1
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Kuo WH, Wright SJ, Small LL, Olsen KM. De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation. BMC Biol 2024; 22:165. [PMID: 39113037 PMCID: PMC11305067 DOI: 10.1186/s12915-024-01962-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/24/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND White clover (Trifolium repens) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features a well-studied polymorphism for cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using a newly generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at cyanogenesis genes play a role in the ability of white clover to rapidly adapt to local environments. We also examined questions on subgenome evolution in this recently evolved allotetraploid species and on chromosomal rearrangements in the broader IRLC legume clade. RESULTS Integration of PacBio HiFi, Omni-C, Illumina, and linkage map data yielded a completely de novo genome assembly for white clover (created without a priori sequence assignment to subgenomes). We find that white clover has undergone extensive transposon diversification since its origin but otherwise shows highly conserved genome organization and composition with its diploid progenitors. Unlike some other clover species, its chromosomal structure is conserved with other IRLC legumes. We further find extensive evidence of CNVs at the major cyanogenesis loci; these contribute to quantitative variation in the cyanogenic phenotype and to local adaptation across wild North American populations. CONCLUSIONS This work provides a case study documenting the role of CNVs in local adaptation in a plant species, and it highlights the value of pan-genome data for identifying contributions of structural variants to adaptation in nature.
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Affiliation(s)
- Wen-Hsi Kuo
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Sara J Wright
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Present address: Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ, 08028, USA
| | - Linda L Small
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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2
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Porter SS, Dupin SE, Denison RF, Kiers ET, Sachs JL. Host-imposed control mechanisms in legume-rhizobia symbiosis. Nat Microbiol 2024:10.1038/s41564-024-01762-2. [PMID: 39095495 DOI: 10.1038/s41564-024-01762-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/17/2024] [Indexed: 08/04/2024]
Abstract
Legumes are ecologically and economically important plants that contribute to nutrient cycling and agricultural sustainability, features tied to their intimate symbiosis with nitrogen-fixing rhizobia. Rhizobia vary dramatically in quality, ranging from highly growth-promoting to non-beneficial; therefore, legumes must optimize their symbiosis with rhizobia through host mechanisms that select for beneficial rhizobia and limit losses to non-beneficial strains. In this Perspective, we examine the considerable scientific progress made in decoding host control over rhizobia, empirically examining both molecular and cellular mechanisms and their effects on rhizobia symbiosis and its benefits. We consider pre-infection controls, which require the production and detection of precise molecular signals by the legume to attract and select for compatible rhizobia strains. We also discuss post-infection mechanisms that leverage the nodule-level and cell-level compartmentalization of symbionts to enable host control over rhizobia development and proliferation in planta. These layers of host control each contribute to legume fitness by directing host resources towards a narrowing subset of more-beneficial rhizobia.
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Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Simon E Dupin
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - R Ford Denison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Joel L Sachs
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, USA.
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3
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Liu T, Liu H, Xian W, Liu Z, Yuan Y, Fan J, Xiang S, Yang X, Liu Y, Liu S, Zhang M, Shen Y, Jiao Y, Cheng S, Doyle JJ, Xie F, Li J, Tian Z. Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39092779 DOI: 10.1111/jipb.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024]
Abstract
Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.
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Affiliation(s)
- Tengfei Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyue Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Zhi Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shi-jiazhuang, 050035, China
| | - Yaqin Yuan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingwei Fan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuaiying Xiang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shulin Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanting Shen
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuannian Jiao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jeff J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, 14853, New York, USA
| | - Fang Xie
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jiayang Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Zhixi Tian
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Ye K, Bu F, Zhong L, Dong Z, Ma Z, Tang Z, Zhang Y, Yang X, Xu X, Wang E, Lucas WJ, Huang S, Liu H, Zheng J. Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics. Nat Commun 2024; 15:6387. [PMID: 39080318 PMCID: PMC11289483 DOI: 10.1038/s41467-024-50737-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
Legumes acquire nitrogen-fixing ability by forming root nodules. Transferring this capability to more crops could reduce our reliance on nitrogen fertilizers, thereby decreasing environmental pollution and agricultural production costs. Nodule organogenesis is complex, and a comprehensive transcriptomic atlas is crucial for understanding the underlying molecular events. Here, we utilized spatial transcriptomics to investigate the development of nodules in the model legume, Lotus japonicus. Our investigation has identified the developmental trajectories of two critical regions within the nodule: the infection zone and peripheral tissues. We reveal the underlying biological processes and provide gene sets to achieve symbiosis and material exchange, two essential aspects of nodulation. Among the candidate regulatory genes, we illustrate that LjNLP3, a transcription factor belonging to the NIN-LIKE PROTEIN family, orchestrates the transition of nodules from the differentiation to maturation. In summary, our research advances our understanding of nodule organogenesis and provides valuable data for developing symbiotic nitrogen-fixing crops.
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Affiliation(s)
- Keyi Ye
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China.
| | - Fengjiao Bu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | | | - Zhaonian Dong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Zhaoxu Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhanpeng Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Yu Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
- School of Agriculture, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - William J Lucas
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, 95616, USA
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
- National Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Huan Liu
- BGI Research, Wuhan, 430074, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
| | - Jianshu Zheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China.
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5
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Li M, Pu J, Jia C, Luo D, Zhou Q, Fang X, Nie B, Liu W, Nan Z, Searle IR, Fang L, Liu Z. The genome of Vicia sativa ssp. amphicarpa provides insights into the role of terpenoids in antimicrobial resistance within subterranean fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39039964 DOI: 10.1111/tpj.16939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024]
Abstract
Vicia sativa ssp. amphicarpa is a unique forage crop capable of simultaneously producing fruits above and below ground, representing a typical amphicarpic plant. In this study, we sequenced and assembled seven pseudo-chromosomes of the genome of V. sativa ssp. amphicarpa (n = 7) yielding a genome size of 1.59 Gb, with a total annotation of 48 932 protein-coding genes. Long terminal repeat (LTR) elements constituted 62.28% of the genome, significantly contributing to the expansion of genome size. Phylogenetic analysis revealed that the divergence between V. sativa ssp. amphicarpa and V. sativa was around 0.88 million years ago (MYA). Comparative transcriptomic and metabolomic analysis of aerial and subterranean pod shells showed biosynthesis of terpenoids in the subterranean pod shells indicating a correlation between the antimicrobial activity of subterranean pod shells and the biosynthesis of terpenoids. Furthermore, functional validation indicates that overexpression of VsTPS5 and VsTPS16 enhances terpenoid biosynthesis for antibacterial activity. Metabolomic analysis suggests the involvement of terpenoids in the antimicrobial properties of subterranean pod shells. Deciphering the genome of V. sativa ssp. amphicarpa elucidated the molecular mechanisms behind the antimicrobial properties of subterranean fruits in amphicarpic plants, providing valuable insights for the study of amphicarpic plant biology.
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Affiliation(s)
- Mingyu Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jun Pu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Chenglin Jia
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Dong Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Qiang Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiangling Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Bin Nie
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Wenxian Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Iain Robert Searle
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
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6
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Zhang G, Yang J, Zhang C, Jiao B, Panero JL, Cai J, Zhang ZR, Gao LM, Gao T, Ma H. Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution. PLANT COMMUNICATIONS 2024; 5:100851. [PMID: 38409784 PMCID: PMC11211554 DOI: 10.1016/j.xplc.2024.100851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain, owing to limited sampling. Here, we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes. Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae, with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups, respectively. Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera. Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology, including capitulum inflorescences and bilaterally symmetric flowers, potentially promoting the diversification of Asteraceae. Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers. This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Caifei Zhang
- Wuhan Botanical Garden and Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bohan Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - José L Panero
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Lijiang National Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan 674100, China.
| | - Tiangang Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA.
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7
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Huang XZ, Gong SD, Shang XH, Gao M, Zhao BY, Xiao L, Shi PL, Zeng WD, Cao S, Wu ZD, Song JM, Chen LL, Yan HB. High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus. DNA Res 2024; 31:dsae017. [PMID: 38809753 PMCID: PMC11149379 DOI: 10.1093/dnares/dsae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 04/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024] Open
Abstract
Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.
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Affiliation(s)
- Xuan-Zhao Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Shao-Da Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Xiao-hong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Ping-li Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Wen-dan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Zheng-dan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Hua-bing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
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8
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Cao J, Zhu H, Gao Y, Hu Y, Li X, Shi J, Chen L, Kang H, Ru D, Ren B, Liu B. Chromosome-level genome assembly and characterization of the Calophaca sinica genome. DNA Res 2024; 31:dsae011. [PMID: 38590243 DOI: 10.1093/dnares/dsae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/26/2024] [Accepted: 04/06/2024] [Indexed: 04/10/2024] Open
Abstract
Calophaca sinica is a rare plant endemic to northern China which belongs to the Fabaceae family and possesses rich nutritional value. To support the preservation of the genetic resources of this plant, we have successfully generated a high-quality genome of C. sinica (1.06 Gb). Notably, transposable elements (TEs) constituted ~73% of the genome, with long terminal repeat retrotransposons (LTR-RTs) dominating this group of elements (~54% of the genome). The average intron length of the C. sinica genome was noticeably longer than what has been observed for closely related species. The expansion of LTR-RTs and elongated introns emerged had the largest influence on the enlarged genome size of C. sinica in comparison to other Fabaceae species. The proliferation of TEs could be explained by certain modes of gene duplication, namely, whole genome duplication (WGD) and dispersed duplication (DSD). Gene family expansion, which was found to enhance genes associated with metabolism, genetic maintenance, and environmental stress resistance, was a result of transposed duplicated genes (TRD) and WGD. The presented genomic analysis sheds light on the genetic architecture of C. sinica, as well as provides a starting point for future evolutionary biology, ecology, and functional genomics studies centred around C. sinica and closely related species.
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Affiliation(s)
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yingqi Gao
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yue Hu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Xuejiao Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jianwei Shi
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Luqin Chen
- Taiyuan Botanical Garden, Taiyuan, China
| | - Hao Kang
- Taiyuan Botanical Garden, Taiyuan, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | | | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
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Chen R, Meng S, Wang A, Jiang F, Yuan L, Lei L, Wang H, Fan W. The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis. PLANT COMMUNICATIONS 2024:100944. [PMID: 38733080 DOI: 10.1016/j.xplc.2024.100944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health, but a lack of genomic resources has hindered their breeding and utilization. Here, we present chromosome-level reference genomes for the two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), the three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb), and Acacia confusa (566 Mb), and the two pioneer and hedgerow trees Leucaena leucocephala (1338 Mb) and Mimosa bimucronata (641 Mb). Phylogenetic inference shows that the mimosoid clade has a much higher evolutionary rate than the other clades of Caesalpinioideae. Macrosynteny comparison suggests that the fusion and breakage of an unstable chromosome are responsible for the difference in basic chromosome number (13 or 14) for Caesalpinioideae. After an ancient whole-genome duplication (WGD) shared by all Caesalpinioideae species (CWGD, ∼72.0 million years ago [MYA]), there were two recent successive WGD events, LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA), in L. leucocephala. Thereafter, ∼40% gene loss and genome-size contraction have occurred during the diploidization process in L. leucocephala. To investigate secondary metabolites, we identified all gene copies involved in mimosine metabolism in these species and found that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. We also identified the set of all potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than that based on previous transcriptome-derived unigenes. Our results and genomic resources will facilitate biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.
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Affiliation(s)
- Rong Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sihan Meng
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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10
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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11
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Bruneau A, de Queiroz LP, Ringelberg JJ, Borges LM, Bortoluzzi RLDC, Brown GK, Cardoso DBOS, Clark RP, Conceição ADS, Cota MMT, Demeulenaere E, de Stefano RD, Ebinger JE, Ferm J, Fonseca-Cortés A, Gagnon E, Grether R, Guerra E, Haston E, Herendeen PS, Hernández HM, Hopkins HCF, Huamantupa-Chuquimaco I, Hughes CE, Ickert-Bond SM, Iganci J, Koenen EJM, Lewis GP, de Lima HC, de Lima AG, Luckow M, Marazzi B, Maslin BR, Morales M, Morim MP, Murphy DJ, O’Donnell SA, Oliveira FG, Oliveira ACDS, Rando JG, Ribeiro PG, Ribeiro CL, Santos FDS, Seigler DS, da Silva GS, Simon MF, Soares MVB, Terra V. Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification. PHYTOKEYS 2024; 240:1-552. [PMID: 38912426 PMCID: PMC11188994 DOI: 10.3897/phytokeys.240.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 11/19/2023] [Indexed: 06/25/2024]
Abstract
Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Ceratonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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Affiliation(s)
- Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke E., Montreal (QC) H1X 2B2, CanadaUniversité de MontréalMontrealCanada
| | - Luciano Paganucci de Queiroz
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UKUniversity of EdinburghEdinburghUnited Kingdom
| | - Leonardo M. Borges
- Universidade Federal de São Carlos, Departamento de Botânica, Rodovia Washington Luís, Km 235, 13565-905, São Carlos, SP, BrazilUniversidade Federal de São CarlosSão CarlosBrazil
| | - Roseli Lopes da Costa Bortoluzzi
- Programa de Pós-graduação em Produção Vegetal, Universidade do Estado de Santa Catarina, Centro de Ciências Agroveterinárias, Avenida Luiz de Camões 2090, 88520-000, Lages, Santa Catarina, BrazilUniversidade do Estado de Santa CatarinaSanta CatarinaBrazil
| | - Gillian K. Brown
- Queensland Herbarium and Biodiversity Science, Department of Environment and Science, Toowong, Queensland, 4066, AustraliaQueensland Herbarium and Biodiversity ScienceToowongAustralia
| | - Domingos B. O. S. Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Pacheco Leão 915, 22460-030, Rio de Janeiro, RJ, BrazilInstituto de Pesquisas Jardim Botânico do Rio de JaneiroRio de JaneiroBrazil
- Programa de Pós-Graduação em Biodiversidade e Evolução (PPGBioEvo), Instituto de Biologia, Universidade Federal de Bahia (UFBA), Rua Barão de Jeremoabo, s.n., Ondina, 40170-115, Salvador, BA, BrazilUniversidade Federal de BahiaSalvadorBrazil
| | - Ruth P. Clark
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Adilva de Souza Conceição
- Programa de Pós-graduação em Diversidade Vegetal, Universidade do Estado da Bahia, Herbário HUNEB, Campus VIII, Rua do Gangorra 503, 48608-240, Paulo Afonso, Bahia, BrazilUniversidade do Estado da BahiaBahiaBrazil
| | - Matheus Martins Teixeira Cota
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Else Demeulenaere
- Center for Island Sustainability and Sea Grant, University of Guam, UOG Station, Mangilao, 96923, GuamUniversity of GuamMangilaoGuam
| | - Rodrigo Duno de Stefano
- Centro de Investigación Científica de Yucatán, A.C. (CICY), Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo; CP 97205, Mérida, Yucatán, MexicoCentro de Investigación Científica de Yucatán, A.C.MéridaMexico
| | - John E. Ebinger
- Eastern Illinois University, Charleston, IL 61920, USAEastern Illinois UniversityCharlestonUnited States of America
| | - Julia Ferm
- Department of Ecology, Environment and Plant Sciences, 10691, Stockholm University, Stockholm, SwedenStockholm UniversityStockholmSweden
| | - Andrés Fonseca-Cortés
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Edeline Gagnon
- Department of Integrative Biology, University of Guelph, 50 Stone Road, Guelph (ON) N1G 2W1, CanadaRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
- Chair of Phytopathology, Technical University Munich, 85354 Freising, GermanyUniversity of GuelphGuelphCanada
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UKTechnical University MunichFreisingGermany
| | - Rosaura Grether
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, Apdo. Postal 55-535, 09340 Ciudad de México, MexicoUniversidad Autónoma Metropolitana-IztapalapaCiudad de MéxicoMexico
| | - Ethiéne Guerra
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, Bloco IV - Prédio 43433, Porto Alegre, RS, 91501-970, BrazilUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | - Elspeth Haston
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UKTechnical University MunichFreisingGermany
| | - Patrick S. Herendeen
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USAChicago Botanic GardenGlencoeUnited States of America
| | - Héctor M. Hernández
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510 Ciudad de México, MexicoUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Helen C. F. Hopkins
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Isau Huamantupa-Chuquimaco
- Herbario Alwyn Gentry (HAG), Universidad Nacional Amazónica de Madre de Dios (UNAMAD), AV. Jorge Chávez N°1160, Madre de Dios, PeruUniversidad Nacional Amazónica de Madre de DiosMadre de DiosPeru
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
| | - Stefanie M. Ickert-Bond
- Department of Biology & Wildlife & Herbarium (ALA) at the University of Alaska Museum of the North, University of Alaska Fairbanks, P.O. Box 756960, Fairbanks AK 99775-6960, USAUniversity of Alaska FairbanksFairbanksUnited States of America
| | - João Iganci
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, Bloco IV - Prédio 43433, Porto Alegre, RS, 91501-970, BrazilUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Programa de Pós-Graduação em Fisiologia Vegetal, Universidade Federal de Pelotas, Instituto de Biologia, Campus Universitário Capão do Leão, Passeio André Dreyfus, Departamento de Botânica, Prédio 21, Pelotas, Rio Grande do Sul, 96010-900, BrazilUniversidade Federal de PelotasPelotasBrazil
| | - Erik J. M. Koenen
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Faculté des Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt, 50, 1050 Bruxelles, BelgiumUniversité Libre de BruxellesBruxellesBelgium
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Haroldo Cavalcante de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Pacheco Leão 915, 22460-030, Rio de Janeiro, RJ, BrazilInstituto de Pesquisas Jardim Botânico do Rio de JaneiroRio de JaneiroBrazil
- Instituto Nacional da Mata Atlântica / INMA-MCTI, Av. José Ruschi, 4, Centro, 29650-000, Santa Teresa, Espírito Santo, BrazilInstituto Nacional da Mata AtlânticaSanta TeresaBrazil
| | - Alexandre Gibau de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Pacheco Leão 915, 22460-030, Rio de Janeiro, RJ, BrazilInstituto de Pesquisas Jardim Botânico do Rio de JaneiroRio de JaneiroBrazil
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USACornell UniversityIthacaUnited States of America
| | - Brigitte Marazzi
- Natural History Museum of Canton Ticino, Viale C. Cattaneo 4, 6900 Lugano, SwitzerlandNatural History Museum of Canton TicinoLuganoSwitzerland
| | - Bruce R. Maslin
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia, 6983, AustraliaWestern Australian HerbariumBentley Delivery CentreAustralia
- Singapore Herbarium, 1 Cluny Road, Singapore, SingaporeSingapore HerbariumSingaporeSingapore
| | - Matías Morales
- Instituto de Recursos Biológicos, CIRN–CNIA, INTA. N. Repetto & Los Reseros s.n., Hurlingham, Buenos Aires, ArgentinaInstituto de Recursos BiológicosBuenos AiresArgentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, ArgentinaConsejo Nacional de Investigaciones Científicas y TécnicasCiudad Autónoma de Buenos AiresArgentina
| | - Marli Pires Morim
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Pacheco Leão 915, 22460-030, Rio de Janeiro, RJ, BrazilInstituto de Pesquisas Jardim Botânico do Rio de JaneiroRio de JaneiroBrazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Melbourne, Victoria, 3004, AustraliaRoyal Botanic Gardens VictoriaVictoriaAustralia
| | - Shawn A. O’Donnell
- Geography and Environmental Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne, NE1 8ST, UKNorthumbria UniversityNewcastle upon TyneUnited Kingdom
| | - Filipe Gomes Oliveira
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Ana Carla da Silva Oliveira
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Juliana Gastaldello Rando
- Programa de Pós-graduação em Ciências Ambientais, Universidade Federal do Oeste da Bahia, Rua Professor José Seabra Lemos 316, 47800-021, Barreiras, Bahia, BrazilUniversidade Federal do Oeste da BahiaBarreirasBrazil
| | - Pétala Gomes Ribeiro
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Carolina Lima Ribeiro
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Felipe da Silva Santos
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Campus, Novo Horizonte. 44036-900, Feira de Santana, BA, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - David S. Seigler
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USAUniversity of IllinoisUrbanaUnited States of America
| | - Guilherme Sousa da Silva
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-876, São Paulo/SP, BrazilUniversidade Estadual de CampinasSão PauloBrazil
| | - Marcelo F. Simon
- Empresa Brasileira de Pesquisa Agropecuária (Embrapa) Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Caixa Postal 02372, 70770-917, Brasília/DF, BrazilEmpresa Brasileira de Pesquisa AgropecuáriaBrasíliaBrazil
| | - Marcos Vinícius Batista Soares
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, Bloco IV - Prédio 43433, Porto Alegre, RS, 91501-970, BrazilUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | - Vanessa Terra
- Instituto de Biologia, Universidade Federal de Santa Maria, 97105-900, Santa Maria/RS, BrazilUniversidade Federal de Santa MariaSanta MariaBrazil
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Jia H, Lin J, Lin Z, Wang Y, Xu L, Ding W, Ming R. Haplotype-resolved genome of Mimosa bimucronata revealed insights into leaf movement and nitrogen fixation. BMC Genomics 2024; 25:334. [PMID: 38570736 PMCID: PMC10993578 DOI: 10.1186/s12864-024-10264-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Mimosa bimucronata originates from tropical America and exhibits distinctive leaf movement characterized by a relative slow speed. Additionally, this species possesses the ability to fix nitrogen. Despite these intriguing traits, comprehensive studies have been hindered by the lack of genomic resources for M. bimucronata. RESULTS To unravel the intricacies of leaf movement and nitrogen fixation, we successfully assembled a high-quality, haplotype-resolved, reference genome at the chromosome level, spanning 648 Mb and anchored in 13 pseudochromosomes. A total of 32,146 protein-coding genes were annotated. In particular, haplotype A was annotated with 31,035 protein-coding genes, and haplotype B with 31,440 protein-coding genes. Structural variations (SVs) and allele specific expression (ASE) analyses uncovered the potential role of structural variants in leaf movement and nitrogen fixation in M. bimucronata. Two whole-genome duplication (WGD) events were detected, that occurred ~ 2.9 and ~ 73.5 million years ago. Transcriptome and co-expression network analyses revealed the involvement of aquaporins (AQPs) and Ca2+-related ion channel genes in leaf movement. Moreover, we also identified nodulation-related genes and analyzed the structure and evolution of the key gene NIN in the process of symbiotic nitrogen fixation (SNF). CONCLUSION The detailed comparative genomic and transcriptomic analyses provided insights into the mechanisms governing leaf movement and nitrogen fixation in M. bimucronata. This research yielded genomic resources and provided an important reference for functional genomic studies of M. bimucronata and other legume species.
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Affiliation(s)
- Haifeng Jia
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jishan Lin
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570100, China
| | - Zhicong Lin
- College of Environment and Biological Engineering, Putian University, Putian, 351100, China
| | - Yibin Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liangwei Xu
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjie Ding
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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13
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Farmer TA, Jansen RK. Out of Place: Phylogenomics resolves the placement of Eurasian taxa and sheds light on origin of Thermopsideae in North America. Mol Phylogenet Evol 2024; 193:108024. [PMID: 38341005 DOI: 10.1016/j.ympev.2024.108024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/16/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
The North American Thermopsideae (Fabaceae: Papilionoideae), a monophyletic group comprising the North American endemic genus Baptisia, and the paraphyletic Eurasian-North American disjunct Thermopsis, is nested within the tribe Sophoreae. Previous phylogenetic studies have identified two East Asian taxa within the North American Thermopsideae, suggesting two independent dispersal events between North America-East Asia. More recent studies have also placed a third taxon, Vuralia turcica, an endemic species from Turkey, among the North American Thermopsideae. The presence of three geographically distant Eurasian taxa within a relatively young clade of North American origin is unprecedented among papilionoid legumes, and the biogeographic implications of this observation are not clear. To investigate this matter, 1540 low-copy nuclear genes and complete plastomes were obtained from 36 taxa across the core genistoids, including 26 newly sequenced taxa. Nuclear and plastome based maximum likelihood (ML) and ASTRAL analyses were conducted based on varying degrees of taxon coverage and read mapping consensus threshold values. Additional analyses were performed to estimate divergence times and to reconstruct biogeographic history. The results strongly support a previously undetected Old World clade, presently composed of V. turcica and T. chinensis, which diverged from the ancestor of the North American lineage during the mid to late Miocene. A single and recent North America-East Asia dispersal involving T. lupinoides is reported. Furthermore, the traditional inclusion of the genus Ammopiptanthus among Thermopsideae is not supported, and the monotypic generic status of Vuralia is called into question. A relatively high degree of cytonuclear discordance is reported within each sub-clade of the North American Thermopsideae. This finding is likely attributable to the high degree of interspecific hybridization reported within these groups and raises the need for more rigorous genome-scale testing to better delimit species within each of the reticulating subclades. Subjects: Biodiversity, Biogeography, Evolutionary Studies, Genetics, Plant Science.
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Affiliation(s)
- Todd A Farmer
- University of Texas at Austin, Department of Integrative Biology, Austin, TX, USA.
| | - Robert K Jansen
- University of Texas at Austin, Department of Integrative Biology, Austin, TX, USA
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Lu Y, Chen X, Yu H, Zhang C, Xue Y, Zhang Q, Wang H. Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:488-505. [PMID: 38173092 DOI: 10.1111/tpj.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Phanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high-coverage PacBio and Hi-C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes: Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole-genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele-specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high-quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.
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Affiliation(s)
- Yongbin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Xiao Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Chao Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Yajie Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China
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15
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Massaro I, Poethig RS, Sinha NR, Leichty AR. Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa. G3 (BETHESDA, MD.) 2024; 14:jkad284. [PMID: 38096217 PMCID: PMC10917515 DOI: 10.1093/g3journal/jkad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/01/2023] [Indexed: 03/08/2024]
Abstract
The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.
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Affiliation(s)
- Isabelle Massaro
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Neelima R Sinha
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Aaron R Leichty
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- USDA Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, USA
- 800 Buchanan Street, Albany, CA 94710, USA
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16
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Yang X, Zheng S, Wang X, Wang J, Ali Shah SB, Wang Y, Gao R, Xu Z. Advances in pharmacology, biosynthesis, and metabolic engineering of Scutellaria-specialized metabolites. Crit Rev Biotechnol 2024; 44:302-318. [PMID: 36581326 DOI: 10.1080/07388551.2022.2149386] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 12/31/2022]
Abstract
Scutellaria Linn., which belongs to the family Lamiaceae, is a commonly used medicinal plant for heat clearing and detoxification. In particular, the roots of S. baicalensis and the entire herb of S. barbata have been widely used in traditional medicine for thousands of years. The main active components of Scutellaria, including: baicalein, wogonin, norwogonin, scutellarein, and their glycosides have potential or existing drug usage. However, the wild resources of Scutellaria plants have been overexploited, and degenerated germplasm resources cannot fulfill the requirements of chemical extraction and clinical usage. Metabolic engineering and green production via microorganisms provide alternative strategies for greater efficiency in the production of natural products. Here, we review the progress of: pharmacological investigations, multi-omics, biosynthetic pathways, and metabolic engineering of various Scutellaria species and their active compounds. In addition, based on multi-omics data, we systematically analyze the phylogenetic relationships of Scutellaria and predict candidate transcription factors related to the regulation of active flavonoids. Finally, we propose the prospects of directed evolution of core enzymes and genome-assisted breeding to alleviate the shortage of plant resources of Scutellaria. This review provides important insights into the sustainable utilization and development of Scutellaria resources.
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Affiliation(s)
- Xinyi Yang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Sihao Zheng
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Xiaotong Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Jing Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Syed Basit Ali Shah
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yu Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ranran Gao
- The Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhichao Xu
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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17
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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18
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Wang M, Zhang R, Shu JP, Zheng XL, Wu XY, Chen JB, Wang MN, Shen H, Yan YH. Whole Genome Duplication Events Likely Contributed to the Aquatic Adaptive Evolution of Parkerioideae. PLANTS (BASEL, SWITZERLAND) 2024; 13:521. [PMID: 38498522 PMCID: PMC10893450 DOI: 10.3390/plants13040521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
As the only aquatic lineage of Pteridaceae, Parkerioideae is distinct from many xeric-adapted species of the family and consists of the freshwater Ceratopteris species and the only mangrove ferns from the genus Acrostichum. Previous studies have shown that whole genome duplication (WGD) has occurred in Parkerioideae at least once and may have played a role in their adaptive evolution; however, more in-depth research regarding this is still required. In this study, comparative and evolutionary transcriptomics analyses were carried out to identify WGDs and explore their roles in the environmental adaptation of Parkerioideae. Three putative WGD events were identified within Parkerioideae, two of which were specific to Ceratopteris and Acrostichum, respectively. The functional enrichment analysis indicated that the lineage-specific WGD events have played a role in the adaptation of Parkerioideae to the low oxygen concentrations of aquatic habitats, as well as different aquatic environments of Ceratopteris and Acrostichum, such as the adaptation of Ceratopteris to reduced light levels and the adaptation of Acrostichum to high salinity. Positive selection analysis further provided evidence that the putative WGD events may have facilitated the adaptation of Parkerioideae to changes in habitat. Moreover, the gene family analysis indicated that the plasma membrane H+-ATPase (AHA), vacuolar H+-ATPase (VHA), and suppressor of K+ transport growth defect 1 (SKD1) may have been involved in the high salinity adaptation of Acrostichum. Our study provides new insights into the evolution and adaptations of Parkerioideae in different aquatic environments.
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Affiliation(s)
- Meng Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Rui Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (R.Z.); (H.S.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Jiang-Ping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xi-Long Zheng
- School of Traditional Medicine Materials Resource, Guangdong Pharmaceutical University, Yunfu 527322, China;
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Jian-Bing Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Mei-Na Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
| | - Hui Shen
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (R.Z.); (H.S.)
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yue-Hong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China; (M.W.); (J.-P.S.); (X.-Y.W.); (J.-B.C.); (M.-N.W.)
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19
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Fan J, Deng M, Li B, Fan G. Genome-Wide Identification of the Paulownia fortunei Aux/IAA Gene Family and Its Response to Witches' Broom Caused by Phytoplasma. Int J Mol Sci 2024; 25:2260. [PMID: 38396939 PMCID: PMC10889751 DOI: 10.3390/ijms25042260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
The typical symptom of Paulownia witches' broom (PaWB), caused by phytoplasma infection, is excessive branching, which is mainly triggered by auxin metabolism disorder. Aux/IAA is the early auxin-responsive gene that participates in regulating plant morphogenesis such as apical dominance, stem elongation, lateral branch development, and lateral root formation. However, no studies have investigated the response of the Aux/IAA gene family to phytoplasma infection in Paulownia fortunei. In this study, a total of 62 Aux/IAA genes were found in the genome. Phylogenetic analysis showed that PfAux/IAA genes could be divided into eight subgroups, which were formed by tandem duplication and fragment replication. Most of them had a simple gene structure, and several members lacked one or two conserved domains. By combining the expression of PfAux/IAA genes under phytoplasma stress and SA-treated phytoplasma-infected seedlings, we found that PfAux/IAA13/33/45 may play a vital role in the occurrence of PaWB. Functional analysis based on homologous relationships showed a strong correlation between PfAux/IAA45 and branching. Protein-protein interaction prediction showed that PfARF might be the binding partner of PfAux/IAA, and the yeast two-hybrid assay and bimolecular fluorescent complementary assay confirmed the interaction of PfAux/IAA45 and PfARF13. This study provides a theoretical basis for further understanding the function of the PfAux/IAA gene family and exploring the regulatory mechanism of branching symptoms caused by PaWB.
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Affiliation(s)
- Jiaming Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (J.F.); (M.D.); (B.L.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Minjie Deng
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (J.F.); (M.D.); (B.L.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Bingbing Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (J.F.); (M.D.); (B.L.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (J.F.); (M.D.); (B.L.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
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20
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Ha YH, Chang KS, Gil HY. Characteristics of chloroplast and mitochondrial genomes and intracellular gene transfer in the Korean endemic shrub, Sophora koreensis Nakai (Fabaceae). Gene 2024; 894:147963. [PMID: 37926173 DOI: 10.1016/j.gene.2023.147963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea
| | - Kae Sun Chang
- DMZ Botanic Garden, Korea National Arboretum, Yanggu-gun, Gangwon-do 24564, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-si, Gyeonggi-do 11186, Republic of Korea.
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Estrada-Castillón E, Villarreal-Quintanilla JÁ, Cuéllar-Rodríguez G, Encina-Domínguez JA, Martínez-Ávalos JG, Mora-Olivo A, Sánchez-Salas J. The Fabaceae in Northeastern Mexico (Subfamily Caesalpinioideae, Mimosoideae Clade, Tribes Mimoseae, Acacieae, and Ingeae). PLANTS (BASEL, SWITZERLAND) 2024; 13:403. [PMID: 38337936 PMCID: PMC10857220 DOI: 10.3390/plants13030403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
A synoptic compendium of the legumes of the Mimosoideae clade in northeastern Mexico is presented for the first time, including changes in their botanical nomenclature and retypification of genera. Furthermore, based on new information recently published, the taxonomic limits of several new genera segregated from Acacia (Acaciella, Mariosousa, Senegalia, and Vachellia) and Prosopis (Neltuma and Strombocarpa) are clarified and included. Based on field work, collection of botanical samples over the past 30 years, and reviewing botanical materials in national and international herbaria, we have completed the diversity of legumes of the Mimosoideae clade of northeastern Mexico. Three tribes (Acacieae, Ingeae, and Mimosaeae), 22 genera, 92 species, and 19 infraspecific categories were recorded. Only the genus Painteria is endemic to Mexico. Eighty-eight species are native to Mexico, and four are exotic: Acacia salicina, Neptunia prostrata, Neltuma chilensis and Albizia lebbeck. Twenty-eight species are endemic to Mexico, nine species are endemic to northeastern Mexico, and four species are endemic to only one state in Mexico. The 22 registered genera represent 44% and 65% of the generic flora of the Mimosoideae clade for Mexico and the planet, respectively, while the 92 species registered represent 3% and 18% of the species of the clade Mimosoideae for the planet and Mexico, respectively. According to the new nomenclature of legumes, the number of genera in the Mimosoideae clade in northern Mexico has increased from 19 to 24.
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Affiliation(s)
- Eduardo Estrada-Castillón
- Facultad de Ciencias Forestales, Universidad Autónoma de Nuevo León, Linares 67700, Mexico; (E.E.-C.); (G.C.-R.)
| | | | - Gerardo Cuéllar-Rodríguez
- Facultad de Ciencias Forestales, Universidad Autónoma de Nuevo León, Linares 67700, Mexico; (E.E.-C.); (G.C.-R.)
| | - Juan Antonio Encina-Domínguez
- Departamento de Botánica, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico; (J.Á.V.-Q.); (J.A.E.-D.)
| | | | - Arturo Mora-Olivo
- Instituto de Ecología Aplicada, Universidad Autónoma de Tamaulipas, Ciudad Victoria 87019, Mexico;
| | - Jaime Sánchez-Salas
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Gómez Palacio 35010, Mexico;
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22
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Sun C, Chen Y, Zheng D, Zhong Y, Luo S, Meng S, Qian L, Wei D, Liu Y, Dai S, Zhou R. The complete mitochondrial genome of Bauhinia variegata (Leguminosae). Mitochondrial DNA B Resour 2024; 9:128-132. [PMID: 38259357 PMCID: PMC10802806 DOI: 10.1080/23802359.2024.2305712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The mitogenome of Bauhinia variegate was assembled and characterized in this study. The mitogenome size was 437,271 bp, and its GC content was 45.5%. 36 protein-coding genes, 17 tRNAs and 3 rRNAs were annotated in the mitogenome. A total of 12 MTPTs, ranging from 71 bp to 3562 bp, were identified in the mitogenome and covered 1.46% (6373 bp) of the mitogenome. Phylogenetic analysis of 15 species of Leguminosae based on 23 core protein-coding genes showed that B. variegata was sister to Tylosema esculentum, another member from the subfamily Cercidoideae. The mitogenome of B. variegata provides a valuable genetic resource for further phylogenetic studies of this family.
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Affiliation(s)
- Chenyu Sun
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, China
| | - Yong Chen
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Danjing Zheng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Yan Zhong
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, China
| | - Shukai Luo
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Shiyuan Meng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Lei Qian
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Dan Wei
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou, China
| | - Ying Liu
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, China
| | - Seping Dai
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Renchao Zhou
- School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, China
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Kang L, Li C, Qin A, Liu Z, Li X, Zeng L, Yu H, Wang Y, Song J, Chen R. Identification and Expression Analysis of the Nucleotidyl Transferase Protein (NTP) Family in Soybean ( Glycine max) under Various Abiotic Stresses. Int J Mol Sci 2024; 25:1115. [PMID: 38256188 PMCID: PMC10816777 DOI: 10.3390/ijms25021115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3' end of RNA. In plants, NTPs can regulate RNA stability by influencing 3' end modifications, which in turn affect plant growth, development, stress responses, and disease resistance. Although the functions of NTP family members have been extensively studied in Arabidopsis, rice, and maize, there is limited knowledge about NTP genes in soybeans. In this study, we identified 16 members of the NTP family in soybeans, including two subfamilies (G1 and G2) with distinct secondary structures, conserved motifs, and domain distributions at the protein level. Evolutionary analysis of genes in the NTP family across multiple species and gene collinearity analysis revealed a relatively conserved evolutionary pattern. Analysis of the tertiary structure of the proteins showed that NTPs have three conserved aspartic acids that bind together to form a possible active site. Tissue-specific expression analysis indicated that some NTP genes exhibit tissue-specific expression, likely due to their specific functions. Stress expression analysis showed significant differences in the expression levels of NTP genes under high salt, drought, and cold stress. Additionally, RNA-seq analysis of soybean plants subjected to salt and drought stress further confirmed the association of soybean NTP genes with abiotic stress responses. Subcellular localization experiments revealed that GmNTP2 and GmNTP14, which likely have similar functions to HESO1 and URT1, are located in the nucleus. These research findings provide a foundation for further investigations into the functions of NTP family genes in soybeans.
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Affiliation(s)
- Liqing Kang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Changgen Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Aokang Qin
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Zehui Liu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Xuanyue Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Liming Zeng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Hongyang Yu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Yihua Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Jianbo Song
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (L.K.); (C.L.); (A.Q.); (Z.L.); (X.L.); (L.Z.); (H.Y.); (Y.W.)
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24
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Zhang Y, Fu Y, Xian W, Li X, Feng Y, Bu F, Shi Y, Chen S, van Velzen R, Battenberg K, Berry AM, Salgado MG, Liu H, Yi T, Fournier P, Alloisio N, Pujic P, Boubakri H, Schranz ME, Delaux PM, Wong GKS, Hocher V, Svistoonoff S, Gherbi H, Wang E, Kohlen W, Wall LG, Parniske M, Pawlowski K, Normand P, Doyle JJ, Cheng S. Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis. PLANT COMMUNICATIONS 2024; 5:100671. [PMID: 37553834 PMCID: PMC10811378 DOI: 10.1016/j.xplc.2023.100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
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Affiliation(s)
- Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuan Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fengjiao Bu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Robin van Velzen
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Marco G Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Hui Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Valerie Hocher
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sergio Svistoonoff
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Hassen Gherbi
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Luis G Wall
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Jeffrey J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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25
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Yuan L, Lei L, Jiang F, Wang A, Chen R, Wang H, Meng S, Fan W. The genomes of 5 underutilized Papilionoideae crops provide insights into root nodulation and disease resistance. Gigascience 2024; 13:giae063. [PMID: 39190925 PMCID: PMC11348429 DOI: 10.1093/gigascience/giae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/22/2024] [Accepted: 08/01/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND The Papilionoideae subfamily contains a large amount of underutilized legume crops, which are important for food security and human sustainability. However, the lack of genomic resources has hindered the breeding and utilization of these crops. RESULTS Here, we present chromosome-level reference genomes for 5 underutilized diploid Papilionoideae crops: sword bean (Canavalia gladiata), scarlet runner bean (Phaseolus coccineus), winged bean (Psophocarpus tetragonolobus), smooth rattlebox (Crotalaria pallida), and butterfly pea (Clitoria ternatea), with assembled genome sizes of 0.62 Gb, 0.59 Gb, 0.71 Gb, 1.22 Gb, and 1.72 Gb, respectively. We found that the long period of higher long terminal repeat retrotransposon activity is the major reason that the genome size of smooth rattlebox and butterfly pea is enlarged. Additionally, there have been no recent whole-genome duplication (WGD) events in these 5 species except for the shared papilionoid-specific WGD event (∼55 million years ago). Then, we identified 5,328 and 10,434 species-specific genes between scarlet runner bean and common bean, respectively, which may be responsible for their phenotypic and functional differences and species-specific functions. Furthermore, we identified the key genes involved in root-nodule symbiosis (RNS) in all 5 species and found that the NIN gene was duplicated in the early Papilionoideae ancestor, followed by the loss of 1 gene copy in smooth rattlebox and butterfly pea lineages. Last, we identified the resistance (R) genes for plant defenses in these 5 species and characterized their evolutionary history. CONCLUSIONS In summary, this study provides chromosome-scale reference genomes for 3 grain and vegetable beans (sword bean, scarlet runner bean, winged bean), along with genomes for a green manure crop (smooth rattlebox) and a food dyeing crop (butterfly pea). These genomes are crucial for studying phylogenetic history, unraveling nitrogen-fixing RNS evolution, and advancing plant defense research.
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Affiliation(s)
- Lihua Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Lihong Lei
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Rong Chen
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sihan Meng
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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26
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Zhang Q, Folk RA, Mo ZQ, Ye H, Zhang ZY, Peng H, Zhao JL, Yang SX, Yu XQ. Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae). Mol Phylogenet Evol 2023; 188:107912. [PMID: 37648181 DOI: 10.1016/j.ympev.2023.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/09/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of selection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discordance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.
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Affiliation(s)
- Qiong Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, MS 39762, United States
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hang Ye
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Zhao-Yuan Zhang
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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27
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Yang L, Harris AJ, Wen F, Li Z, Feng C, Kong H, Kang M. Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation. Syst Biol 2023; 72:1064-1083. [PMID: 37158589 PMCID: PMC10627561 DOI: 10.1093/sysbio/syad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 04/15/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.
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Affiliation(s)
- Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Fang Wen
- Guangxi Institute of Botany, Guangxi Zhang Autonomous Region and the Chinese Academy of Sciences, 541006 Guilin, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, AZ 85721, USA
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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28
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Yong B, Zhu W, Wei S, Li B, Wang Y, Xu N, Lu J, Chen Q, He C. Parallel selection of loss-of-function alleles of Pdh1 orthologous genes in warm-season legumes for pod indehiscence and plasticity is related to precipitation. THE NEW PHYTOLOGIST 2023; 240:863-879. [PMID: 37501344 DOI: 10.1111/nph.19150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Pod dehiscence facilitates seed dispersal in wild legumes but results in yield loss in cultivated legumes. The evolutionary genetics of the legume pod dehiscence trait remain largely elusive. We characterized the pod dehiscence of chromosome segment substitution lines of Glycine max crossed with Glycine soja and found that the gene underlying the predominant quantitative trait locus (QTL) of soybean pod-shattering trait was Pod dehiscence 1 (Pdh1). A few rare loss-of-function (LoF) Pdh1 alleles were identified in G. soja, while only an allele featuring a premature stop codon was selected for pod indehiscence in cultivated soybean and spread to low-precipitation regions with increased frequency. Moreover, correlated interactions among Pdh1's haplotype, gene expression, and environmental changes for the developmental plasticity of the pod dehiscence trait were revealed in G. max. We found that orthologous Pdh1 genes specifically originated in warm-season legumes and their LoF alleles were then parallel-selected during the domestication of legume crops. Our results provide insights into the convergent evolution of pod dehiscence in warm-season legumes, facilitate an understanding of the intricate interactions between genetic robustness and environmental adaptation for developmental plasticity, and guide the breeding of new legume varieties with pod indehiscence.
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Affiliation(s)
- Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Nan Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Li JX, Meng Y, Nie ZL, Tu TY. The complete plastid genome sequence of Lysidice brevicalyx (Fabaceae: Detarioideae), an arbor species endemic to China. Mitochondrial DNA B Resour 2023; 8:1003-1006. [PMID: 37746035 PMCID: PMC10515688 DOI: 10.1080/23802359.2023.2259041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023] Open
Abstract
The plastid genome of Lysidice brevicalyx was successfully assembled using Illumina sequencing reads for the first time. The complete plastid genome of L. brevicalyx is a circular structure of 159,084 bp with a GC content of 36.4%. It comprises a large single-copy (LSC) region of 87,783 bp, a small single-copy (SSC) region of 19,557 bp, and two inverted repeat regions (IRA and IRB) of 25,872 bp, each. The plastome of L. brevicalyx contains a total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. The phylogenetic analysis strongly supports the monophyly of Lysidice. This study provides the first complete plastid genome sequence of L. brevicalyx and contributes to our understanding of the molecular characteristics and evolutionary relationships of this plant species.
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Affiliation(s)
- Jian-Xin Li
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
- Plant Science Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Tie-Yao Tu
- Plant Science Center, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
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30
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Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Wang Z, Zhang X, Lei W, Zhu H, Wu S, Liu B, Ru D. Chromosome-level genome assembly and population genomics of Robinia pseudoacacia reveal the genetic basis for its wide cultivation. Commun Biol 2023; 6:797. [PMID: 37524773 PMCID: PMC10390555 DOI: 10.1038/s42003-023-05158-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023] Open
Abstract
Urban greening provides important ecosystem services and ideal places for urban recreation and is a serious consideration for municipal decision-makers. Among the tree species cultivated in urban green spaces, Robinia pseudoacacia stands out due to its attractive flowers, fragrances, high trunks, wide adaptability, and essential ecosystem services. However, the genomic basis and consequences of its wide-planting in urban green spaces remains unknown. Here, we report the chromosome-level genome assembly of R. pseudoacacia, revealing a genome size of 682.4 Mb and 33,187 protein-coding genes. More than 99.3% of the assembly is anchored to 11 chromosomes with an N50 of 59.9 Mb. Comparative genomic analyses among 17 species reveal that gene families related to traits favoured by urbanites, such as wood formation, biosynthesis, and drought tolerance, are notably expanded in R. pseudoacacia. Our population genomic analyses further recover 11 genes that are under recent selection. Ultimately, these genes play important roles in the biological processes related to flower development, water retention, and immunization. Altogether, our results reveal the evolutionary forces that shape R. pseudoacacia cultivated for urban greening. These findings also present a valuable foundation for the future development of agronomic traits and molecular breeding strategies for R. pseudoacacia.
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Affiliation(s)
- Zefu Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiao Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China.
| | - Weixiao Lei
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hui Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Shengdan Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China.
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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Yang LL, Zhang XY, Wang LY, Li YG, Li XT, Yang Y, Su Q, Chen N, Zhang YL, Li N, Deng CL, Li SF, Gao WJ. Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species. BMC Genomics 2023; 24:423. [PMID: 37501164 PMCID: PMC10373317 DOI: 10.1186/s12864-023-09530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/22/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Long terminal repeat (LTR)-retrotransposons (LTR-RTs) are ubiquitous and make up the majority of nearly all sequenced plant genomes, whereas their pivotal roles in genome evolution, gene expression regulation as well as their epigenetic regulation are still not well understood, especially in a large number of closely related species. RESULTS Here, we analyzed the abundance and dynamic evolution of LTR-RTs in 54 species from an economically and agronomically important family, Fabaceae, and also selected two representative species for further analysis in expression of associated genes, transcriptional activity and DNA methylation patterns of LTR-RTs. Annotation results revealed highly varied proportions of LTR-RTs in these genomes (5.1%~68.4%) and their correlation with genome size was highly positive, and they were significantly contributed to the variance in genome size through species-specific unique amplifications. Almost all of the intact LTR-RTs were inserted into the genomes 4 Mya (million years ago), and more than 50% of them were inserted in the last 0.5 million years, suggesting that recent amplifications of LTR-RTs were an important force driving genome evolution. In addition, expression levels of genes with intronic, promoter, and downstream LTR-RT insertions of Glycine max and Vigna radiata, two agronomically important crops in Fabaceae, showed that the LTR-RTs located in promoter or downstream regions suppressed associated gene expression. However, the LTR-RTs within introns promoted gene expression or had no contribution to gene expression. Additionally, shorter and younger LTR-RTs maintained higher mobility and transpositional potential. Compared with the transcriptionally silent LTR-RTs, the active elements showed significantly lower DNA methylation levels in all three contexts. The distributions of transcriptionally active and silent LTR-RT methylation varied across different lineages due to the position of LTR-RTs located or potentially epigenetic regulation. CONCLUSION Lineage-specific amplification patterns were observed and higher methylation level may repress the activity of LTR-RTs, further influence evolution in Fabaceae species. This study offers valuable clues into the evolution, function, transcriptional activity and epigenetic regulation of LTR-RTs in Fabaceae genomes.
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Affiliation(s)
- Long-Long Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Xin-Yu Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Li-Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yan-Ge Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Xiao-Ting Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yi Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Qing Su
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Ning Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China.
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Ghosh Dasgupta M, Senthilkumar S, Muthulakshmi E, Balasubramanian A. The draft genome reveals early duplication event in Pterocarpus santalinus: an endemic timber species. PLANTA 2023; 258:27. [PMID: 37358820 DOI: 10.1007/s00425-023-04190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
MAIN CONCLUSION A 541 Mb draft genome of Pterocarpus santalinus is presented and evidence of whole-genome duplication in the Eocene period with expansion of drought responsive gene families is documented. Pterocarpus santalinus Linn. f., popularly known as Red Sanders, is a deciduous tree, endemic to southern parts of Eastern Ghats in India. The heartwood is highly valued in the international market due to its deep red colour, fragrant heartwood and wavy grained texture. In the present study, a high-quality draft genome of P. santalinus was assembled using short and long reads generated from Illumina and Oxford Nanopore Sequencing platforms, respectively. The haploid genome size was estimated at 541 Mb and the hybrid assembly showed 99.60% genome completeness. A total of 51,713 consensus gene set were predicted with 31,437 annotated genes. The age of the whole-genome duplication event in the species was dated at 30-39 mya with 95% confidence suggesting early genome duplication event during the Eocene period. Concurrently, phylogenomic assessment of seven Papilionoideae members including P. santalinus grouped the species based on the tribal classification and established divergence of the tribe Dalbergieae from tribe Trifolieae at ~ 54.20 mya. A significant expansion of water deprivation/drought responsive gene families documented in the study probably explains the occurrence of the species in dry rocky patches. Additionally, re-sequencing of six diverse genotypes predicted one variant every 27 bases. This report presents the first draft genome in the genus Pterocarpus and the unprecedented genomic information generated is expected to accelerate population divergence studies in the species in relation to its endemic nature, support trait-based breeding programme and aid in development of diagnostic tools for timber forensics.
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Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India.
| | - Shanmugavel Senthilkumar
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India
| | - Eswaran Muthulakshmi
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India
| | - Aiyar Balasubramanian
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India
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Abstract
Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.
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Affiliation(s)
- Peng Xu
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen 518054, China.
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Zhang G, Hu Y, Huang MZ, Huang WC, Liu DK, Zhang D, Hu H, Downing JL, Liu ZJ, Ma H. Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1204-1225. [PMID: 36738233 DOI: 10.1111/jipb.13462] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/03/2023] [Indexed: 05/13/2023]
Abstract
Orchidaceae (with >28,000 orchid species) are one of the two largest plant families, with economically and ecologically important species, and occupy global and diverse niches with primary distribution in rainforests. Among orchids, 70% grow on other plants as epiphytes; epiphytes contribute up to ~50% of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes, thereby contributing to the health of these ecosystems. Orchids account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of epiphytism. Extensive phylogenetic studies of Orchidaceae and subgroups have ;been crucial for understanding relationships among many orchid lineages, although some uncertainties remain. For example, in the largest subfamily Epidendroideae with nearly all epiphytic orchids, relationships among some tribes and many subtribes are still controversial, hampering evolutionary analyses of epiphytism. Here we obtained 1,450 low-copy nuclear genes from 610 orchid species, including 431 with newly generated transcriptomes, and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and subtribes. We also provide generally well-supported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies. Molecular clock analyses estimated the Orchidaceae origin at ~132 million years ago (Ma) and divergences of most subtribes from 52 to 29 Ma. Character reconstruction supports at least 14 parallel origins of epiphytism; one such origin was placed at the most recent common ancestor of ~95% of epiphytic orchids and linked to modern rainforests. Ten occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary, contributing to ~80% of the Orchidaceae diversity. This study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and new insights into the evolution of epiphytism in vascular plants.
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Affiliation(s)
- Guojin Zhang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ming-Zhong Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Chang Huang
- Shanghai Chenshan Botanical Garden, Songjiang, Shanghai, 201602, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haihua Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jason L Downing
- Fairchild Tropical Botanic Garden, Coral Gables, Florida, 33156, USA
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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Huang J, Xu W, Zhai J, Hu Y, Guo J, Zhang C, Zhao Y, Zhang L, Martine C, Ma H, Huang CH. Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants. PLANT COMMUNICATIONS 2023:100595. [PMID: 36966360 PMCID: PMC10363554 DOI: 10.1016/j.xplc.2023.100595] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/02/2023] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.
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Affiliation(s)
- Jie Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China; Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Weibin Xu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Junwen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | | | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, State College, PA 16802, USA.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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37
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Yao G, Zhang YQ, Barrett C, Xue B, Bellot S, Baker WJ, Ge XJ. A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biol 2023; 21:50. [PMID: 36882831 PMCID: PMC9993706 DOI: 10.1186/s12915-023-01544-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research. RESULTS Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support. CONCLUSIONS The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.
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Affiliation(s)
- Gang Yao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yu-Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Present Address: College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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Bhatia H, Srivastava G, Mehrotra R. Legumes from the Paleocene sediments of India and their ecological significance. PLANT DIVERSITY 2023; 45:199-210. [PMID: 37069925 PMCID: PMC10105134 DOI: 10.1016/j.pld.2022.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 06/17/2023]
Abstract
During the early Paleogene, greenhouse gases created warm global climates. These warm climates redistributed the habitat of marine and terrestrial biota globally. Understanding the ecology of biotas under extremely warm climates is important to decipher their behavior in future climate warming. Here we report two new legume fossils (Leguminocarpum meghalayensis Bhatia, Srivastava et Mehrotra sp. nov., and Parvileguminophyllum damalgiriensis Bhatia, Srivastava et Mehrotra sp. nov.) from the late Paleocene sediments of Tura Formation of Meghalaya, northeast India. Globally, the Paleocene legume fossil records indicate that legumes most likely immigrated to India from Africa via the Ladakh-Kohistan Arc during the early Paleogene. Moreover, previously reconstructed climate data from the Tura Formation indicate that legumes were well adapted to a warm seasonal climate with monsoon rains.
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Affiliation(s)
- Harshita Bhatia
- Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow 226 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gaurav Srivastava
- Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow 226 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - R.C. Mehrotra
- Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow 226 007, India
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Cheng L, Li M, Wang Y, Han Q, Hao Y, Qiao Z, Zhang W, Qiu L, Gong A, Zhang Z, Li T, Luo S, Tang L, Liu D, Yin H, Lu S, Balbuena TS, Zhao Y. Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population. FRONTIERS IN PLANT SCIENCE 2023; 14:1114284. [PMID: 36890899 PMCID: PMC9986275 DOI: 10.3389/fpls.2023.1114284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yachao Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Lin Qiu
- Institute of Forestry Science, Xinyang Forestry Bureau, Xinyang, Henan, China
| | - Andong Gong
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhihan Zhang
- College of Engineering and Technology, Northeast Forestry University, Harbin, China
| | - Tao Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Shanshan Luo
- College of Agriculture, Guizhou University, Guiyang, China
| | - Linshuang Tang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Daliang Liu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Hao Yin
- College of Agriculture, Guizhou University, Guiyang, China
| | - Song Lu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal, Brazil
| | - Yiyong Zhao
- College of Agriculture, Guizhou University, Guiyang, China
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. ANNALS OF BOTANY 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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Li J, Shen J, Wang R, Chen Y, Zhang T, Wang H, Guo C, Qi J. The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution. PLANT COMMUNICATIONS 2023; 4:100422. [PMID: 35957520 PMCID: PMC9860166 DOI: 10.1016/j.xplc.2022.100422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 05/27/2023]
Abstract
Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation. Polyploidization events have been extensively studied in some Fabaceae plants, but the occurrence of new genes is still concealed, owing to a lack of genomic information on certain species of the basal clade of Fabaceae. Cercis chinensis (Cercidoideae) is one such species; it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae. To facilitate genomic studies on Fabaceae, we performed genome sequencing of C. chinensis and obtained a 352.84 Mb genome, which was further assembled into seven pseudochromosomes with 30 612 predicted protein-coding genes. Compared with other legume genomes, that of C. chinensis exhibits no lineage-specific polyploidization event. Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae. Among them, dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes. They differ significantly from established genes in coding sequence length, exon number, guanine-cytosine content, and expression patterns among tissues. Functional analysis revealed that many new genes are related to asparagine metabolism. This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.
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Affiliation(s)
- Jinglong Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jingting Shen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haifeng Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
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Czyż KB, Taylor CM, Kawaliło M, Koczyk G. Gain or Loss? Evidence for Legume Predisposition to Symbiotic Interactions with Rhizobia via Loss of Pathogen-Resistance-Related Gene Families. Int J Mol Sci 2022; 23:ijms232416003. [PMID: 36555644 PMCID: PMC9783688 DOI: 10.3390/ijms232416003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Nodulation is a hallmark yet non-universal characteristic of legumes. It is unknown whether the mechanisms underlying nitrogen-fixing symbioses evolved within legumes and the broader nitrogen-fixing clade (NFC) repeatedly de novo or based on common ancestral pathways. Ten new transcriptomes representing members from the Cercidoideae and Caesalpinioideae subfamilies were supplemented with published omics data from 65 angiosperms, to investigate how gene content correlates with nodulation capacity within Fabaceae and the NFC. Orthogroup analysis categorized annotated genes into 64150 orthogroups, of which 19 were significantly differentially represented between nodulating versus non-nodulating NFC species and were most commonly absent in nodulating taxa. The distribution of six over-represented orthogroups within Viridiplantae representatives suggested that genomic evolution events causing gene family expansions, including whole-genome duplications (WGDs), were unlikely to have facilitated the development of stable symbioses within Fabaceae as a whole. Instead, an absence of representation of 13 orthogroups indicated that losses of genes involved in trichome development, defense and wounding responses were strongly associated with rhizobial symbiosis in legumes. This finding provides novel evidence of a lineage-specific predisposition for the evolution and/or stabilization of nodulation in Fabaceae, in which a loss of pathogen resistance genes may have allowed for stable mutualistic interactions with rhizobia.
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Affiliation(s)
- Katarzyna B. Czyż
- Biometry and Bioinformatics Team, Institute of Plant Genetics Polish Academy of Science, 60-479 Poznań, Poland
- Correspondence:
| | - Candy M. Taylor
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Michał Kawaliło
- Biometry and Bioinformatics Team, Institute of Plant Genetics Polish Academy of Science, 60-479 Poznań, Poland
| | - Grzegorz Koczyk
- Biometry and Bioinformatics Team, Institute of Plant Genetics Polish Academy of Science, 60-479 Poznań, Poland
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Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae. Chromosome Res 2022; 30:477-492. [PMID: 35715657 DOI: 10.1007/s10577-022-09702-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 01/25/2023]
Abstract
The tribe Phaseoleae includes several legume crops with assembled genomes. Comparative genomic studies have evidenced the preservation of large genomic blocks among legumes, although chromosome dynamics during Phaseoleae evolution has not been investigated. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We identified GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata and searched for GBs in different genomes of the Phaseolinae (P. lunatus) and Glycininae (Amphicarpaea edgeworthii) subtribes and Spatholobus suberectus (sister to Phaseolinae and Glycininae), using Medicago truncatula as the outgroup. We also used oligo-FISH probes of two P. vulgaris chromosomes to paint the orthologous chromosomes of two non-sequenced Phaseolinae species. We inferred the APK as having n = 11 and 19 GBs (A to S), hypothesizing five chromosome fusions that reduced the ancestral legume karyotype to n = 11. We identified the rearrangements among the APK and the subtribes and species, with extensive centromere repositioning in Phaseolus. We also reconstructed the chromosome number reduction in S. suberectus. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.
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Chen D, Zhang T, Chen Y, Ma H, Qi J. Tree2GD: a phylogenomic method to detect large-scale gene duplication events. Bioinformatics 2022; 38:5317-5321. [PMID: 36218394 DOI: 10.1093/bioinformatics/btac669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/11/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy. RESULTS Here, we present Tree2GD, an integrated method to identify large-scale gene duplication events by automatically perform multiple procedures, including sequence alignment, recognition of homolog, gene tree/species tree reconciliation, Ks distribution of gene duplicates and synteny analyses. Application of Tree2GD on 2 datasets, 12 metazoan genomes and 68 angiosperms, successfully identifies all reported whole-genome duplication events exhibited by these species, showing effectiveness and efficiency of Tree2GD on phylogenomic analyses of large-scale gene duplications. AVAILABILITY AND IMPLEMENTATION Tree2GD is written in Python and C++ and is available at https://github.com/Dee-chen/Tree2gd. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Duoyuan Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.,Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hong Ma
- Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
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Jiang D, Liao L, Xing H, Chen Z, Luo X, Li HL. Interplay of Ecological Opportunities and Functional Traits Drives the Evolution and Diversification of Millettiod Legumes (Fabaceae). Genes (Basel) 2022; 13:genes13122220. [PMID: 36553487 PMCID: PMC9777679 DOI: 10.3390/genes13122220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Understanding the striking diversity of the angiosperms is a paramount issue in biology and of interest to biologists. The Millettiod legumes is one of the most hyper-diverse groups of the legume family, containing many economically important medicine, furniture and craft species. In the present study, we explore how the interplay of past climate change, ecological opportunities and functional traits' evolution may have triggered diversification of the Millettiod legumes. Using a comprehensive species-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that three dramatic accumulations of the Millettiod legumes occurred during the Miocene. The rapid diversification of the Millettiod legumes in the Miocene was driven by ecological opportunities created by the emergence of new niches and range expansion. Additionally, habit shifts and the switch between biomes might have facilitated the rapid diversification of the Millettiod legumes. The Millettiod legumes provide an excellent case for supporting the idea that the interplay of functional traits, biomes, and climatic and geographic factors drives evolutionary success.
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Xie DF, Xie C, Ren T, Song BN, Zhou SD, He XJ. Plastid phylogenomic insights into relationships, divergence, and evolution of Apiales. PLANTA 2022; 256:117. [PMID: 36376499 DOI: 10.1007/s00425-022-04031-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/06/2022] [Indexed: 06/16/2023]
Abstract
Members of Apiales are monophyletic and radiated in the Late Cretaceous. Fruit morphologies are critical for Apiales evolution and negative selection and mutation pressure play important roles in environmental adaptation. Apiales include many foods, spices, medicinal, and ornamental plants, but the phylogenetic relationships, origin and divergence, and adaptive evolution remain poorly understood. Here, we reconstructed Apiales phylogeny based on 72 plastid genes from 280 species plastid genomes representing six of seven families of this order. Highly supported phylogenetic relationships were detected, which revealed that each family of Apiales is monophyletic and confirmed that Pennanticeae is a member of Apiales. Genera Centella and Dickinsia are members of Apiaceae, and the genus Hydrocotyle previously classified into Apiaceae is confirmed to belong to Araliaceae. Besides, coalescent phylogenetic analysis and gene trees cluster revealed ten genes that can be used for distinguishing species among families of Apiales. Molecular dating suggested that the Apiales originated during the mid-Cretaceous (109.51 Ma), with the families' radiation occurring in the Late Cretaceous. Apiaceae species exhibit higher differentiation compared to other families. Ancestral trait reconstruction suggested that fruit morphological evolution may be related to shifts in plant types (herbaceous or woody), which in turn is related to the distribution areas and species numbers. Codon bias and positive selection analyses suggest that negative selection and mutation pressure may play important roles in environmental adaptation of Apiales members. Our results improve the phylogenetic framework of Apiales and provide insights into the origin, divergence, and adaptive evolution of this order and its members.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Chuan Xie
- Sichuan Academy of Forestry, Chengdu, 610081, Sichuan, People's Republic of China
| | - Ting Ren
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Bo-Ni Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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Cheng L, Han Q, Chen F, Li M, Balbuena TS, Zhao Y. Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae. Front Genet 2022; 13:1031705. [PMID: 36406110 PMCID: PMC9670182 DOI: 10.3389/fgene.2022.1031705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Hybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited. We proposed the conception and method of identifying allopolyploidy events by phylogenomics. The reconciliation and summary of nuclear multi-labeled gene family trees were adopted to untangle hybridization events from next-generation data in our novel phylogenomic approach. Given horticulturalists’ relatively clear cultivated crossbreeding history, the water lily family is a suitable case for examining recent allopolyploidy events. Here, we reconstructed and confirmed the well-resolved nuclear phylogeny for the Nymphaeales family in the context of geological time as a framework for identifying hybridization signals. We successfully identified two possible allopolyploidy events with the parental lineages for the hybrids in the family Nymphaeaceae based on summarization from multi-labeled gene family trees of Nymphaeales. The lineages where species Nymphaea colorata and Nymphaea caerulea are located may be the progenitors of horticultural cultivated species Nymphaea ‘midnight’ and Nymphaea ‘Woods blue goddess’. The proposed hybridization hypothesis is also supported by horticultural breeding records. Our methodology can be widely applied to identify hybridization events and theoretically facilitate the genome breeding design of hybrid plants.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-oil Tree Biology and High-Value Utilization, Xinyang Normal University, Xinyang, Henan, China
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-oil Tree Biology and High-Value Utilization, Xinyang Normal University, Xinyang, Henan, China
| | - Fei Chen
- College of Tropical Crops, Hainan University, Haikou, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-oil Tree Biology and High-Value Utilization, Xinyang Normal University, Xinyang, Henan, China
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, UNESP, São Paulo, Brazil
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Yiyong Zhao, ,
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McLay TGB, Murphy DJ, Holmes GD, Mathews S, Brown GK, Cantrill DJ, Udovicic F, Allnutt TR, Jackson CJ. A genome resource for Acacia, Australia's largest plant genus. PLoS One 2022; 17:e0274267. [PMID: 36240205 PMCID: PMC9565413 DOI: 10.1371/journal.pone.0274267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022] Open
Abstract
Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes.
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Affiliation(s)
- Todd G. B. McLay
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Gareth D. Holmes
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Sarah Mathews
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Gillian K. Brown
- Queensland Herbarium, Department of Environment and Science, Toowong, Queensland, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | | | - Chris J. Jackson
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
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50
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de Faria SM, Ringelberg JJ, Gross E, Koenen EJM, Cardoso D, Ametsitsi GKD, Akomatey J, Maluk M, Tak N, Gehlot HS, Wright KM, Teaumroong N, Songwattana P, de Lima HC, Prin Y, Zartman CE, Sprent JI, Ardley J, Hughes CE, James EK. The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes. THE NEW PHYTOLOGIST 2022; 235:2365-2377. [PMID: 35901264 PMCID: PMC9541511 DOI: 10.1111/nph.18321] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/31/2022] [Indexed: 05/12/2023]
Abstract
Nitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2 -fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen-fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane-bound symbiosomes (SYMs). Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs. We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species-rich pantropical legume clade.
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Affiliation(s)
- Sergio M. de Faria
- Embrapa Agrobiologia465 km 07, SeropédicaRio de JaneiroBR23891‐000Brazil
| | - Jens J. Ringelberg
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Eduardo Gross
- Departamento de Ciências Agrárias e AmbientaisUniversidade Estadual de Santa Cruz (UESC)IlhéusBA45662‐900Brazil
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN‐TREE)Instituto de Biologia, Universidade Federal de Bahia (UFBA)Rua Barão de Jeremoabo, s.n., OndinaSalvador40170‐115BABrazil
| | | | - John Akomatey
- CSIR‐Forestry Research Institute of GhanaFUMESUAPO Box UP 63 KNUSTKumasiGhana
| | - Marta Maluk
- The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Nisha Tak
- Department of Botany, BNF and Microbial Genomics Lab.Center of Advanced Study, Jai Narain Vyas UniversityJodhpur342001RajasthanIndia
| | - Hukam S. Gehlot
- Department of Botany, BNF and Microbial Genomics Lab.Center of Advanced Study, Jai Narain Vyas UniversityJodhpur342001RajasthanIndia
| | | | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhonratchasima30000Thailand
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhonratchasima30000Thailand
| | - Haroldo C. de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (JBRJ/MMA)Rua Pacheco Leão 915Rio de Janeiro22460‐030RJBrazil
- Instituto Nacional da Mata Atlântica (INMA‐MCTI)Av. José Ruschi 4Santa Teresa29650‐000ESBrazil
| | - Yves Prin
- CIRAD, UMR LSTMCampus de Baillarguet34398Montpellier Cedex 5France
| | - Charles E. Zartman
- Departamento de BiodiversidadeInstituto Nacional de Pesquisas da Amazônia (INPA)Av. André Araújo Aleixo, Caixa Postal 478Manaus69060‐001AMBrazil
| | - Janet I. Sprent
- Division of Plant SciencesUniversity of Dundee at The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Julie Ardley
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWA6150Australia
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Euan K. James
- The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
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