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Luo L, Fang D, Wang F, Lin Q, Sahu SK, Song Y, Kang J, Guang X, Liu M, Luo S, Hao G, Liu H, Guo X. The chromosome-level genomes of the herbal magnoliids Warburgia ugandensis and Saururus chinensis. Sci Data 2024; 11:554. [PMID: 38816414 PMCID: PMC11139940 DOI: 10.1038/s41597-024-03229-9] [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: 07/27/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Warburgia ugandensis and Saururus chinensis are two of the most important medicinal plants in magnoliids and are widely utilized in traditional Kenya and Chinese medicine, respectively. The absence of higher-quality reference genomes has hindered research on the medicinal compound biosynthesis mechanisms of these plants. We report the chromosome-level genome assemblies of W. ugandensis and S. chinensis, and generated 1.13 Gb and 0.53 Gb genomes from 74 and 27 scaffolds, respectively, using BGI-DIPSEQ, Nanopore, and Hi-C sequencing. The scaffold N50 lengths were 82.97 Mb and 48.53 Mb, and the assemblies were anchored to 14 and 11 chromosomes of W. ugandensis and S. chinensis, respectively. In total, 24,739 and 20,561 genes were annotated, and 98.5% and 98% of the BUSCO genes were fully represented, respectively. The chromosome-level genomes of W. ugandensis and S. chinensis will be valuable resources for understanding the genetics of these medicinal plants, studying the evolution of magnoliids and angiosperms and conserving plant genetic resources.
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Affiliation(s)
- Liuming Luo
- College of Life Science, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiongqiong Lin
- College of Life Science, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | - Yali Song
- BGI Research, Beijing, 102601, China
| | | | - Xuanmin Guang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Shixiao Luo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Gang Hao
- College of Life Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- BGI Research, Wuhan, 430074, China.
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Friis EM, Crane PR, Pedersen KR, Marone F. Cretaceous chloranthoids: early prominence, extinct diversity and missing links. ANNALS OF BOTANY 2024; 133:225-260. [PMID: 38597914 PMCID: PMC11005782 DOI: 10.1093/aob/mcad137] [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: 05/01/2023] [Accepted: 09/07/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND The Chloranthaceae comprise four extant genera (Hedyosmum, Ascarina, Chloranthus and Sarcandra), all with simple flowers. Molecular phylogenetics indicates that the Chloranthaceae diverged very early in angiosperm evolution, although how they are related to eudicots, magnoliids, monocots and Ceratophyllum is uncertain. Fossil pollen similar to that of Ascarina and Hedyosmum has long been recognized in the Early Cretaceous, but over the last four decades evidence of extinct Chloranthaceae based on other types of fossils has expanded dramatically and contributes significantly to understanding the evolution of the family. SCOPE Studies of fossils from the Cretaceous, especially mesofossils of Early Cretaceous age from Portugal and eastern North America, recognized diverse flowers, fruits, seeds, staminate inflorescences and stamens of extinct chloranthoids. These early chloranthoids include forms related to extant Hedyosmum and also to the Ascarina, Chloranthus and Sarcandra clade. In the Late Cretaceous there are several occurrences of distinctive fossil androecia related to extant Chloranthus. The rich and still expanding Cretaceous record of Chloranthaceae contrasts with a very sparse Cenozoic record, emphasizing that the four extant genera are likely to be relictual, although speciation within the genera might have occurred in relatively recent times. In this study, we describe three new genera of Early Cretaceous chloranthoids and summarize current knowledge on the extinct diversity of the group. CONCLUSIONS The evolutionary lineage that includes extant Chloranthaceae is diverse and abundantly represented in Early Cretaceous mesofossil floras that provide some of the earliest evidence of angiosperm reproductive structures. Extinct chloranthoids, some of which are clearly in the Chloranthaceae crown group, fill some of the morphological gaps that currently separate the extant genera, help to illuminate how some of the unusual features of extant Chloranthaceae evolved and suggest that Chloranthaceae are of disproportionate importance for a more refined understanding of ecology and phylogeny of early angiosperm diversification.
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Affiliation(s)
- Else Marie Friis
- Department of Geoscience, University of Aarhus, Høegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Peter R Crane
- Oak Spring Garden Foundation, 1776 Loughborough Lane, Upperville, VA 20184, USA
- Yale School of the Environment, Yale University, New Haven, CT 06511, USA
| | - Kaj Raunsgaard Pedersen
- Department of Geoscience, University of Aarhus, Høegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
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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: 0] [Impact Index Per Article: 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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Mahajan S, Chakraborty A, Bisht MS, Sil T, Sharma VK. Genome sequencing and functional analysis of a multipurpose medicinal herb Tinospora cordifolia (Giloy). Sci Rep 2024; 14:2799. [PMID: 38307917 PMCID: PMC10837142 DOI: 10.1038/s41598-024-53176-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Tinospora cordifolia (Willd.) Hook.f. & Thomson, also known as Giloy, is among the most important medicinal plants that have numerous therapeutic applications in human health due to the production of a diverse array of secondary metabolites. To gain genomic insights into the medicinal properties of T. cordifolia, the genome sequencing was carried out using 10× Genomics linked read and Nanopore long-read technologies. The draft genome assembly of T. cordifolia was comprised of 1.01 Gbp, which is the genome sequenced from the plant family Menispermaceae. We also performed the genome size estimation for T. cordifolia, which was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed. The genome and transcriptome assemblies were used to construct the gene set, resulting in 17,245 coding gene sequences. Further, the phylogenetic position of T. cordifolia was also positioned as basal eudicot by constructing a genome-wide phylogenetic tree using multiple species. Further, a comprehensive comparative evolutionary analysis of gene families contraction/expansion and multiple signatures of adaptive evolution was performed. The genes involved in benzyl iso-quinoline alkaloid, terpenoid, lignin and flavonoid biosynthesis pathways were found with signatures of adaptive evolution. These evolutionary adaptations in genes provide genomic insights into the presence of diverse medicinal properties of this plant. The genes involved in the common symbiosis signalling pathway associated with endosymbiosis (Arbuscular Mycorrhiza) were found to be adaptively evolved. The genes involved in adventitious root formation, peroxisome biogenesis, biosynthesis of phytohormones, and tolerance against abiotic and biotic stresses were also found to be adaptively evolved in T. cordifolia.
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Affiliation(s)
- Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Titas Sil
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India.
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Xiang Y, Zhang T, Zhao Y, Dong H, Chen H, Hu Y, Huang CH, Xiang J, Ma H. Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:228-251. [PMID: 38351714 DOI: 10.1111/jipb.13618] [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: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024]
Abstract
Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary-fruit "modules" each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single-seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole-genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.
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Affiliation(s)
- Yezi Xiang
- State Key Laboratory of Genetic Engineering, 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
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, 27708, NC, USA
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, 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
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering, 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
| | - Hongjin Dong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Hongyi Chen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Yi Hu
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering, 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
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, 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, 16802, PA, USA
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Yu X, Feng Y, Zhang J. Characterization of the Complete Mitochondrial Genome of Wintersweet ( Chimonanthus praecox) and Comparative Analysis within Magnoliids. Life (Basel) 2024; 14:182. [PMID: 38398691 PMCID: PMC10890521 DOI: 10.3390/life14020182] [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: 01/08/2024] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as "La Mei" in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (-0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T's and G's in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution.
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Affiliation(s)
- Xianxian Yu
- College of Urban and Environmental Sciences, Xuchang University, Xuchang 461000, China;
| | - Yanlei Feng
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China;
| | - Jie Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
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R N, Kh M, Hegde SN, Begum N, Kukkupuni SK, Gowda M, Narendran P. De novo genome assembly and annotation of the medicinal plant Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thom's. Funct Integr Genomics 2023; 23:330. [PMID: 37935874 DOI: 10.1007/s10142-023-01262-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]
Abstract
Indian natural climbing shrub Tinospora cordifolia, often known as "Guduchi" and "Amrita," is a highly esteemed medicinal plant in the Indian system of medicine (ISM). It is a member of the Menispermaceae family which consists of a rich source of protein, micronutrients, and rich source of bioactive components which are used in treating various systemic diseases. The current study was designed to know the biological characterization of the plant genome and biosynthesis of plant metabolites essential for its medicinal applications. Tinospora cordifolia's complete genome was sequenced using Illumina HiSeq2500 sequencing technology. The draft genome was assembled through a de novo method. An integrative genome annotation approach was used to perform functional gene prediction. The pathway analysis was carried out using the KEGG database. The total genome size obtained after genome assembly was 894 Mb with an N50 of 9148 bp. The integrative annotation approach resulted in 35,111 protein-coding genes. In addition, genes responsible for the synthesis of syringin, a secondary metabolite found in plants, were identified. In comparison to the standard drug (dopamine, rasagiline, and selegiline), syringin's molecular docking exhibited a greater binding affinity from the range of - 4.3 to - 6.6 kcal/mol for all the targets of Parkinson's disease and for Alzheimer's targets; it has shown the maximum potency from the range of - 6.5 to - 7.4 kcal/mol with respect to the standard drug (donepezil, galantamine, and rivastigmine). This study provides the genomic information of Tinospora cordifolia which is helpful in understanding genomic insights and metabolic pathways connected to the corresponding plant genome and predicts the possible useful effect for the molecular characterization of therapeutic drugs.
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Affiliation(s)
- Namitha R
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Manasa Kh
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Santhosh N Hegde
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Noorunnisa Begum
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Subrahmanya Kumar Kukkupuni
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Malali Gowda
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India.
| | - Pavithra Narendran
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India.
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Renner SS. A time tree for the evolution of insect, vertebrate, wind, and water pollination in the angiosperms. THE NEW PHYTOLOGIST 2023; 240:464-465. [PMID: 37564031 DOI: 10.1111/nph.19201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
This article is a Commentary on Stephens et al. (2023), 240: 880–891.
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Affiliation(s)
- Susanne S Renner
- Department of Biology, Washington University, St Louis, MO, 63130, USA
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Wang S, Gao J, Li Z, Chen K, Pu W, Feng C. Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships in Nicotiana. FRONTIERS IN PLANT SCIENCE 2023; 14:1205683. [PMID: 37575947 PMCID: PMC10421670 DOI: 10.3389/fpls.2023.1205683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
Introduction Nicotiana L. (Solanaceae) is of great scientific and economic importance, and polyploidization has been pivotal in shaping this genus. Despite many previous studies on the Nicotiana phylogenetic relationship and hybridization, evidence from whole genome data is still lacking. Methods In this study, we obtained 995 low-copy genes and plastid transcript fragments from the transcriptome datasets of 26 Nicotiana species, including all sections. We reconstructed the phylogenetic relationship and phylogenetic network of diploid species. Results The incongruence among gene trees showed that the formation of N. sylvestris involved incomplete lineage sorting. The nuclear-plastid discordance and nuclear introgression absence indicated that organelle capture from section Trigonophyllae was involved in forming section Petunioides. Furthermore, we analyzed the evolutionary origin of polyploid species and dated the time of hybridization events based on the analysis of PhyloNet, sequence similarity search, and phylogeny of subgenome approaches. Our results highly evidenced the hybrid origins of five polyploid sections, including sections Nicotiana, Repandae, Rusticae, Polydicliae, and Suaveolentes. Notably, we provide novel insights into the hybridization event of section Polydicliae and Suaveolentes. The section Polydicliae formed from a single hybridization event between maternal progenitor N. attenuata and paternal progenitor N. undulata; the N. sylvestris (paternal progenitor) and the N. glauca (maternal progenitor) were involved in the formation of section Suaveolentes. Discussion This study represents the first exploration of Nicotiana polyploidization events and phylogenetic relationships using the high-throughput RNA-seq approach. It will provide guidance for further studies in molecular systematics, population genetics, and ecological adaption studies in Nicotiana and other related species.
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Affiliation(s)
- Shuaibin Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Junping Gao
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Zhaowu Li
- Puai Medical College, Shaoyang University, Shaoyang, China
| | - Kai Chen
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Wenxuan Pu
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Chen Feng
- Jiangxi Provincial Key Laboratory of ex-situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
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Wu Y, Ge Y, Hu H, Stidham TA, Li Z, Bailleul AM, Zhou Z. Intra-gastric phytoliths provide evidence for folivory in basal avialans of the Early Cretaceous Jehol Biota. Nat Commun 2023; 14:4558. [PMID: 37507397 PMCID: PMC10382595 DOI: 10.1038/s41467-023-40311-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Angiosperms became the dominant plant group in early to middle Cretaceous terrestrial ecosystems, coincident with the timing of the earliest pulse of bird diversification. While living birds and angiosperms exhibit strong interactions across pollination/nectivory, seed dispersal/frugivory, and folivory, documentation of the evolutionary origins and construction of that ecological complexity remains scarce in the Mesozoic. Through the first study of preserved in situ dietary derived phytoliths in a nearly complete skeleton of the early diverging avialan clade Jeholornithidae, we provide direct dietary evidence that Jeholornis consumed leaves likely from the magnoliid angiosperm clade, and these results lend further support for early ecological connections among the earliest birds and angiosperms. The broad diet of the early diverging avialan Jeholornis including at least fruits and leaves marks a clear transition in the early evolution of birds in the establishment of an arboreal (angiosperm) herbivore niche in the Early Cretaceous occupied largely by birds today. Morphometric reanalysis of the lower jaw of Jeholornis further supports a generalized morphology shared with other herbivorous birds, including an extant avian folivore, the hoatzin.
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Affiliation(s)
- Yan Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, 100044, Beijing, China
| | - Yong Ge
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, 100044, Beijing, China
- Department of Archaeology and Anthropology, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Han Hu
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK
| | - Thomas A Stidham
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, 100044, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhiheng Li
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, 100044, Beijing, China.
| | - Alida M Bailleul
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, 100044, Beijing, China
| | - Zhonghe Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, 100044, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
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11
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Wu Z, Zhang T, Li J, Chen S, Grin IR, Zharkov DO, Yu B, Li H. Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet. FRONTIERS IN PLANT SCIENCE 2023; 14:1185440. [PMID: 37332716 PMCID: PMC10272600 DOI: 10.3389/fpls.2023.1185440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.
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Affiliation(s)
- Zhirui Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Tingyue Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jinna Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Inga R. Grin
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
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12
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Benítez-Villaseñor A, Granados Mendoza C, Wanke S, Peñafiel Cevallos M, Freire ME, Lemmon EM, Lemmon AR, Magallón S. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 2023; 181:107714. [PMID: 36708940 DOI: 10.1016/j.ympev.2023.107714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Anchored Hybrid Enrichment (AHE) is a tool for capturing orthologous regions of the nuclear genome shared in low or single copy across lineages. Despite the increasing number of studies using this method, its usefulness to estimate relationships at deeper taxonomic levels in plants has not been fully explored. Here we present a proof of concept about the performance of nuclear loci obtained with AHE to infer phylogenetic relationships and explore the use of gene sampling schemes to estimate divergence times in Asterales. We recovered low-copy nuclear loci using the AHE method from herbarium material and silica-preserved samples. Maximum likelihood, Bayesian inference, and coalescence approaches were used to reconstruct phylogenomic relationships. Dating analyses were conducted under a multispecies coalescent approach by jointly inferring species tree and divergence times with random gene sampling schemes and multiple calibrations. We recovered 403 low-copy nuclear loci for 63 species representing nine out of eleven families of Asterales. Phylogenetic hypotheses were congruent among the applied methods and previously published results. Analyses with concatenated datasets were strongly supported, but coalescence-based analyses showed low support for the phylogenetic position of families Argophyllaceae and Alseuosmiaceae. Estimated family ages were congruent among gene sampling schemes, with the mean age for Asterales around 130 Myr. Our study documents the usefulness of AHE for resolving phylogenetic relationships at deep phylogenetic levels in Asterales. Observed phylogenetic inconsistencies were possibly due to the non-inclusion of families Phellinceae and Pentaphragmataceae. Random gene sampling schemes produced consistent age estimates with coalescence and species tree relaxed clock approaches.
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Affiliation(s)
- Adriana Benítez-Villaseñor
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, C.P.04510 Ciudad de México, Mexico.
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Marcia Peñafiel Cevallos
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - M Efraín Freire
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, United States.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306-4120, United States.
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico.
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13
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Xue JY, Li Z, Hu SY, Kao SM, Zhao T, Wang JY, Wang Y, Chen M, Qiu Y, Fan HY, Liu Y, Shao ZQ, Van de Peer Y. The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1021-1034. [PMID: 36602036 PMCID: PMC7614262 DOI: 10.1111/tpj.16097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Saururus chinensis, an herbaceous magnoliid without perianth, represents a clade of early-diverging angiosperms that have gone through woodiness-herbaceousness transition and pollination obstacles: the characteristic white leaves underneath inflorescence during flowering time are considered a substitute for perianth to attract insect pollinators. Here, using the newly sequenced S. chinensis genome, we revisited the phylogenetic position of magnoliids within mesangiosperms, and recovered a sister relationship for magnoliids and Chloranthales. By considering differentially expressed genes, we identified candidate genes that are involved in the morphogenesis of the white leaves in S. chinensis. Among those genes, we verified - in a transgenic experiment with Arabidopsis - that increasing the expression of the "pseudo-etiolation in light" gene (ScPEL) can inhibit the biosynthesis of chlorophyll. ScPEL is thus likely responsible for the switches between green and white leaves, suggesting that changes in gene expression may underlie the evolution of pollination strategies. Despite being an herbaceous plant, S. chinensis still has vascular cambium and maintains the potential for secondary growth as a woody plant, because the necessary machinery, i.e., the entire gene set involved in lignin biosynthesis, is well preserved. However, similar expression levels of two key genes (CCR and CAD) between the stem and other tissues in the lignin biosynthesis pathway are possibly associated with the herbaceous nature of S. chinensis. In conclusion, the S. chinensis genome provides valuable insights into the adaptive evolution of pollination in Saururaceae and reveals a possible mechanism for the evolution of herbaceousness in magnoliids.
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Affiliation(s)
- Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shu-Min Kao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jie-Yu Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yue Wang
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Min Chen
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yichun Qiu
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Hai-Yun Fan
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Liu
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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14
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Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships. Mol Genet Genomics 2023; 298:399-411. [PMID: 36592219 DOI: 10.1007/s00438-022-01991-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Species in Gentiana section Cruciata are important alpine plants with a center of diversity and speciation in Qinghai-Tibet Plateau (QTP), and some of these species are sympatrically distributed in northeastern QTP. Studies on genome features and natural selection signatures of sympatric species in section Crucata have been impeded by a lack of genomic resources. Here, we showed transcript characterizations and molecular footprints of selection effects on G. straminea, G. dahurica and G. officinalis based on the comparative transcriptome. A total of 62.97 Gb clean reads were obtained with unigene numbers per species ranging from 141,819 to 236,408 after assembly. We found that these three species had similar distribution of functional categories in different databases, and key enzyme-encoding genes involved in the iridoids biosynthesis were also obtained. The selective pressure analyses indicated that most paired orthologs between these three species were subject to negative selection, and only a low proportion of the orthologs that underwent positive selection were detected. We found that some positive selected genes were involved in "catalytic activity", "metabolic process", "response to stimulus" and "response to stress". Besides, large numbers of SSR primer pairs with transferabilities were successfully designed based on the available transcriptome datasets of three Gentiana species. The phylogenetic relationships reconstructed based on 352 single-copy nuclear genes provided a rough phylogenetic framework for this genus and confirmed the monophyly of section Cruciata. Our study not only provides insights for the natural selection effects on sympatric Gentiana species, but also enhances future genetic breeding or evolutionary studies on Qinjiao species.
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15
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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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16
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Duan Y, Fu S, Ye Z, Bu W. Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification. ZOOL SCR 2023. [DOI: 10.1111/zsc.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yujie Duan
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
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17
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Hu H, Sun P, Yang Y, Ma J, Liu J. Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36647606 DOI: 10.1111/jipb.13455] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.
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Affiliation(s)
- Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Pengchuan Sun
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianxiang Ma
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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18
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Shen Z, Ding X, Cheng J, Wu F, Yin H, Wang M. Phylogenetic studies of magnoliids: Advances and perspectives. FRONTIERS IN PLANT SCIENCE 2023; 13:1100302. [PMID: 36726671 PMCID: PMC9885158 DOI: 10.3389/fpls.2022.1100302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Magnoliids are the largest flowering plant clades outside of the eudicots and monocots, which are distributed worldwide and have high economic, ornamental and ecological values. Eudicots, monocots and magnoliids are the three major clades of Mesangiospermae, and their phylogenetic relationship is one of the most interesting issues. In recent years, with the continuous accumulation of genomic information, the evolutionary status of magnoliids has become a hot spot in plant phylogenetic research. Although great efforts have been made to study the evolution of magnoliids using molecular data from several representative species such as nuclear genome, plastid genome, mitochondrial genome, and transcriptome, the results of current studies on the phylogenetic status of magnoliids are inconsistent. Here, we systematically describe the current understanding of the molecular research on magnoliid phylogeny and review the differences in the evolutionary state of magnoliids. Understanding the research approaches and limitations of magnoliid phylogeny can guide research strategies to further improve the study of the phylogenetic evolution of magnoliids.
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Affiliation(s)
- Zhiguo Shen
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Xin Ding
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Jianming Cheng
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Fangfang Wu
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Minyan Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
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19
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Kasianov AS, Klepikova AV, Mayorov AV, Buzanov GS, Logacheva MD, Penin AA. Interspecific comparison of gene expression profiles using machine learning. PLoS Comput Biol 2023; 19:e1010743. [PMID: 36626392 PMCID: PMC9879537 DOI: 10.1371/journal.pcbi.1010743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/26/2023] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Interspecific gene comparisons are the keystones for many areas of biological research and are especially important for the translation of knowledge from model organisms to economically important species. Currently they are hampered by the low resolution of methods based on sequence analysis and by the complex evolutionary history of eukaryotic genes. This is especially critical for plants, whose genomes are shaped by multiple whole genome duplications and subsequent gene loss. This requires the development of new methods for comparing the functions of genes in different species. Here, we report ISEEML (Interspecific Similarity of Expression Evaluated using Machine Learning)-a novel machine learning-based algorithm for interspecific gene classification. In contrast to previous studies focused on sequence similarity, our algorithm focuses on functional similarity inferred from the comparison of gene expression profiles. We propose novel metrics for expression pattern similarity-expression score (ES)-that is suitable for species with differing morphologies. As a proof of concept, we compare detailed transcriptome maps of Arabidopsis thaliana, the model species, Zea mays (maize) and Fagopyrum esculentum (common buckwheat), which are species that represent distant clades within flowering plants. The classifier resulted in an AUC of 0.91; under the ES threshold of 0.5, the specificity was 94%, and sensitivity was 72%.
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Affiliation(s)
- Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Mayorov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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20
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Costa FP, Schrago CG, Mello B. Assessing the relative performance of fast molecular dating methods for phylogenomic data. BMC Genomics 2022; 23:798. [PMID: 36460948 PMCID: PMC9719170 DOI: 10.1186/s12864-022-09030-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
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Affiliation(s)
- Fernanda P. Costa
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Carlos G. Schrago
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Beatriz Mello
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
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21
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Che X, Lai W, Wang S, Wang X, Hu W, Chen H, Xie X, Tang M. Multiple PHT1 family phosphate transporters are recruited for mycorrhizal symbiosis in Eucalyptus grandis and conserved PHT1;4 is a requirement for the arbuscular mycorrhizal symbiosis. TREE PHYSIOLOGY 2022; 42:2020-2039. [PMID: 35512354 DOI: 10.1093/treephys/tpac050] [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: 06/09/2021] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Eucalypts engage in a mutualistic endosymbiosis with arbuscular mycorrhizal (AM) fungi to acquire mineral nutrients from soils, particularly inorganic phosphate (Pi). In return, the host plant provides organic carbons to its fungal partners. However, the mechanism by which the Eucalyptus plants acquire Pi released from the AM fungi has remained elusive. In this study, we investigated the characterization of potential PHOSPHATE TRANSPORTER1 (PHT1) family Pi transporters in AM symbiosis in Eucalyptus grandis W. Hill ex Maiden. We show that multiple PHT1 family Pi transporters were recruited for AM symbiosis in E. grandis. We further report that EgPT4, an E. grandis member of the PHT1 family, is conserved across angiosperms and is exclusively expressed in AM roots with arbuscule-containing cells and localizes to the periarbuscular membrane (PAM). EgPT4 was able to complement a yeast mutant strain defective in all inorganic Pi transporters and mediate Pi uptake. Importantly, EgPT4 is essential for improved E. grandis growth, total phosphorus concentration and arbuscule development during symbiosis. Moreover, silencing of EgPT4 led to the induction of polyphosphate accumulation relevant genes of Rhizophagus irregularis DAOM 197198. Collectively, our results unravel a pivotal role for EgPT4 in symbiotic Pi transport across the PAM required for arbuscule development in E. grandis.
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Affiliation(s)
- Xianrong Che
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Wenzhen Lai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Sijia Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Xinyang Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
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22
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Wang Z, Li Y, Sun P, Zhu M, Wang D, Lu Z, Hu H, Xu R, Zhang J, Ma J, Liu J, Yang Y. A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots. BMC Biol 2022; 20:216. [PMID: 36195948 PMCID: PMC9533543 DOI: 10.1186/s12915-022-01420-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
Background Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. Results Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. Conclusions Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01420-1.
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Affiliation(s)
- Zhenyue Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mingjia Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Dandan Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Hongyin Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Renping Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China. .,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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23
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Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet. Int J Mol Sci 2022; 23:ijms231911573. [PMID: 36232881 PMCID: PMC9569505 DOI: 10.3390/ijms231911573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 12/04/2022] Open
Abstract
As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.
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24
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Xu KW, Wei XF, Lin CX, Zhang M, Zhang Q, Zhou P, Fang YM, Xue JY, Duan YF. The chromosome-level holly ( Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change. FRONTIERS IN PLANT SCIENCE 2022; 13:982323. [PMID: 36072321 PMCID: PMC9441949 DOI: 10.3389/fpls.2022.982323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/04/2022] [Indexed: 05/30/2023]
Abstract
The Ilex L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, Ilex species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of Ilex latifolia, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered I. latifolia as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in I. latifolia. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of I. latifolia leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of I. latifolia. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of I. latifolia, providing a data basis and promising clues for further applications.
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Affiliation(s)
- Ke-Wang Xu
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xue-Fen Wei
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Chen-Xue Lin
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Min Zhang
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Jiangsu Academy of Forestry, Nanjing, China
| | - Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Peng Zhou
- Jiangsu Academy of Forestry, Nanjing, China
| | - Yan-Ming Fang
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Yi-Fan Duan
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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25
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Xu X, Li X, Wang D. New Insights Into the Backbone Phylogeny and Character Evolution of Corydalis (Papaveraceae) Based on Plastome Data. FRONTIERS IN PLANT SCIENCE 2022; 13:926574. [PMID: 35991421 PMCID: PMC9389321 DOI: 10.3389/fpls.2022.926574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 05/27/2023]
Abstract
A robust backbone phylogeny is fundamental for developing a stable classification and is instructive for further research. However, it was still not available for Corydalis DC., a species-rich (> 500 species), ecologically and medically important, but taxonomically notoriously difficult genus. Here, we constructed backbone phylogeny and estimated the divergence of Corydalis based on the plastome data from 39 Corydalis species (32 newly sequenced), which represent ca. 80% of sections and series across this genus. Our phylogenetic analyses recovered six fully supported main clades (I-VI) and provided full support for the majority of lineages within Corydalis. Section Archaeocapnos was unexpectedly turned out to be sister to the rest of the subg. Corydalis s. l. (clades IV-VI), thus treating as a distinct clade (clade III) to render all the main clades monophyletic. Additionally, some unusual plastome structural rearrangements were constantly detected within Corydalis and were proven to be lineage-specific in this study, which, in turn, provided further support to our phylogeny. A segment containing five genes (trnV-UAC-rbcL) in the plastome's LSC region was either normally located downstream of the ndhC gene in clade I species or translocated downstream of the atpH gene in clade II species or translocated to downstream of the trnK-UUU gene in clade III-VI species. The unique large inversion (ca. 50 kb) in the plastome LSC region of clade III species, representing an intermediate stage of the above translocation in clades IV-VI, firmly supported clade III as a distinct and early diverged clade within this large lineage (clades III-VI). Our phylogeny contradicted substantially with the morphology-based taxonomy, rejected the treatment of tuberous species as an independent evolutionary group, and proved that some commonly used diagnostic characters (e.g., root and rhizome) were results of convergent evolution, suggestive of unreliability in Corydalis. We dated the origin of crown Corydalis to the early Eocene (crown age 49.08 Ma) and revealed possible explosive radiation around 25 Ma, coinciding with the drastic uplift of the Qinghai-Tibetan Plateau in Oligocene and Miocene. This study provided the most reliable and robust backbone phylogeny of Corydalis to date and shed some new insights on the evolution of Corydalis.
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Affiliation(s)
- Xiaodong Xu
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xuexiu Li
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Dong Wang
- School of Life Sciences, Central China Normal University, Wuhan, China
- Bio-Resources key Laboratory of Shaanxi Province, Shaanxi University of Technology, Hanzhong, China
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26
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Liu L, Zhang Y, Tumi L, Suni ML, Arakaki M, Burgess KS, Ge X. Genetic markers in Andean
Puya
species (Bromeliaceae) with implications on plastome evolution and phylogeny. Ecol Evol 2022; 12:e9159. [PMID: 35919393 PMCID: PMC9336176 DOI: 10.1002/ece3.9159] [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: 01/20/2022] [Revised: 06/19/2022] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%–37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein‐coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69–78 tandem repeats, 45–60 SSRs (simple sequence repeats), and 8–22 repeat structures among 13 species. Four protein‐coding genes were identified under positive site‐specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.
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Affiliation(s)
- Lu Liu
- 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
- University of Chinese Academy of Sciences Beijing 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
- College of Pharmacy Shaanxi University of Chinese Medicine Xi'an China
| | - Liscely Tumi
- Facultad de Ciencias Biológicas Universidad Nacional Mayor de San Marcos Lima Peru
| | - Mery L. Suni
- Facultad de Ciencias Biológicas Universidad Nacional Mayor de San Marcos Lima Peru
| | - Mónica Arakaki
- Facultad de Ciencias Biológicas Universidad Nacional Mayor de San Marcos Lima Peru
| | - Kevin S. Burgess
- Department of Biology, Columbus State University University System of Georgia Columbus Georgia USA
| | - 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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27
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Cheng L, Li M, Han Q, Qiao Z, Hao Y, Balbuena TS, Zhao Y. Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity. BIOLOGY 2022; 11:biology11071007. [PMID: 36101388 PMCID: PMC9311850 DOI: 10.3390/biology11071007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary The Theaceae includes more than 300 species of great morphological diversity and has immense economic, cultural, and ornamental values. However, the evolutionary history of this family remains elusive. We integrated 91 genomes and transcriptome datasets of Theaceae and successfully resolved the phylogeny of Theaceae including relatives of cultivated tea plants from both extensive low-copy and multi-copy nuclear gene markers. Bayes-based molecular dating revealed that the ancestor of the tea family originated slightly earlier than the K-Pg boundary (Mass extinction events including the extinction of dinosaurs) with early diversification of three tribes associated with the Early Eocene Climatic Optimum. Further speciation analysis suggested a sole significant diversification shift rate in the common ancestor of Camellia associated with the Mid-Miocene Climatic Optimum. Collectively, polyploidy events, and key morphological innovation characters, such as pericarp with seed coat hardening, could possibly contribute to the Theaceae species diversity. Abstract Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed. Our results maximumly supported that the tribes Stewartieae and Gordonieae are successive sister groups to the tribe Theeae from both coalescent and super matrix ML tree analyses. Moreover, in the most evolved tribe, Theeae, the monophyletic genera Pyrenaria, Apterosperma, and Polyspora are the successive sister groups of Camellia. We also yield a well-resolved relationship of Camellia, which contains the vast majority of Theaceae species richness. Molecular dating suggests that Theaceae originated in the late L-Cretaceous, with subsequent early radiation under the Early Eocene Climatic Optimal (EECO) for the three tribes. A diversification rate shift was detected in the common ancestors of Camellia with subsequent acceleration in speciation rate under the climate optimum in the early Miocene. These results provide a phylogenetic framework and new insights into factors that likely have contributed to the survival of Theaceae, especially a successful radiation event of genus Camellia members to subtropic/tropic regions. These novel findings will facilitate the efficient conservation and utilization of germplasm resources for breeding cultivated tea and oil-tea. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Theaceae.
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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 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal 14884-900, Brazil;
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence:
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28
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Wu Z, Chen H, Pan Y, Feng H, Fang D, Yang J, Wang Y, Yang J, Sahu SK, Liu J, Xing Y, Wang X, Liu M, Luo X, Gao P, Li L, Liu Z, Yang H, Liu X, Xu X, Liu H, Wang E. Genome of Hippophae rhamnoides provides insights into a conserved molecular mechanism in actinorhizal and rhizobial symbioses. THE NEW PHYTOLOGIST 2022; 235:276-291. [PMID: 35118662 DOI: 10.1111/nph.18017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Sea buckthorn (Hippophae rhamnoides), a horticulturally multipurpose species in the family Elaeagnaceae, can build associations with Frankia actinomycetes to enable symbiotic nitrogen-fixing. Currently, no high-quality reference genome is available for an actinorhizal plant, which greatly hinders the study of actinorhizal symbiotic nodulation. Here, by combining short-read, long-read and Hi-C sequencing technologies, we generated a chromosome-level reference genome of H. rhamnoides (scaffold N50: 65 Mb, and genome size: 730 Mb) and predicted 30 812 protein-coding genes mainly on 12 pseudochromosomes. Hippophae rhamnoides was found to share a high proportion of symbiotic nodulation genes with Medicago truncatula, implying a shared molecular mechanism between actinorhizal and rhizobial symbioses. Phylogenetic analysis clustered the three paralogous NODULE INCEPTION (NIN) genes of H. rhamnoides with those of other nodulating species, forming the NIN group that most likely evolved from the ancestral NLP group. The genome of H. rhamnoides will help us to decipher the underlying genetic programming of actinorhizal symbiosis, and our high-quality genome and transcriptomic resources will make H. rhamnoides a new excellent model plant for actinorhizal symbiosis research.
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Affiliation(s)
- Zefeng Wu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Hongyun Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Ya Pan
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Huan Feng
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jun Yang
- Shanghai Chenshan Plant Science Research Center (CAS), Shanghai, 210602, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Jianling Liu
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Yu'e Xing
- Jinzhong Institute of Forestry, Jinzhong, Shanxi, 030600, China
| | - Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xinyue Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Peng Gao
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Lifeng Li
- Jinzhong Municipal Planning and Natural Resources Bureau, Jinzhong, Shanxi, 030600, China
| | - Zhongjian 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, Fujian, 350002, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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Deng R, Li W, Berhow MA, Jander G, Zhou S. Phenolic sucrose esters: evolution, regulation, biosynthesis, and biological functions. PLANT MOLECULAR BIOLOGY 2022; 109:369-383. [PMID: 33783685 DOI: 10.1007/s11103-021-01142-y] [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: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Phenolic sucrose esters (PSEs) are a diverse group of specialized metabolites that are present in several angiosperm lineages. Phylogenetic reconstruction and structural variation suggest that these metabolites may have evolved independently in monocots and dicots. Constitutive variation in PSE abundance across plant organs and developmental stages is correlated with transcriptional regulation of the upstream phenylpropanoid pathway, whereas pathogen induction is regulated by stress-related phytohormones such as ethylene. Shared structural features of PSEs indicate that their biosynthesis may involve one or more hydroxycinnamoyl transferases and BAHD acetyltransferases, which could be identified by correlative analyses of multi-omics datasets. Elucidation of the core biosynthetic pathway of PSEs will be essential for more detailed studies of the biological function of these compounds and their potential medicinal and agricultural applications.
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Affiliation(s)
- Renyu Deng
- 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, 440307, China
| | - Wei 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, 440307, China
| | - Mark A Berhow
- Functional Foods Research Unit, Agricultural Research Service, USDA, National Center for Agricultural Utilization Research, 1815 N, University Street, Peoria, IL, 61604, USA
| | - Georg Jander
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Shaoqun Zhou
- 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, 440307, China.
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30
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Ye F, Kment P, Rédei D, Luo JY, Wang YH, Kuechler SM, Zhang WW, Chen PP, Wu HY, Wu YZ, Sun XY, Ding L, Wang YR, Xie Q. Diversification of the phytophagous lineages of true bugs (Insecta: Hemiptera: Heteroptera) shortly after that of the flowering plants. Cladistics 2022; 38:403-428. [PMID: 35349192 DOI: 10.1111/cla.12501] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 12/20/2022] Open
Abstract
More than 95% of phytophagous true bug (Hemiptera: Heteroptera) species belong to four superfamilies: Miroidea (Cimicomorpha), Pentatomoidea, Coreoidea, and Lygaeoidea (all Pentatomomorpha). These iconic groups of highly diverse, overwhelmingly phytophagous insects include several economically prominent agricultural and silvicultural pest species, though their evolutionary history has not yet been well resolved. In particular, superfamily- and family-level phylogenetic relationships of these four lineages have remained controversial, and the divergence times of some crucial nodes for phytophagous true bugs have hitherto been little known, which hampers a better understanding of the evolutionary processes and patterns of phytophagous insects. In the present study, we used 150 species and concatenated nuclear and mitochondrial protein-coding genes and rRNA genes to infer the phylogenetic relationships within the Terheteroptera (Cimicomorpha + Pentatomomorpha) and estimated their divergence times. Our results support the monophyly of Cimicomorpha, Pentatomomorpha, Miroidea, Pentatomoidea, Pyrrhocoroidea, Coreoidea, and Lygaeoidea. The phylogenetic relationships across phytophagous lineages are largely congruent at deep nodes across the analyses based on different datasets and tree-reconstructing methods with just a few exceptions. Estimated divergence times and ancestral state reconstructions for feeding habit indicate that phytophagous true bugs explosively radiated in the Early Cretaceous-shortly after the angiosperm radiation-with the subsequent diversification of the most speciose clades (Mirinae, Pentatomidae, Coreinae, and Rhyparochromidae) in the Late Cretaceous.
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Affiliation(s)
- Fei Ye
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Petr Kment
- Department of Entomology, National Museum, Praha, Czech Republic
| | | | - Jiu-Yang Luo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yan-Hui Wang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Stefan M Kuechler
- Department of Animal Ecology II, University of Bayreuth, Bayreuth, Germany
| | | | - Ping-Ping Chen
- Netherlands Centre of Biodiversity Naturalis, Leiden, Netherlands
| | - Hao-Yang Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Xiao-Ya Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Lu Ding
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yue-Ran Wang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiang Xie
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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31
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Hou Z, Ma X, Shi X, Li X, Yang L, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomic insights into a Mesoproterozoic-Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae). Nat Commun 2022; 13:1610. [PMID: 35318329 PMCID: PMC8941102 DOI: 10.1038/s41467-022-29282-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/09/2022] [Indexed: 01/09/2023] Open
Abstract
The Ulvophyceae, a major group of green algae, is of particular evolutionary interest because of its remarkable morphological and ecological diversity. Its phylogenetic relationships and diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- and concatenation-based approaches to reconstruct the phylogeny of the Ulvophyceae and to explore the sources of conflict in previous phylogenomic studies. The Ulvophyceae is recovered as a paraphyletic group, with the Bryopsidales being a sister group to the Chlorophyceae, and the remaining taxa forming a clade (Ulvophyceae sensu stricto). Molecular clock analyses with different calibration strategies emphasize the large impact of fossil calibrations, and indicate a Meso-Neoproterozoic origin of the Ulvophyceae (sensu stricto), earlier than previous estimates. The results imply that ulvophyceans may have had a profound influence on oceanic redox structures and global biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition. “Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
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Affiliation(s)
- Zheng Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xi Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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32
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Szandar K, Krawczyk K, Myszczyński K, Ślipiko M, Sawicki J, Szczecińska M. Breaking the limits - multichromosomal structure of an early eudicot Pulsatilla patens mitogenome reveals extensive RNA-editing, longest repeats and chloroplast derived regions among sequenced land plant mitogenomes. BMC PLANT BIOLOGY 2022; 22:109. [PMID: 35264098 PMCID: PMC8905907 DOI: 10.1186/s12870-022-03492-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The mitogenomes of vascular plants are one of the most structurally diverse molecules. In the present study we characterize mitogenomes of a rare and endangered species Pulsatilla patens. We investigated the gene content and its RNA editing potential, repeats distribution and plastid derived sequences. RESULTS The mitogenome structure of early divergent eudicot, endangered Pulsatilla patens does not support the master chromosome hypothesis, revealing the presence of three linear chromosomes of total length 986 613 bp. The molecules are shaped by the presence of extremely long, exceeding 87 kbp repeats and multiple chloroplast-derived regions including nearly complete inverted repeat. Since the plastid IR content of Ranunculales is very characteristic, the incorporation into mitogenome could be explained rather by intracellular transfer than mitochondrial HGT. The mitogenome contains almost a complete set of genes known from other vascular plants with exception of rps10 and sdh3, the latter being present but pseudogenized. Analysis of long ORFs enabled the identification of genes which are rarely present in plant mitogenomes, including RNA and DNA polymerases, albeit their presence even at species level is variable. Mitochondrial transcripts of P. patens were edited with a high frequency, which exceeded the level known in other analyzed angiosperms, despite the strict qualification criteria of counting the editing events and taking into analysis generally less frequently edited leaf transcriptome. The total number of edited sites was 902 and nad4 was identified as the most heavily edited gene with 65 C to U changes. Non-canonical, reverse U to C editing was not detected. Comparative analysis of mitochondrial genes of three Pulsatilla species revealed a level of variation comparable to chloroplast CDS dataset and much higher infrageneric differentiation than in other known angiosperm genera. The variation found in CDS of mitochondrial genes is comparable to values found among Pulsatilla plastomes. Despite the complicated mitogenome structure, 14 single copy regions of 329 kbp, not splitted by repeats or plastid-derived sequences (MTPT), revealed the potential for phylogenetic, phylogeographic and population genetics studies by revealing intra- and interspecific collinearity. CONCLUSIONS This study provides valuable new information about mitochondrial genome of early divergent eudicots, Pulsatilla patens, revealed multi-chromosomal structure and shed new light on mitogenomics of early eudicots.
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Affiliation(s)
- Kamil Szandar
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Kamil Myszczyński
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland.
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Monika Szczecińska
- Department of Ecology and Environmental Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10- 727, Olsztyn, Poland.
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33
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Choi IS, Cardoso D, de Queiroz LP, de Lima HC, Lee C, Ruhlman TA, Jansen RK, Wojciechowski MF. Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics. FRONTIERS IN PLANT SCIENCE 2022; 13:823190. [PMID: 35283880 PMCID: PMC8905342 DOI: 10.3389/fpls.2022.823190] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/31/2022] [Indexed: 05/31/2023]
Abstract
Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
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Affiliation(s)
- In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - 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 da Bahia, Salvador, Brazil
| | - Luciano P. de Queiroz
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Haroldo C. de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
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34
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Wang W, Gao L, Cui X. A New Year's spotlight on two years of publication. PLANT COMMUNICATIONS 2022; 3:100274. [PMID: 35059635 PMCID: PMC8760135 DOI: 10.1016/j.xplc.2021.100274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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35
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Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:808156. [PMID: 35498716 PMCID: PMC9038950 DOI: 10.3389/fpls.2022.808156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 05/03/2023]
Abstract
The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.
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Affiliation(s)
- Ting Yang
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sunil Kumar Sahu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- *Correspondence: Sunil Kumar Sahu,
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yang Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Weixue Mu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Xin Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Huan Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Bojian Zhong,
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36
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Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE. Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). PHYTOKEYS 2022; 205:3-58. [PMID: 36762007 PMCID: PMC9848904 DOI: 10.3897/phytokeys.205.85866] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 05/05/2023]
Abstract
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
- Present address: 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
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, Capão do Leão 96010-900, Rio Grande do Sul, BrazilUniversidade Federal de PelotasRio Grande do SulBrazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, 91501-970, BrazilUniversidade Federal do Rio Grande do SulRio Grande do SulBrazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n – Novo Horizonte, 44036-900, Feira de Santana, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, AustraliaRoyal Botanic Gardens VictoriaMelbourneAustralia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB)ParisFrance
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, CanadaUniversité de MontréalMontrealCanada
| | - 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
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UKAccelerated Taxonomy Department, Royal Botanic GardensRichmondUnited Kingdom
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
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Shen Z, Li W, Li Y, Liu M, Cao H, Provart N, Ding X, Sun M, Tang Z, Yue C, Cao Y, Yuan D, Zhang L. The red flower wintersweet genome provides insights into the evolution of magnoliids and the molecular mechanism for tepal color development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1662-1678. [PMID: 34624152 DOI: 10.1111/tpj.15533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Wintersweet (Chimonanthus praecox) is one of the most important ornamental plants. Its color is mainly determined by the middle tepals. However, the molecular mechanisms underlying the intriguing flower color development among different wintersweet groups are still largely unknown. In addition, wintersweet belongs to magnoliids, and the phylogenetic position of magnoliids remains to be determined conclusively. Here, the whole genome of red flower wintersweet, a new wintersweet type, was sequenced and assembled with high quality. The genome comprised 11 super-scaffolds (chromosomes) with a total size of 737.03 Mb. Based on the analyses of the long branch attraction, incomplete lineage sorting, sparse taxon sampling, and other factors, we suggest that a bifurcating tree may not fully represent the complex early diversification of the angiosperms and that magnoliids are most likely sister to the eudicots. The wintersweet genome appears to have undergone two whole-genome duplication (WGD) events: a recent WGD event representing an independent event specific to the Calycanthaceae and an ancient WGD event shared by Laurales. By integrating genomic, transcriptomic, and metabolomic data, CpANS1 and the transcription factor CpMYB1 were found to play key roles in regulating tepal color development, whereas CpMYB1 needs to form a complex with bHLH and WD40 to fully perform its regulatory function. The present study not only provides novel insights into the evolution of magnoliids and the molecular mechanism for flower color development, but also lays the foundation for subsequent functional genomics study and molecular breeding of wintersweet.
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Affiliation(s)
- Zhiguo Shen
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, Henan, 450008, People's Republic of China
| | - Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China
| | - Yanli Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China
| | - Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China
| | - Heping Cao
- US Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, 70124, USA
| | - Nicholas Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Xin Ding
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, Henan, 450008, People's Republic of China
| | - Meng Sun
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, Henan, 450008, People's Republic of China
| | - Zhenghui Tang
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, Henan, 450008, People's Republic of China
| | - Changping Yue
- Forestry Research Institute of Yanling County, Xuchang, Henan, 461200, People's Republic of China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, People's Republic of China
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Sun W, Li Z, Xiang S, Ni L, Zhang D, Chen D, Qiu M, Zhang Q, Xiao L, Din L, Li Y, Liao X, Liu X, Jiang Y, Zhang P, Ni H, Wang Y, Yue Y, Wu X, Din X, Huang W, Wang Z, Ma X, Liu B, Zou X, Van de Peer Y, Liu Z, Zou S. The Euscaphis japonica genome and the evolution of malvids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1382-1399. [PMID: 34587334 PMCID: PMC9298382 DOI: 10.1111/tpj.15518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.
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Guo X, Fang D, Sahu SK, Yang S, Guang X, Folk R, Smith SA, Chanderbali AS, Chen S, Liu M, Yang T, Zhang S, Liu X, Xu X, Soltis PS, Soltis DE, Liu H. Chloranthus genome provides insights into the early diversification of angiosperms. Nat Commun 2021; 12:6930. [PMID: 34836973 PMCID: PMC8626473 DOI: 10.1038/s41467-021-26922-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.
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Affiliation(s)
- Xing Guo
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Dongming Fang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Sunil Kumar Sahu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shuai Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Xuanmin Guang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ryan Folk
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 United States of America
| | - Stephen A. Smith
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 United States of America
| | - Andre S. Chanderbali
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Sisi Chen
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.9227.e0000000119573309South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650 China
| | - Min Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ting Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shouzhou Zhang
- grid.9227.e0000000119573309Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Xin Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839BGI-Fuyang, BGI-Shenzhen, Fuyang, 236009 China
| | - Xun Xu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pamela S. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Douglas E. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America ,grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, FL 32611 United States of America
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
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Ma J, Sun P, Wang D, Wang Z, Yang J, Li Y, Mu W, Xu R, Wu Y, Dong C, Shrestha N, Liu J, Yang Y. The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms. Nat Commun 2021; 12:6929. [PMID: 34836967 PMCID: PMC8626421 DOI: 10.1038/s41467-021-26931-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Most extant angiosperms belong to Mesangiospermae, which comprises eudicots, monocots, magnoliids, Chloranthales and Ceratophyllales. However, phylogenetic relationships between these five lineages remain unclear. Here, we report the high-quality genome of a member of the Chloranthales lineage (Chloranthus sessilifolius). We detect only one whole genome duplication within this species and find that polyploidization events in different Mesangiospermae lineage are mutually independent. We also find that the members of all floral development-related gene lineages are present in C. sessilifolius despite its extremely simplified flower. The AP1 and PI genes, however, show a weak floral tissue-specialized expression. Our phylogenomic analyses suggest that Chloranthales and magnoliids are sister groups, and both are together sister to the clade comprising Ceratophyllales and eudicots, while the monocot lineage is sister to all other Mesangiospermae. Our findings suggest that in addition to hybridization, incomplete lineage sorting may largely account for phylogenetic inconsistencies between the observed gene trees.
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Affiliation(s)
- Jianxiang Ma
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dandan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhenyue Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jiao Yang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Renping Xu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Wu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Congcong Dong
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China.
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Li HT, Luo Y, Gan L, Ma PF, Gao LM, Yang JB, Cai J, Gitzendanner MA, Fritsch PW, Zhang T, Jin JJ, Zeng CX, Wang H, Yu WB, Zhang R, van der Bank M, Olmstead RG, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Yi TS, Li DZ. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol 2021; 19:232. [PMID: 34711223 PMCID: PMC8555322 DOI: 10.1186/s12915-021-01166-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. RESULTS Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. CONCLUSIONS We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lu Gan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10025, USA
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hong Wang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195-5325, USA
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, England, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Qin L, Hu Y, Wang J, Wang X, Zhao R, Shan H, Li K, Xu P, Wu H, Yan X, Liu L, Yi X, Wanke S, Bowers JE, Leebens-Mack JH, dePamphilis CW, Soltis PS, Soltis DE, Kong H, Jiao Y. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. NATURE PLANTS 2021; 7:1239-1253. [PMID: 34475528 PMCID: PMC8445822 DOI: 10.1038/s41477-021-00990-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/22/2021] [Indexed: 05/04/2023]
Abstract
Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.
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Affiliation(s)
- Liuyu Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoliang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanying Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lumei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Stefan Wanke
- Institute of Botany, Dresden University of Technology, Dresden, Germany
| | - John E Bowers
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | | | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Li X, Zhao Y, Tu X, Li C, Zhu Y, Zhong H, Liu ZJ, Wu S, Zhai J. Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers. PLANT DIVERSITY 2021; 43:281-291. [PMID: 34485770 PMCID: PMC8390927 DOI: 10.1016/j.pld.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 06/13/2023]
Abstract
The wood sorrel family, Oxalidaceae, is mainly composed of annual or perennial herbs, a few shrubs, and trees distributed from temperate to tropical zones. Members of Oxalidaceae are of high medicinal, ornamental, and economic value. Despite the rich diversity and value of Oxalidaceae, few molecular markers or plastomes are available for phylogenetic analysis of the family. Here, we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family, as well as the plastome of Rourea microphylla in the closely related family Connaraceae. The eight plastomes ranged in length from 150,673 bp (Biophytum sensitivum) to 156,609 bp (R. microphylla). Genome annotations revealed a total of 129-131 genes, including 83-84 protein-coding genes, eight rRNA genes, 37 tRNA genes, and two to three pseudogenes. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. The smaller plastomes of herbs B. sensitivum and three Oxalis species are associated with variations in IR region sizes, intergenic region variation, and gene or intron loss. We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae. The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae. Our research also supported the monophyly of the COM (Celastrales, Oxalidales, and Malpighiales) clade.
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Affiliation(s)
- Xiaoping Li
- 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
| | - Yamei Zhao
- 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
| | - Xiongde Tu
- 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
| | - Chengru Li
- 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
| | - Yating Zhu
- 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
| | - Hui Zhong
- 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
| | - 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
| | - Shasha Wu
- 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
| | - Junwen Zhai
- 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
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Guo XM, Wang ZF, Zhang Y, Wang RJ. Chromosomal-level assembly of the Leptodermis oblonga (Rubiaceae) genome and its phylogenetic implications. Genomics 2021; 113:3072-3082. [PMID: 34246693 DOI: 10.1016/j.ygeno.2021.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 11/26/2022]
Abstract
Rubiaceae is the fourth largest and a taxonomically complex family of angiosperms. Many species in this family harbor low reproductive isolation and frequently exhibit inconsistent phenotypic characteristics. Therefore, taxonomic classification and their phylogenetic relationships in the Rubiaceae family is challenging, especially in the genus Leptodermis. Considering the low taxonomic confusion and wide distribution, Leptodermis oblonga is selected as a representative Leptodermis for genome sequencing. The assemblies resulted in 497 Mbp nuclear and 155,100 bp chloroplast genomes, respectively. Using the nuclear genome as a reference, SNPs were called from 37 Leptodermis species or varieties. The phylogenetic tree based on SNPs exhibited high resolution for species delimitation of the complex and well-resolved phylogenetic relationships in the genus. Moreover, 28,987 genes were predicted in the nuclear genome and used for comparative genomics study. As the first chromosomal-level genome of the subfamily Rubioideae in Rubiaceae, it will provide fruitfully evolutionary understanding in the family.
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Affiliation(s)
- Xiao-Ming Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Feng Wang
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China
| | - Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China; University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Jiang Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, China.
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Baker WJ, Bailey P, Barber V, Barker A, Bellot S, Bishop D, Botigué LR, Brewer G, Carruthers T, Clarkson JJ, Cook J, Cowan RS, Dodsworth S, Epitawalage N, Françoso E, Gallego B, Johnson MG, Kim JT, Leempoel K, Maurin O, McGinnie C, Pokorny L, Roy S, Stone M, Toledo E, Wickett NJ, Zuntini AR, Eiserhardt WL, Kersey PJ, Leitch IJ, Forest F. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Syst Biol 2021; 71:301-319. [PMID: 33983440 PMCID: PMC8830076 DOI: 10.1093/sysbio/syab035] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal}
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}{}$\%$\end{document}) and 2333 genera (17\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]
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Affiliation(s)
- William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Vanessa Barber
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Abigail Barker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - David Bishop
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Laura R Botigué
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - James J Clarkson
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Jeffrey Cook
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom
| | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan T Kim
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Computer Science, School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Plant Biotechnology and Genomics (CBGP) UPM-INIA, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Malcolm Stone
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Eduardo Toledo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | | | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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Wu JY, Xue JY, Van de Peer Y. Evolution of NLR Resistance Genes in Magnoliids: Dramatic Expansions of CNLs and Multiple Losses of TNLs. FRONTIERS IN PLANT SCIENCE 2021; 12:777157. [PMID: 34992620 PMCID: PMC8724549 DOI: 10.3389/fpls.2021.777157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 05/05/2023]
Abstract
Magnoliids are the third-largest group of angiosperms and occupy a critical position in angiosperm evolution. In the past years, due to the lack of sequenced genomes, the disease resistance gene (R gene) profile of magnoliids remains poorly understood. By the genome-wide identification of 1,832 NLR genes from seven magnoliid genomes, we built a framework for the evolution of magnoliid R genes. TNL genes were completely absent from five magnoliids, presumably due to immune pathway deficiencies. A total of 74 ancestral R genes (70 CNLs, 3 TNLs, and 1 RNL) were recovered in a common ancestor of magnoliids, from which all current NLR gene repertoires were derived. Tandem duplication served as the major drive for NLR genes expansion in seven magnoliid genomes, as most surveyed angiosperms. Due to recent rapid expansions, most magnoliids exhibited "a first expansion followed by a slight contraction and a further stronger expansion" evolutionary pattern, while both Litsea cubeba and Persea americana showed a two-times-repeated pattern of "expansion followed by contraction." The transcriptome analysis of seven different tissues of Saururus chinensis revealed a low expression of most NLR genes, with some R genes displaying a relatively higher expression in roots and fruits. Overall, our study sheds light on the evolution of NLR genes in magnoliids, compensates for insufficiency in major angiosperm lineages, and provides an important reference for a better understanding of angiosperm NLR genes.
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Affiliation(s)
- Jia-Yi Wu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology (CAS), Nanjing, China
- *Correspondence: Jia-Yu Xue, ;
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Department of Plant Biotechnology and Bioinformatics, VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Yves Van de Peer, ;
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47
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Yang Q, Fu GF, Wu ZQ, Li L, Zhao JL, Li QJ. Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China. FRONTIERS IN PLANT SCIENCE 2021; 12:774482. [PMID: 35082807 PMCID: PMC8784687 DOI: 10.3389/fpls.2021.774482] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/08/2021] [Indexed: 05/11/2023]
Abstract
Chloroplasts are critical to plant survival and adaptive evolution. The comparison of chloroplast genomes could provide insight into the adaptive evolution of closely related species. To identify potential adaptive evolution in the chloroplast genomes of four montane Zingiberaceae taxa (Cautleya, Roscoea, Rhynchanthus, and Pommereschea) that inhabit distinct habitats in the mountains of Yunnan, China, the nucleotide sequences of 13 complete chloroplast genomes, including five newly sequenced species, were characterized and compared. The five newly sequenced chloroplast genomes (162,878-163,831 bp) possessed typical quadripartite structures, which included a large single copy (LSC) region, a small single copy (SSC) region, and a pair of inverted repeat regions (IRa and IRb), and even though the structure was highly conserved among the 13 taxa, one of the rps19 genes was absent in Cautleya, possibly due to expansion of the LSC region. Positive selection of rpoA and ycf2 suggests that these montane species have experienced adaptive evolution to habitats with different sunlight intensities and that adaptation related to the chloroplast genome has played an important role in the evolution of Zingiberaceae taxa.
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Affiliation(s)
- Qian Yang
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Gao-Fei Fu
- 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, China
| | - Zhi-Qiang Wu
- 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, China
| | - Li Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- *Correspondence: Jian-Li Zhao,
| | - Qing-Jun Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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