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Ma H, Zhang E, An Y, Wei Y, Zhang L. Characterization of the complete chloroplast genome of the rare medicinal plant: Mandragora caulescens (Solanaceae). Mitochondrial DNA B Resour 2024; 9:812-817. [PMID: 38911521 PMCID: PMC11191837 DOI: 10.1080/23802359.2024.2368213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024] Open
Abstract
In this study, we assembled high-quality chloroplast genomes of Mandragora caulescens through a reference-guided approach using high-throughput Illumina sequencing reads. The resulting chloroplast genome assembly displayed a typical quadripartite structural organization, comprising a large single-copy (LSC) region of 85,233 bp, two inverted repeat (IR) regions of 25,685 bp each, and a small single-copy (SSC) region of 18,207 bp. The chloroplast genome harbored 141 complete genes, and its overall GC content was 38.0%. In maximum-likelihood (ML) and Bayesian inference (BI) trees, the 19 Solanaceae species formed a monophyletic group, dividing into two main clades. M. caulescens and Nicandra physalodes formed a monophyletic group, suggesting a close relationship between the two species. The M. caulescens cp genome presented in this study lays a good foundation for further genetic and genomic studies of the Solanaceae.
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Affiliation(s)
- Heqin Ma
- School of Biological Science & Engineering, Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, North Minzu University, Yinchuan, PR China
| | - Erdong Zhang
- School of Biological Science & Engineering, Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, North Minzu University, Yinchuan, PR China
| | - Yajing An
- School of Biological Science & Engineering, Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, North Minzu University, Yinchuan, PR China
| | - Yuqing Wei
- School of Biological Science & Engineering, Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, North Minzu University, Yinchuan, PR China
| | - Lei Zhang
- School of Biological Science & Engineering, Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, North Minzu University, Yinchuan, PR China
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Javaid N, Ramzan M, Jabeen S, Du Y, Anwar M, Xiqiang S. The chloroplast genome of Chrozophora sabulosa Kar. & Kir. and its exploration in the evolutionary position uncertainty of genus Chrozophora. BMC Genomics 2024; 25:597. [PMID: 38877411 PMCID: PMC11177538 DOI: 10.1186/s12864-024-10366-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 04/29/2024] [Indexed: 06/16/2024] Open
Abstract
Chrozophora sabulosa Kar. & Kir. is a biennial herbaceous plant that belongs to the Euphorbiaceae family and has medicinal properties. This research aimed to identify the genetic characteristics and phylogenetic position of the Chrozophora genus within the Euphorbiaceae family. The evolutionary position of the Chrozophora genus was previously unknown due to insufficient research. Therefore, to determine the evolutionary link between C. sabulosa and other related species, we conducted a study using the NGS Illumina platform to sequence the C. sabulosa chloroplast (cp.) genome. The study results showed that the genome was 156,488 bp in length. It had a quadripartite structure consisting of two inverted repeats (IRb and IRa) of 24,649-bp, separated by an 87,696-bp LSC region and a 19,494-bp SSC region. The CP genome contained 113 unique genes, including four rRNA genes, 30 tRNA genes, and 79 CDS genes. In the second copy of the inverted repeat, there were 18 duplicated genes. The C. sabulosa lacks the petD, petB, rpl2, and rps16 intron. The analysis of simple sequence repeats (SSRs) revealed 93 SSR loci of 22 types and 78 oligonucleotide repeats of four kinds. The phylogenetic investigation showed that the Chrozophora genus evolved paraphyletically from other members of the Euphorbiaceae family. To support the phylogenetic findings, we selected species from the Euphorbiaceae and Phyllanthaceae families to compare with C. sabulosa for Ks and Ka substitution rates, InDels investigation, IR contraction and expansion, and SNPs analysis. The results of these comparative studies align with the phylogenetic findings. We identified six highly polymorphic regions shared by both families, which could be used as molecular identifiers for the Chrozophora genus (rpl33-rps18, rps18-rpl20, rps15-ycf1, ndhG-ndhI, psaI-ycf4, petA-psbJ). The cp. genome sequence of C. sabulosa reveals the evolution of plastid sequences in Chrozophora species. This is the first time the cp. genome of a Chrozophora genus has been sequenced, serving as a foundation for future sequencing of other species within the Chrozophoreae tribe and facilitating in-depth taxonomic research. The results of this research will also aid in identifying new Chrozophora species.
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Affiliation(s)
- Nida Javaid
- The Islamia University, Bahawalpur, Pakistan
| | | | | | - Yanjun Du
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs,School of Rural Revitalization), Hainan University, Haikou, P.R. China
| | - Muhammad Anwar
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs,School of Rural Revitalization), Hainan University, Haikou, P.R. China.
- Key Laboratory of Genetic and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou, P.R. China.
- , Haikou, P.R. China.
| | - Song Xiqiang
- Key Laboratory of Genetic and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou, P.R. China.
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Zhang L, Zhang E, Wei Y, Zheng G. Phylogenetic analysis and divergence time estimation of Lycium species in China based on the chloroplast genomes. BMC Genomics 2024; 25:569. [PMID: 38844874 PMCID: PMC11155141 DOI: 10.1186/s12864-024-10487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Lycium is an economically and ecologically important genus of shrubs, consisting of approximately 70 species distributed worldwide, 15 of which are located in China. Despite the economic and ecological importance of Lycium, its phylogeny, interspecific relationships, and evolutionary history remain relatively unknown. In this study, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of 15 species, including subspecies, of the genus Lycium from China. RESULTS We sequenced and annotated 15 CPGs in this study. Comparative analysis of these genomes from these Lycium species revealed a typical quadripartite structure, with a total sequence length ranging from 154,890 to 155,677 base pairs (bp). The CPGs was highly conserved and moderately differentiated. Through annotation, we identified a total of 128-132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the junctions of the IRb/LSC region were located in rps19 in all Lycium species, IRb/SSC between the ycf1 and ndhF genes, and SSC/IRa within the ycf1 gene. Sequence variation in the SSC region exceeded that in the IR region. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the 15 Lycium species. Comparative analyses revealed five hotspot regions in the CPG: trnR(UCU), atpF-atpH, ycf3-trnS(GGA), trnS(GGA), and trnL-UAG, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the 15 Lycium species formed a monophyletic group and were divided into two typical subbranches and three minor branches. Molecular dating suggested that Lycium diverged from its sister genus approximately 17.7 million years ago (Mya) and species diversification within the Lycium species of China primarily occurred during the recent Pliocene epoch. CONCLUSION The divergence time estimation presented in this study will facilitate future research on Lycium, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Erdong Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Yuqing Wei
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Guoqi Zheng
- Key Laboratory of the Ministry of Education for Protection and Utilization of Special Biological Resources in the Western, School of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China.
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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Han S, Zhang S, Yi R, Bi D, Ding H, Yang J, Ye Y, Xu W, Wu L, Zhuo R, Kan X. Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae). ANNALS OF BOTANY 2024; 133:585-604. [PMID: 38359907 PMCID: PMC11037489 DOI: 10.1093/aob/mcae017] [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: 01/05/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND AND AIMS Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale 'barcodes' (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes. METHODS To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes). KEY RESULTS Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic. CONCLUSIONS This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- School of Basic Medical Sciences, Wannan Medical College, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Liu J, Zhou SZ, Liu YL, Zhao BY, Yu D, Zhong MC, Jiang XD, Cui WH, Zhao JX, Qiu J, Liu LM, Guo ZH, Li HT, Tan DY, Hu JY, Li DZ. Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae. PLANT COMMUNICATIONS 2024:100878. [PMID: 38475995 DOI: 10.1016/j.xplc.2024.100878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Zhao Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Bin-Yan Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongmei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jiu-Xia Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Qiu
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Liang-Min Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dun-Yan Tan
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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Xiao TW, Song F, Vu DQ, Feng Y, Ge XJ. The evolution of ephemeral flora in Xinjiang, China: insights from plastid phylogenomic analyses of Brassicaceae. BMC PLANT BIOLOGY 2024; 24:111. [PMID: 38360561 PMCID: PMC10868009 DOI: 10.1186/s12870-024-04796-0] [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: 07/07/2023] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND The ephemeral flora of northern Xinjiang, China, plays an important role in the desert ecosystems. However, the evolutionary history of this flora remains unclear. To gain new insights into its origin and evolutionary dynamics, we comprehensively sampled ephemeral plants of Brassicaceae, one of the essential plant groups of the ephemeral flora. RESULTS We reconstructed a phylogenetic tree using plastid genomes and estimated their divergence times. Our results indicate that ephemeral species began to colonize the arid areas in north Xinjiang during the Early Miocene and there was a greater dispersal of ephemeral species from the surrounding areas into the ephemeral community of north Xinjiang during the Middle and Late Miocene, in contrast to the Early Miocene or Pliocene periods. CONCLUSIONS Our findings, together with previous studies, suggest that the ephemeral flora originated in the Early Miocene, and species assembly became rapid from the Middle Miocene onwards, possibly attributable to global climate changes and regional geological events.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Duc Quy Vu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Feng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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Berthelier TH, Cabanac SC, Callot C, Bellec A, Mathé C, Jamet E, Dunand C. Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three Brassicaceae Species. Int J Mol Sci 2024; 25:1938. [PMID: 38339216 PMCID: PMC10856686 DOI: 10.3390/ijms25031938] [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: 12/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Climate change is expected to intensify the occurrence of abiotic stress in plants, such as hypoxia and salt stresses, leading to the production of reactive oxygen species (ROS), which need to be effectively managed by various oxido-reductases encoded by the so-called ROS gene network. Here, we studied six oxido-reductases families in three Brassicaceae species, Arabidopsis thaliana as well as Nasturtium officinale and Eutrema salsugineum, which are adapted to hypoxia and salt stress, respectively. Using available and new genomic data, we performed a phylogenomic analysis and compared RNA-seq data to study genomic and transcriptomic adaptations. This comprehensive approach allowed for the gaining of insights into the impact of the adaptation to saline or hypoxia conditions on genome organization (gene gains and losses) and transcriptional regulation. Notably, the comparison of the N. officinale and E. salsugineum genomes to that of A. thaliana highlighted changes in the distribution of ohnologs and homologs, particularly affecting class III peroxidase genes (CIII Prxs). These changes were specific to each gene, to gene families subjected to duplication events and to each species, suggesting distinct evolutionary responses. The analysis of transcriptomic data has allowed for the identification of genes related to stress responses in A. thaliana, and, conversely, to adaptation in N. officinale and E. salsugineum.
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Affiliation(s)
- Thomas Horst Berthelier
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Sébastien Christophe Cabanac
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, France; (C.C.); (A.B.)
| | - Arnaud Bellec
- Centre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, France; (C.C.); (A.B.)
| | - Catherine Mathé
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
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9
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Liu J, Hu JY, Li DZ. Remarkable mitochondrial genome heterogeneity in Meniocus linifolius (Brassicaceae). PLANT CELL REPORTS 2024; 43:36. [PMID: 38200362 DOI: 10.1007/s00299-023-03102-w] [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: 08/22/2023] [Accepted: 11/06/2023] [Indexed: 01/12/2024]
Abstract
KEY MESSAGE Detailed analyses of 16 genomes identified a remarkable acceleration of mutation rate, hence mitochondrial sequence and structural heterogeneity, in Meniocus linifolius (Brassicaceae). The powerhouse, mitochondria, in plants feature high levels of structural variation, while the encoded genes are normally conserved. However, the substitution rates and spectra of mitochondria DNA within the Brassicaceae, a family with substantial scientific and economic importance, have not been adequately deciphered. Here, by analyzing three newly assembled and 13 known mitochondrial genomes (mitogenomes), we report the highly variable genome structure and mutation rates in Brassicaceae. The genome sizes and GC contents are 196,604 bp and 46.83%, 288,122 bp and 44.79%, and 287,054 bp and 44.93%, for Meniocus linifolius (Mli), Crucihimalaya lasiocarpa (Cla), and Lepidium sativum (Lsa), respectively. In total, 29, 33, and 34 protein-coding genes (PCGs) and 14, 18, and 18 tRNAs are annotated for Mli, Cla, and Lsa, respectively, while all mitogenomes contain one complete circular molecule with three rRNAs and abundant RNA editing sites. The Mli mitogenome features four conformations likely mediated by the two pairs of long repeats, while at the same time seems to have an unusual evolutionary history due to higher GC content, loss of more genes and sequences, but having more repeats and plastid DNA insertions. Corroborating with these, an ambiguous phylogenetic position with long branch length and elevated synonymous substitution rate in nearly all PCGs are observed for Mli. Taken together, our results reveal a high level of mitogenome heterogeneity at the family level and provide valuable resources for further understanding the evolutionary pattern of organelle genomes in Brassicaceae.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity, Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity, Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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10
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Hendriks KP, Kiefer C, Al-Shehbaz IA, Bailey CD, Hooft van Huysduynen A, Nikolov LA, Nauheimer L, Zuntini AR, German DA, Franzke A, Koch MA, Lysak MA, Toro-Núñez Ó, Özüdoğru B, Invernón VR, Walden N, Maurin O, Hay NM, Shushkov P, Mandáková T, Schranz ME, Thulin M, Windham MD, Rešetnik I, Španiel S, Ly E, Pires JC, Harkess A, Neuffer B, Vogt R, Bräuchler C, Rainer H, Janssens SB, Schmull M, Forrest A, Guggisberg A, Zmarzty S, Lepschi BJ, Scarlett N, Stauffer FW, Schönberger I, Heenan P, Baker WJ, Forest F, Mummenhoff K, Lens F. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol 2023; 33:4052-4068.e6. [PMID: 37659415 DOI: 10.1016/j.cub.2023.08.026] [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: 02/03/2023] [Revised: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 09/04/2023]
Abstract
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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Affiliation(s)
- Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany; Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands.
| | - Christiane Kiefer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM 88003, USA
| | - Alex Hooft van Huysduynen
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lachezar A Nikolov
- Department of Molecular, Cell and Developmental Biology, University of California, 610 Charles E. Young Dr. S., Los Angeles, CA 90095, USA
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | | | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Lesosechnaya Ulitsa, 25, Barnaul, Altai Krai, Russia
| | - Andreas Franzke
- Heidelberg Botanic Garden, Heidelberg University, Im Neuenheimer Feld 361, 69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Óscar Toro-Núñez
- Departamento de Botánica, Universidad de Concepción, Barrio Universitario, Concepción, Chile
| | - Barış Özüdoğru
- Department of Biology, Hacettepe University, Beytepe, Ankara 06800, Türkiye
| | - Vanessa R Invernón
- Sorbonne Université, Muséum National d'Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP 39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Nora Walden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Nikolai M Hay
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip Shushkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mats Thulin
- Department of Organismal Biology, Uppsala University, Norbyvägen 18, 752 36 Uppsala, Sweden
| | | | - Ivana Rešetnik
- Department of Biology, University of Zagreb, Marulićev trg 20/II, 10000 Zagreb, Croatia
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Dúbravská cesta 9, 845 23 Bratislava, Slovakia
| | - Elfy Ly
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, 307 University Ave., Fort Collins, CO 80523-1170, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Barbara Neuffer
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Robert Vogt
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Christian Bräuchler
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Heimo Rainer
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Steven B Janssens
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31 - box 2435, 3001 Leuven, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Michaela Schmull
- Harvard University Herbaria, 22 Divinity Ave., Cambridge, MA 02138, USA
| | - Alan Forrest
- Centre for Middle Eastern Plants, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Alessia Guggisberg
- ETH Zürich, Institut für Integrative Biologie, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Sue Zmarzty
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Brendan J Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, Clunies Ross St, Acton, ACT 2601, Australia
| | - Neville Scarlett
- La Trobe University, Plenty Road and Kingsbury Dr., Bundoora, VIC 3086, Australia
| | - Fred W Stauffer
- Conservatory and Botanic Gardens of Geneva, CP 60, Chambésy, 1292 Geneva, Switzerland
| | - Ines Schönberger
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | - Peter Heenan
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Frederic Lens
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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11
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Uribe M, Brabec J, Chaparro-Gutiérrez JJ, Hermosilla C. Neglected zoonotic helminthiases in wild canids: new insights from South America. Front Vet Sci 2023; 10:1235182. [PMID: 37635759 PMCID: PMC10450927 DOI: 10.3389/fvets.2023.1235182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
The global threat of neglected tropical diseases (NTDs) constitutes a public health issue in underdeveloped countries. Zoonotic helminthiases are the most common human NTD agents in developing countries in sub-Saharan Africa, Asia, and the Americas, causing a global burden of disease that exceeds that of more recognized infectious diseases such as malaria and tuberculosis. Wild canids are well-known mammals that act as natural reservoirs of zoonotic-relevant helminthiasis worldwide, thus playing a pivotal role in their epidemiology and transmission to humans. Here we evaluate the occurrence of zoonotic gastrointestinal helminths in two Neotropical wild canid species from the Amazonian and Andean regions of Colombia, i.e., the bush dog (Speothos venaticus) and the crab-eating fox (Cerdocyon thous). We recovered tapeworm proglottids from bush dog fecal samples and identified them molecularly as the canine-specific lineage of Dipylidium caninum by using cytochrome c oxidase subunit I (cox1) gene sequences. Moreover, examination of a crab-eating fox during necropsy revealed the presence of non-embryonated eggs of the neglected nematode Lagochilascaris cf. minor, in addition to eggs and gravid proglottids of the cestode Spirometra mansoni. These findings represent the first report of zoonotic-relevant cestodes, i.e., D. caninum ("canine genotype"), S. mansoni, and the nematode L. cf. minor, in bush dogs and crab-eating foxes as final hosts. The occurrence of these zoonotic helminthiases in wild canid species calls for regular monitoring programs to better understand the epidemiology and transmission routes of neglected dipylidiasis, lagochilascariosis, and sparganosis in South America.
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Affiliation(s)
- Manuel Uribe
- Biomedical Research Center Seltersberg (BFS), Institute of Parasitology, Justus Liebig University Giessen, Gießen, Germany
- CIBAV Research Group, Veterinary Medicine School, Universidad de Antioquia, Medellín, Colombia
| | - Jan Brabec
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | | | - Carlos Hermosilla
- Biomedical Research Center Seltersberg (BFS), Institute of Parasitology, Justus Liebig University Giessen, Gießen, Germany
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12
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Wang W, Qin L, Zhang W, Tang L, Zhang C, Dong X, Miao P, Shen M, Du H, Cheng H, Wang K, Zhang X, Su M, Lu H, Li C, Gao Q, Zhang X, Huang Y, Liang C, Zhou JM, Chen YH. WeiTsing, a pericycle-expressed ion channel, safeguards the stele to confer clubroot resistance. Cell 2023; 186:2656-2671.e18. [PMID: 37295403 DOI: 10.1016/j.cell.2023.05.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/06/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Plant roots encounter numerous pathogenic microbes that often cause devastating diseases. One such pathogen, Plasmodiophora brassicae (Pb), causes clubroot disease and severe yield losses on cruciferous crops worldwide. Here, we report the isolation and characterization of WeiTsing (WTS), a broad-spectrum clubroot resistance gene from Arabidopsis. WTS is transcriptionally activated in the pericycle upon Pb infection to prevent pathogen colonization in the stele. Brassica napus carrying the WTS transgene displayed strong resistance to Pb. WTS encodes a small protein localized in the endoplasmic reticulum (ER), and its expression in plants induces immune responses. The cryoelectron microscopy (cryo-EM) structure of WTS revealed a previously unknown pentameric architecture with a central pore. Electrophysiology analyses demonstrated that WTS is a calcium-permeable cation-selective channel. Structure-guided mutagenesis indicated that channel activity is strictly required for triggering defenses. The findings uncover an ion channel analogous to resistosomes that triggers immune signaling in the pericycle.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| | - Li Qin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Linghui Tang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaojing Dong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pei Miao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Shen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Hangyuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyun Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Min Su
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Huang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
| | - Yu-Hang Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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13
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Wang Y, Zhang CF, Ochieng Odago W, Jiang H, Yang JX, Hu GW, Wang QF. Evolution of 101 Apocynaceae plastomes and phylogenetic implications. Mol Phylogenet Evol 2023; 180:107688. [PMID: 36581140 DOI: 10.1016/j.ympev.2022.107688] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/21/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Apocynaceae are one of the ten species-richest angiosperm families. However, the backbone phylogeny of the family is yet less well supported, and the evolution of plastome structure has not been thoroughly studied for the whole family. Herein, a total of 101 complete plastomes including 35 newly sequenced, 24 reassembled from public raw data and the rest from the NCBI GenBank database, representing 26 of 27 tribes of Apocynaceae, were used for comparative plastome analysis. Phylogenetic analyses were conducted using a combined plastid data matrix of 77 protein-coding genes from 162 taxa, encompassing all tribes and 41 of 49 subtribes of Apocynaceae. Plastome lengths ranged from 150,897 bp in Apocynum venetum to 178,616 bp in Hoya exilis. Six types of boundaries between the inverted repeat (IR) regions and single copy (SC) regions were identified. Different sizes of IR expansion were found in three lineages, including Alyxieae, Ceropegieae and Marsdenieae, suggesting multiple expansion events of the IRs over the SC regions in Apocynaceae. The IR regions of Marsdenieae evolved in two ways: expansion towards the large single copy (LSC) region in Lygisma + Stephanotis + Ruehssia + Gymnema (Cosmopolitan clade), and expansion towards both LSC and small single copy (SSC) region in Dischidia-Hoya alliance and Marsdenia (Asia-Pacific clade). Six coding genes and five non-coding regions were identified as highly variable, including accD, ccsA-ndhD, clpP, matK, ndhF, ndhG-ndhI, trnG(GCC)-trnfM(CAU), trnH(GUG)-psbA, trnY(GUA)-trnE(UUC), ycf1, and ycf2. Maximum likelihood and Bayesian phylogenetic analyses resulted in nearly identical tree topologies and produced a well-resolved backbone comprising 15 consecutive dichotomies that subdivided Apocynaceae into 15 clades. The subfamily Periplocoideae were embedded in the Apocynoid grade and were sister to the Echiteae-Odontadenieae-Mesechiteae clade with high support values. Three tribes (Melodineae, Vinceae, and Willughbeieae), the subtribe Amphineuriinae, and four genera (Beaumontia, Ceropegia, Hoya, and Stephanotis) were not resolved as monophyletic. Our work sheds light on the backbone phylogenetic relationships in the family Apocynaceae and offers insights into the evolution of Apocynaceae plastomes using the most densely sampled plastome dataset to date.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Cai-Fei Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Wyclif Ochieng Odago
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hui Jiang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jia-Xin Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Yin X, Yang D, Zhao Y, Yang X, Zhou Z, Sun X, Kong X, Li X, Wang G, Duan Y, Yang Y, Yang Y. Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies. PLANT COMMUNICATIONS 2023; 4:100427. [PMID: 36056558 PMCID: PMC9860189 DOI: 10.1016/j.xplc.2022.100427] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/30/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Pseudogenes are important resources for investigation of genome evolution and genomic diversity because they are nonfunctional but have regulatory effects that influence plant adaptation and diversification. However, few systematic comparative analyses of pseudogenes in closely related species have been conducted. Here, we present a turnip (Brassica rapa ssp. rapa) genome sequence and characterize pseudogenes among diploid Brassica species/subspecies. The results revealed that the number of pseudogenes was greatest in Brassica oleracea (CC genome), followed by B. rapa (AA genome) and then Brassica nigra (BB genome), implying that pseudogene differences emerged after species differentiation. In Brassica AA genomes, pseudogenes were distributed asymmetrically on chromosomes because of numerous chromosomal insertions/rearrangements, which contributed to the diversity among subspecies. Pseudogene differences among subspecies were reflected in the flavor-related glucosinolate (GSL) pathway. Specifically, turnip had the highest content of pungent substances, probably because of expansion of the methylthioalkylmalate synthase-encoding gene family in turnips; these genes were converted into pseudogenes in B. rapa ssp. pekinensis (Chiifu). RNA interference-based silencing of the gene encoding 2-oxoglutarate-dependent dioxygenase 2, which is also associated with flavor and anticancer substances in the GSL pathway, resulted in increased abundance of anticancer compounds and decreased pungency of turnip and Chiifu. These findings revealed that pseudogene differences between turnip and Chiifu influenced the evolution of flavor-associated GSL metabolism-related genes, ultimately resulting in the different flavors of turnip and Chiifu.
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Affiliation(s)
- Xin Yin
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Danni Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youjie Zhao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, Yunnan, China
| | - Xingyu Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Zhou
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xudong Sun
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiangxiang Kong
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiong Li
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guangyan Wang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yuanwen Duan
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yunqiang Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yongping Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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15
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Liu H, Qiao Q, Ye X, Guo Y, Ye B, Xu Q, Zhou X, Li B. The reference genome and organelle genomes of wasabi (Eutrema japoniacum). Front Genet 2022; 13:1048264. [DOI: 10.3389/fgene.2022.1048264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Wasabi (Eutrema japonicum) is one of the most famous vegetable crops in the family Brassicaceae. However, a limited genomic resource is available, which hinders genomic breeding and understanding of the genetic basis of vital traits. Here, we generated the genome assembly of wasabi using the hybrid genome assembly strategy, which combined the Nanopore long reads and Illumina reads. The genome assembly contains 687M bp and 39,534 high-quality annotated gene models. Besides, we annotated 68.85% of the genomic sequences as repetitive elements, including 43.72% of retrotransposons and 18.99% of DNA transposons. Using the customized pipeline, we also generated the complete organelle genomes of wasabi. This reference genome could provide essential genomic resources for evolution, breeding, and exploring the unique biological traits of wasabi.
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Kaya Y, Aydın ZU, Cai X, Wang X, Dönmez AA. Genome-wide characterization of two Aubrieta taxa: Aubrieta canescens subsp. canescens and Au. macrostyla (Brassicaceae). AOB PLANTS 2022; 14:plac035. [PMID: 36196394 PMCID: PMC9521481 DOI: 10.1093/aobpla/plac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Aubrieta canescens complex is divided into two subspecies, Au. canescens subsp. canescens, Au. canescens subsp. cilicica and a distinct species, Au. macrostyla, based on molecular phylogeny. We generated a draft assembly of Au. canescens subsp. canescens and Au. macrostyla using paired-end shotgun sequencing. This is the first attempt at genome characterization for the genus. In the presented study, ~165 and ~157 Mbp of the genomes of Au. canescens subsp. canescens and Au. macrostyla were assembled, respectively, and a total of 32 425 and 31 372 gene models were predicted in the genomes of the target taxa, respectively. We corroborated the phylogenomic affinity of taxa with some core Brassicaceae species (Clades A and B) including Arabis alpina. The orthology-based tree suggested that Aubrieta species differentiated from A. alpina 1.3-2.0 mya (million years ago). The genome-wide syntenic comparison of two Aubrieta taxa revealed that Au. canescens subsp. canescens (46 %) and Au. macrostyla (45 %) have an almost identical syntenic gene pair ratio. These novel genome assemblies are the first steps towards the chromosome-level assembly of Au. canescens and understanding the genome diversity within the genus.
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Affiliation(s)
| | - Zübeyde Uğurlu Aydın
- Molecular Plant Systematic Laboratory (MOBIS), Department of Biology, Faculty of Science, Hacettepe University, Ankara 06800, Turkey
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ali A Dönmez
- Molecular Plant Systematic Laboratory (MOBIS), Department of Biology, Faculty of Science, Hacettepe University, Ankara 06800, Turkey
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Han TS, Hu ZY, Du ZQ, Zheng QJ, Liu J, Mitchell-Olds T, Xing YW. Adaptive responses drive the success of polyploid yellowcresses ( Rorippa, Brassicaceae) in the Hengduan Mountains, a temperate biodiversity hotspot. PLANT DIVERSITY 2022; 44:455-467. [PMID: 36187546 PMCID: PMC9512641 DOI: 10.1016/j.pld.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/16/2023]
Abstract
Polyploids contribute substantially to plant evolution and biodiversity; however, the mechanisms by which they succeed are still unclear. According to the polyploid adaptation hypothesis, successful polyploids spread by repeated adaptive responses to new environments. Here, we tested this hypothesis using two tetraploid yellowcresses (Rorippa), the endemic Rorippa elata and the widespread Rorippa palustris, in the temperate biodiversity hotspot of the Hengduan Mountains. Speciation modes were resolved by phylogenetic modeling using 12 low-copy nuclear loci. Phylogeographical patterns were then examined using haplotypes phased from four plastid and ITS markers, coupled with historical niche reconstruction by ecological niche modeling. We inferred the time of hybrid origins for both species as the mid-Pleistocene, with shared glacial refugia within the southern Hengduan Mountains. Phylogeographic and ecological niche reconstruction indicated recurrent northward colonization by both species after speciation, possibly tracking denuded habitats created by glacial retreat during interglacial periods. Common garden experiment involving perennial R. elata conducted over two years revealed significant changes in fitness-related traits across source latitudes or altitudes, including latitudinal increases in survival rate and compactness of plant architecture, suggesting gradual adaptation during range expansion. These findings support the polyploid adaptation hypothesis and suggest that the spread of polyploids was aided by adaptive responses to environmental changes during the Pleistocene. Our results thus provide insight into the evolutionary success of polyploids in high-altitude environments.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Zheng-Yan Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Qiang Du
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | | | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
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18
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Zuo (左胜) S, Guo (郭新异) X, Mandáková T, Edginton M, Al-Shehbaz IA, Lysak MA. Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution. PLANT PHYSIOLOGY 2022; 190:403-420. [PMID: 35670733 PMCID: PMC9434143 DOI: 10.1093/plphys/kiac268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/09/2022] [Indexed: 05/20/2023]
Abstract
Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted in the extant c. 17 genera and 60 species endemic to Australia and New Zealand (10 species). As postpolyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. In Microlepidieae, different extents of homoeologous recombination between the two parental subgenomes generated clades marked by slow ("cold") versus fast ("hot") genome diploidization. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, we analyzed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. The four recovered intra-tribal clades mirror the varied diploidization of Microlepidieae genomes, suggesting that the intrinsic genomic features underlying the extent of diploidization are shared among genera and species within one clade. Nevertheless, even congeneric species may exert considerable morphological disparity (e.g. in fruit shape), whereas some species within different clades experience extensive morphological convergence despite the different pace of their genome diploidization. We showed that faster genome diploidization is positively associated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, our results confirm the potential of Microlepidieae as a promising subject for the analysis of postpolyploid genome diploidization in Brassicaceae.
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Affiliation(s)
| | | | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Mark Edginton
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Toowong, QLD 4066, Australia
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Javaid N, Ramzan M, Khan IA, Alahmadi TA, Datta R, Fahad S, Danish S. The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae. BMC PLANT BIOLOGY 2022; 22:384. [PMID: 35918648 PMCID: PMC9344719 DOI: 10.1186/s12870-022-03750-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/13/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. RESULTS The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. CONCLUSION The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.
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Affiliation(s)
- Nida Javaid
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Musarrat Ramzan
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi, Karachi, 75270 Pakistan
| | - Tahani Awad Alahmadi
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Medical City, PO Box-2925, Riyadh, 11461 Saudi Arabia
| | - Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Shah Fahad
- Department of Agronomy, The University of Haripur, Khyber Pakhtunkhwa, Haripur, 22620 Pakistan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
| | - Subhan Danish
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60800 Punjab Pakistan
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20
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Han S, Bi D, Yi R, Ding H, Wu L, Kan X. Plastome evolution of Aeonium and Monanthes (Crassulaceae): insights into the variation of plastomic tRNAs, and the patterns of codon usage and aversion. PLANTA 2022; 256:35. [PMID: 35809200 DOI: 10.1007/s00425-022-03950-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
This study reported 13 new plastomes from Aeonium and Monanthes, and observed new markers for phylogeny and DNA barcoding, such as novel tRNA structures and codon usage bias and aversion. The Macaronesian clade of Crassulaceae consists of three genera: Aichryson, with about 15 species; Monanthes, with about 10 species; Aeonium, with about 40 species. Within this clade, Aeonium, known as "the botanical equivalent of Darwin's finches", is regarded as an excellent model plant for researching adaptive evolution. Differing from the well-resolved relationships among three genera of the Macaronesian clade, the internal branching patterns within the genus Aeonium are largely unclear. In this study, we first reported 13 new plastomes from genus Aeonium and the closely related genus Monanthes. We further performed comprehensive analyses of the plastomes, with focuses on the secondary structures of pttRNAs and the patterns of codon usage and aversion. With a typical circular and quadripartite structure, the 13 plastomes ranged from 149,900 to 151,030 bp in size, and the unique pattern in IR junctions might become a family-specific marker for Crassulaceae species. Surprisingly, the π values of plastomes from Monanthes were almost twice those from Aeonium. Most importantly, we strongly recommend that highly polymorphic regions, novel putative pttRNA structures, patterns of codon usage bias and aversion derived from plastomes might have phylogenetic implications, and could act as new markers for DNA barcoding of plants. The results of phylogenetic analyses strongly supported a clear internal branching pattern in Macaronesian clade (represented by Aeonium and Monanthes), with higher nodal support values. The findings reported here will provide new insights into the variation of pttRNAs, and the patterns of codon usage and aversion of the family Crassulaceae.
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Affiliation(s)
- Shiyun Han
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou, 215000, Jiangsu, China
| | - Ran Yi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Hengwu Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, 241000, Anhui, China.
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21
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Ghaffari S, Abbasi A, Somi MH, Moaddab SY, Nikniaz L, Kafil HS, Ebrahimzadeh Leylabadlo H. Akkermansia muciniphila: from its critical role in human health to strategies for promoting its abundance in human gut microbiome. Crit Rev Food Sci Nutr 2022; 63:7357-7377. [PMID: 35238258 DOI: 10.1080/10408398.2022.2045894] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Akkermansia muciniphila, a frequent colonizer in the gut mucous layer of individuals, has constantly been recognized as a promising candidate for the next generation of probiotics due to its biological advantages from in vitro and in vivo investigations. This manuscript comprehensively reviewed the features of A. muciniphila in terms of its function in host physiology and frequently utilized nutrition using the published peer-reviewed articles, which should present valuable and critical information to scientists, engineers, and even the general population. A. muciniphila is an important bacterium that shows host physiology. However, its physiological advantages in several clinical settings also have excellent potential to become a probiotic. Consequently, it can be stated that there is a coherent and direct relation between the biological activities of the gut microbiota, intestinal dysbiosis/eubiosis, and the population of A. muciniphila in the gut milieu, which is influenced by various genetical and nutritional factors. Current regulatory barriers, the need for large-scale clinical trials, and the feasibility of production must be removed before A muciniphila can be extensively used as a next-generation probiotic.
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Affiliation(s)
- Sima Ghaffari
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amin Abbasi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Yaghoub Moaddab
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Nikniaz
- Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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22
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Sielemann K, Pucker B, Schmidt N, Viehöver P, Weisshaar B, Heitkam T, Holtgräwe D. Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 2022; 23:113. [PMID: 35139817 PMCID: PMC8830136 DOI: 10.1186/s12864-022-08336-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. Results We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. Conclusion In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08336-8.
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Affiliation(s)
- Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.,Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,Institute of Plant Biology, TU Braunschweig, Braunschweig, Germany
| | - Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
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23
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Bruun Asmussen Lange C, Pavlo Hauser T, Deichmann V, Ørgaard M. Hybridization and complex evolution of Barbarea vulgaris and related species (Brassicaceae). Mol Phylogenet Evol 2022; 169:107425. [DOI: 10.1016/j.ympev.2022.107425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 09/15/2020] [Accepted: 01/12/2022] [Indexed: 11/29/2022]
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24
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Gu L, Hou Y, Wang G, Liu Q, Ding W, Weng Q. Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae. PLoS One 2022; 17:e0262813. [PMID: 35077482 PMCID: PMC8789150 DOI: 10.1371/journal.pone.0262813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/05/2022] [Indexed: 11/19/2022] Open
Abstract
Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Guangyi Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Ding
- Colleage of plant protection, Southwest University, Chongqing, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
- * E-mail:
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25
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Brock JR, Mandáková T, McKain M, Lysak MA, Olsen KM. Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa. HORTICULTURE RESEARCH 2022; 9:6497793. [PMID: 35031794 PMCID: PMC8788360 DOI: 10.1093/hr/uhab050] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 05/24/2023]
Abstract
The genus Camelina (Brassicaceae) comprises 7-8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.
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Affiliation(s)
- Jordan R Brock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130 USA
| | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michael McKain
- Department of Biological Sciences, The University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, Alabama, 35487 USA
| | - Martin A Lysak
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130 USA
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26
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Bayat S, Lysak MA, Mandáková T. Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1768-1785. [PMID: 34661331 DOI: 10.1111/tpj.15542] [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: 05/10/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.
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Affiliation(s)
- Soheila Bayat
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Martin A Lysak
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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27
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Chen L, Jin WT, Liu XQ, Wang XQ. New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data. Mol Phylogenet Evol 2021; 166:107341. [PMID: 34740782 DOI: 10.1016/j.ympev.2021.107341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Phylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae. Our study completely resolved the intergeneric relationships of Podocarpaceae represented by all extant genera and revealed that topological conflicts among phylogenetic trees could be attributed to synonymous substitutions. Moreover, we found that two morphological traits, fleshy seed cones and flattened leaves, might be important for Podocarpaceae to adapt to angiosperm-dominated forests and thus could have promoted its species diversification. In addition, our results indicate that Podocarpaceae originated in Gondwana in the late Triassic and both vicariance and dispersal have contributed to its current biogeographic patterns. Our study provides the first robust transcriptome-based phylogeny of Podocarpaceae, an evolutionary framework important for future studies of this family.
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Affiliation(s)
- Luo Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin-Quan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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28
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Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation. Proc Natl Acad Sci U S A 2021; 118:2025711118. [PMID: 34649989 PMCID: PMC8545485 DOI: 10.1073/pnas.2025711118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 12/01/2022] Open
Abstract
Plants’ adaptations to and divergence in arid deserts have long fascinated scientists and the general public. Here, we present a genomic analysis of two congeneric desert plant species that clarifies their evolutionary history and shows that their common ancestor arose from a hybrid polyploidization, which provided genomic foundations for their survival in deserts. The whole-genome duplication was followed by translocation-based rearrangements of the ancestral chromosomes. Rapid evolution of genes in these reshuffled chromosomes contributed greatly to the divergences of the two species in desert microhabitats during which gene flow was continuous. Our results provide insights into plant adaptation in the arid deserts and highlight the significance of polyploidy-driven chromosomal structural variations in species divergence. Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.
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29
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Oliveira MAS, Nunes T, Dos Santos MA, Ferreira Gomes D, Costa I, Van-Lume B, Marques Da Silva SS, Oliveira RS, Simon MF, Lima GSA, Gissi DS, Almeida CCDS, Souza G, Marques A. High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae). Front Genet 2021; 12:727314. [PMID: 34630521 PMCID: PMC8495327 DOI: 10.3389/fgene.2021.727314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.
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Affiliation(s)
| | - Tomáz Nunes
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | | | | | - Iara Costa
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | | | - Ronaldo Simão Oliveira
- Campus Xique Xique, Federal Institute of Education, Science and Technology of Bahia, Xique-Xique, Brazil
| | | | - Gaus S A Lima
- Center of Agronomic Sciences, Federal University of Alagoas, Rio Largo, Brazil
| | - Danilo Soares Gissi
- Department of Biostatistics, Institute of Biosciences-IBB, Plant Biology, Parasitology and Zoology, São Paulo State University-UNESP, Botucatu, Brazil
| | | | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil.,Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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30
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Žerdoner Čalasan A, Hurka H, German DA, Pfanzelt S, Blattner FR, Seidl A, Neuffer B. Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae). Ecol Evol 2021; 11:12697-12713. [PMID: 34594532 PMCID: PMC8462161 DOI: 10.1002/ece3.8015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/06/2021] [Accepted: 07/29/2021] [Indexed: 12/19/2022] Open
Abstract
Capsella is a model plant genus of the Brassicaceae closely related to Arabidopsis. To disentangle its biogeographical history and intrageneric phylogenetic relationships, 282 individuals of all five currently recognized Capsella species were genotyped using a restriction digest-based next-generation sequencing method. Our analysis retrieved two main lineages within Capsella that split c. one million years ago, with western C. grandiflora and C. rubella forming a sister lineage to the eastern lineage consisting of C. orientalis. The split was attributed to continuous latitudinal displacements of the Eurasian steppe belt to the south during Early Pleistocene glacial cycles. During the interglacial cycles of the Late Pleistocene, hybridization of the two lineages took place in the southwestern East European Plain, leading to the allotetraploid C. bursa-pastoris. Extant genetic variation within C. orientalis postdated any extensive glacial events. Ecological niche modeling showed that suitable habitat for C. orientalis existed during the Last Glacial Maximum around the north coast of the Black Sea and in southern Kazakhstan. Such a scenario is also supported by population genomic data that uncovered the highest genetic diversity in the south Kazakhstan cluster, suggesting that C. orientalis originated in continental Asia and migrated north- and possibly eastwards after the last ice age. Post-glacial hybridization events between C. bursa-pastoris and C. grandiflora/rubella in the southwestern East European Plain and the Mediterranean gave rise to C. thracica. Introgression of C. grandiflora/rubella into C. bursa-pastoris resulted in a new Mediterranean cluster within the already existing Eurasian C. bursa-pastoris cluster. This study shows that the continuous displacement and disruption of the Eurasian steppe belt during the Pleistocene was the driving force in the evolution of Capsella.
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Affiliation(s)
| | - Herbert Hurka
- Department 5: Biology/Chemistry, BotanyUniversity of OsnabrückOsnabrückGermany
| | - Dmitry A. German
- South‐Siberian Botanical GardenAltai State UniversityBarnaulRussia
| | - Simon Pfanzelt
- Experimental TaxonomyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Seeland‐GaterslebenGermany
- Munich Botanical GardenMünchenGermany
| | - Frank R. Blattner
- Experimental TaxonomyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Seeland‐GaterslebenGermany
| | - Anna Seidl
- Institute of BotanyDepartment of Integrative Biology and Biodiversity ResearchUniversity of Natural Resources and Life SciencesVienna (BOKU)Austria
| | - Barbara Neuffer
- Department 5: Biology/Chemistry, BotanyUniversity of OsnabrückOsnabrückGermany
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31
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Geng Y, Guan Y, Qiong L, Lu S, An M, Crabbe MJC, Qi J, Zhao F, Qiao Q, Zhang T. Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation. BMC Biol 2021; 19:143. [PMID: 34294107 PMCID: PMC8296595 DOI: 10.1186/s12915-021-01079-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01079-0.
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Affiliation(s)
- Yupeng Geng
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Yabin Guan
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China.,School of Life Sciences, Yunnan University, Kunming, 650504, China
| | - La Qiong
- Research Center for Ecology, College of Science, Tibet University, Lhasa, 850000, China
| | - Shugang Lu
- School of Life Sciences, Yunnan University, Kunming, 650504, China
| | - Miao An
- Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX2 6UD, UK.,Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK.,School of Life Sciences, Shanxi University, Taiyuan, 030006, China
| | - Ji Qi
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Fangqing Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, 650504, China.
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China.
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32
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Guo X, Mandáková T, Trachtová K, Özüdoğru B, Liu J, Lysak MA. Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe. Mol Biol Evol 2021; 38:1695-1714. [PMID: 33331908 PMCID: PMC8097306 DOI: 10.1093/molbev/msaa327] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pervasive hybridization and whole-genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. Although frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (∼60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring postpolyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.
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Affiliation(s)
- Xinyi Guo
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karolína Trachtová
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe, Ankara, Turkey
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Song WC, Feng Q, Zhang YJ, Wu XM, Shi C, Wang S. The complete chloroplast genome sequence of Duranta erecta (Verbenaceae). Mitochondrial DNA B Resour 2021; 6:1832-1833. [PMID: 34124359 PMCID: PMC8183526 DOI: 10.1080/23802359.2021.1934164] [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] [Indexed: 12/02/2022] Open
Abstract
In this study, the complete chloroplast (cp) genome of Duranta erecta was assembled using Illumina sequencing data. The complete cp genome is 149,869 bp in length, including a pair of invert repeats (IRA and IRB) regions of 22,839 bp, large single-copy (LSC) region of 86,201 bp, and small single-copy (SSC) region of 17,990 bp. The G + C content of this cp genome was 38.26%. A total of 128 genes were predicted in the genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis confirmed the phylogenetic relationship between D. erecta and other representative species of Verbenaceae.
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Affiliation(s)
- Wei-cai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Qi Feng
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Yun-jiao Zhang
- Kunming Medical University Haiyuan College, Kunming, China
| | - Xiao-meng Wu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
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Wei-Cai S, Xiao-Fan L, Wang S, Rui-Qing Z, Chao S, Zhang YJ. The complete chloroplast genome sequence of Crassocephalum crepidioides (Benth.) S. Moore. (Asteraceae). Mitochondrial DNA B Resour 2021; 6:1834-1836. [PMID: 34124360 PMCID: PMC8183548 DOI: 10.1080/23802359.2021.1934165] [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] [Indexed: 11/20/2022] Open
Abstract
The complete chloroplast (cp) genome of Crassocephalum crepidioides was sequenced and assembled for the first time. In this study, the total genome size is 150,596 bp in length and demonstrates a typical quadripartite structure containing a large single copy (LSC, 82,575 bp) and a small single copy (SSC, 18,293 bp), separated by a pair of inverted repeats (IRa, IRb) of 24,864 bp. The G + C content of this cp genome was 37.21%. Gene annotation analysis identified 130 genes including 85 protein-coding genes, 37 transfer RNA, and 8 ribosomal RNA genes. The maximum-likelihood phylogenetic analysis result showed that C. crepidioides was closely related to Nannoglottis ravida in the phylogenetic relationship.
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Affiliation(s)
- Song Wei-Cai
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Liu Xiao-Fan
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Zhang Rui-Qing
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Shi Chao
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Yun-Jiao Zhang
- Kunming Medical University Haiyuan College, Kunming, China
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Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. AMERICAN JOURNAL OF BOTANY 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
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Shi D, Li J, Li Y, Li Y, Xie L. The complete chloroplast genome sequence of Gynandropsis gynandra (Cleomaceae). Mitochondrial DNA B Resour 2021; 6:1909-1910. [PMID: 34179471 PMCID: PMC8204997 DOI: 10.1080/23802359.2021.1935339] [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: 11/25/2020] [Accepted: 05/22/2021] [Indexed: 11/01/2022] Open
Abstract
Gynandropsis gynandra (L.) Briquet is a monoecious herb species in the family Cleomaceae. It is an important commercial crop with medicinal and nutritional values. Here, we sequenced, assembled, and analyzed the complete chloroplast genome of G. gynandra. The circular genome is 158,152 bp in size, consisting of two copies of inverted repeat (IR) regions of 26,181 bp, one large single-copy (LSC) region of 87,242 bp, and one small single-copy (SSC) region of 18,548 bp. The overall GC content was 35.81%. A total of 131 genes were annotated, including 37 tRNA genes, 87 protein-coding genes, and seven rRNA genes. Phylogenetic analysis based on 10 chloroplast genome sequences indicated that G. gynandra was more closely related to Tarenaya hassleriana.
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Affiliation(s)
- Dawei Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jinyu Li
- College of Forestry, Nanjing Forestry University, Nanjing, China
- TongJi University School of Medicine, Shanghai, China
| | - Yong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Lei Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis. Sci Rep 2021; 11:11731. [PMID: 34083611 PMCID: PMC8175739 DOI: 10.1038/s41598-021-91071-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
Adrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.
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Yang B, Li L, Liu J, Zhang L. Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau. PLANT DIVERSITY 2021; 43:198-205. [PMID: 34195504 PMCID: PMC8233517 DOI: 10.1016/j.pld.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 05/09/2023]
Abstract
The phylogenetic position of the monotypic woody Parapteropyrum (Polygonaceae) remains controversial. Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae, although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae. In this study, we used plastome data to determine the phylogenetic position of Parapteropyrum (Fagopyrum) tibeticum. Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae: Parapteropyrum (Fagopyrum) tibeticum, Atraphaxis bracteata and Calligonum ebinuricum. Once assembled, plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae. Phylogenetic analyses of Polygonaceae were performed using whole plastome, all plastome genes, and single-copy genes. Plastomes assembled using different reference plastomes did not differ; however, annotations showed small variation. Plastomes of Parapteropyrum (Fagopyrum) tibeticum, A. bracteata and C. ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp, and a total number of plastome genes of about 130. Plastome microsatellites (SSR) ranged in number from 48 to 77. Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum. Furthermore, our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic. Our study provides strong evidence that the woody Parapteropyrum tibeticum, which is distantly related to woody genera sampled here, should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.
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Nishiyama E, Nonogaki M, Yamazaki S, Nonogaki H, Ohshima K. Ancient and recent gene duplications as evolutionary drivers of the seed maturation regulators DELAY OF GERMINATION1 family genes. THE NEW PHYTOLOGIST 2021; 230:889-901. [PMID: 33454982 DOI: 10.1111/nph.17201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
The DELAY OF GERMINATION1 (DOG1) family genes (DFGs) in Arabidopsis thaliana are involved in seed dormancy, reserve accumulation, and desiccation tolerance. Decoding the molecular evolution of DFGs is key to understanding how these seed programs evolved. This article demonstrates that DFGs have diverged in the four lineages DOG1, DOG1-LIKE4 (DOGL4), DOGL5 and DOGL6, whereas DOGL1, DOGL2 and DOGL3 arose separately within the DOG1 lineage. The systematic DFG nomenclature proposed in this article addresses the current issues of inconsistent DFG annotation and highlights DFG genomic synteny in angiosperms. DFG pseudogenes, or collapsed coding sequences, hidden in the genomes of early-diverging angiosperms are documented here. They suggest ancient birth and loss of DFGs over the course of angiosperm evolution. The proposed models suggest that the origin of DFG diversification dates back to the most recent common ancestor of living angiosperms. The presence of a single form of DFG in nonflowering plants is discussed. Phylogenetic analysis of gymnosperm, lycophyte, and liverwort DFGs and similar genes found in mosses and algae suggests that DFGs diverged from the TGACG motif-binding transcription factor genes before the divergence of the bryophyte lineage.
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Affiliation(s)
- Eri Nishiyama
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Mariko Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Satoru Yamazaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Hiroyuki Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Kazuhiko Ohshima
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
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Jiang M, Li Y, Chen H, Wang B, Liu C. Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Lactuca raddeana and Lactuca sativa. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1498-1506. [PMID: 33969207 PMCID: PMC8079048 DOI: 10.1080/23802359.2021.1911700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Lactuca raddeana is a biennial plant of the Lactuca genus belonging to the Asteraceae family. The classification of Lactuca is controversial, and no consistent conclusions have been reached based on the analysis of morphological characters and different molecular markers. Here, we sequenced and assembled the complete chloroplast genome of L. raddeana. This genome has a total length of 152,339 bp, a conservative quartile structure that is composed of a large single-copy (LSC) region of 83,976 bp, a small-copy (SSC) region of 18,521 bp, and a pair of inverted repeats (IRs) of 24,921 bp. The genome contains 112 unique genes, including 79 protein-coding, four rRNA, and 29 tRNA genes. Repeat analysis obtained 17 microsatellite, 16 tandem, and 17 interspersed repeats. Comparison of sequence divergence between L. raddeana and L. sativa found the intergenic spacer trnC-petN exhibited the highest degree of variation. Three phylogenetic trees based on the 72 shared protein, matK gene, and rbcL gene sequences showed that L. raddeana and L. sativa are clustered together. The acquisition and comparative analysis of the chloroplast genome provide a valuable resource for the taxonomic and phylogenetic studies of Lactuca.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Yuning Li
- School of Pharmaceutical Sciences, Xiangnan University, Chenzhou, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Bin Wang
- School of Pharmaceutical Sciences, Xiangnan University, Chenzhou, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
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Muñoz-Gómez S, Suárez-Baron H, Alzate JF, González F, Pabón-Mora N. Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales. FRONTIERS IN PLANT SCIENCE 2021; 12:633227. [PMID: 33897722 PMCID: PMC8063865 DOI: 10.3389/fpls.2021.633227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/08/2021] [Indexed: 05/27/2023]
Abstract
Flavonoids, carotenoids, betalains, and chlorophylls are the plant pigments responsible for floral color. Anthocyanins, a class of flavonoids, are largely responsible for the red, purple, pink, and blue colors. R2R3-MYB genes belonging to subgroup 6 (SG6) are the upstream regulatory factors of the anthocyanin biosynthetic pathway. The canonical members of these genes in Arabidopsis include AtMYB75, AtMYB90, AtMYB113, and AtMYB114. The Aristolochiaceae is an angiosperm lineage with diverse floral groundplans and perianth colors. Saruma henryi exhibits a biseriate perianth with green sepals and yellow petals. All other genera have sepals only, with colors ranging from green (in Lactoris) to a plethora of yellow to red and purple mixtures. Here, we isolated and reconstructed the SG6 R2R3-MYB gene lineage evolution in angiosperms with sampling emphasis in Aristolochiaceae. We found numerous species-specific duplications of this gene lineage in core eudicots and local duplications in Aristolochiaceae for Saruma and Asarum. Expression of SG6 R2R3-MYB genes examined in different developmental stages and plant organs of four Aristolochiaceae species, largely overlaps with red and purple pigments, suggesting a role in anthocyanin and flavonoid synthesis and accumulation. A directed RNA-seq analysis corroborated our RT-PCR analyses, by showing that these structural enzymes activate during perianth development in Aristolochia fimbriata and that the regulatory genes are expressed in correlation with color phenotype. Finally, the reconstruction of the flavonoid and anthocyanin metabolic pathways using predicted peptides from transcriptomic data show that all pivotal enzymes are present in the analyzed species. We conclude that the regulatory genes as well as the biosynthetic pathway are largely conserved across angiosperms. In addition, the Aristolochiaceae emerges as a remarkable group to study the genetic regulatory network for floral color, as their members exhibit an outstanding floral diversity with elaborate color patterns and the genetic complement for SG6 R2R3-MYB genes is simpler than in core eudicot model species.
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Affiliation(s)
- Sarita Muñoz-Gómez
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Harold Suárez-Baron
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica – CNSG, Sede de Investigación Universitaria, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, Bogotá, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
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Nowak MD, Birkeland S, Mandáková T, Roy Choudhury R, Guo X, Gustafsson ALS, Gizaw A, Schrøder‐Nielsen A, Fracassetti M, Brysting AK, Rieseberg L, Slotte T, Parisod C, Lysak MA, Brochmann C. The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Mol Ecol Resour 2021; 21:661-676. [PMID: 33058468 PMCID: PMC7983928 DOI: 10.1111/1755-0998.13280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/26/2020] [Accepted: 10/09/2020] [Indexed: 01/04/2023]
Abstract
The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
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Affiliation(s)
| | | | | | | | - Xinyi Guo
- CEITECMasaryk UniversityBrnoCzech Republic
| | | | - Abel Gizaw
- Natural History MuseumUniversity of OsloOsloNorway
| | | | - Marco Fracassetti
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
| | - Anne K. Brysting
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Loren Rieseberg
- Department of BotanyThe University of British ColumbiaVancouverBCCanada
| | - Tanja Slotte
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
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Griese E, Caarls L, Bassetti N, Mohammadin S, Verbaarschot P, Bukovinszkine’Kiss G, Poelman EH, Gols R, Schranz ME, Fatouros NE. Insect egg-killing: a new front on the evolutionary arms-race between brassicaceous plants and pierid butterflies. THE NEW PHYTOLOGIST 2021; 230:341-353. [PMID: 33305360 PMCID: PMC7986918 DOI: 10.1111/nph.17145] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/04/2020] [Indexed: 05/03/2023]
Abstract
Evolutionary arms-races between plants and insect herbivores have long been proposed to generate key innovations such as plant toxins and detoxification mechanisms that can drive diversification of the interacting species. A novel front-line of plant defence is the killing of herbivorous insect eggs. We test whether an egg-killing plant trait has an evolutionary basis in such a plant-insect arms-race. Within the crucifer family (Brassicaceae), some species express a hypersensitive response (HR)-like necrosis underneath butterfly eggs (Pieridae) that leads to eggs desiccating or falling off the plant. We studied the phylogenetic distribution of this trait, its egg-killing effect on and elicitation by butterflies, by screening 31 Brassicales species, and nine Pieridae species. We show a clade-specific induction of strong, egg-killing HR-like necrosis mainly in species of the Brassiceae tribe including Brassica crops and close relatives. The necrosis is strongly elicited by pierid butterflies that are specialists of crucifers. Furthermore, HR-like necrosis is linked to PR1 defence gene expression, accumulation of reactive oxygen species and cell death, eventually leading to egg-killing. Our findings suggest that the plants' egg-killing trait is a new front on the evolutionary arms-race between Brassicaceae and pierid butterflies beyond the well-studied plant toxins that have evolved against their caterpillars.
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Affiliation(s)
- Eddie Griese
- Biosystematics GroupWageningen UniversityWageningen6700 AAthe Netherlands
- Laboratory of EntomologyWageningen UniversityWageningen6700 AAthe Netherlands
| | - Lotte Caarls
- Biosystematics GroupWageningen UniversityWageningen6700 AAthe Netherlands
- Present address:
Plant BreedingWageningen University and ResearchWageningen6700 AJthe Netherlands
| | - Niccolò Bassetti
- Biosystematics GroupWageningen UniversityWageningen6700 AAthe Netherlands
| | - Setareh Mohammadin
- Biosystematics GroupWageningen UniversityWageningen6700 AAthe Netherlands
| | | | - Gabriella Bukovinszkine’Kiss
- Biosystematics GroupWageningen UniversityWageningen6700 AAthe Netherlands
- Laboratory of GeneticsWageningen UniversityWageningen6700 AAthe Netherlands
| | - Erik H. Poelman
- Laboratory of EntomologyWageningen UniversityWageningen6700 AAthe Netherlands
| | - Rieta Gols
- Laboratory of EntomologyWageningen UniversityWageningen6700 AAthe Netherlands
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityWageningen6700 AAthe Netherlands
| | - Nina E. Fatouros
- Biosystematics GroupWageningen UniversityWageningen6700 AAthe Netherlands
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Birkeland S, Gustafsson ALS, Brysting AK, Brochmann C, Nowak MD. Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae. Mol Biol Evol 2021; 37:2052-2068. [PMID: 32167553 PMCID: PMC7306683 DOI: 10.1093/molbev/msaa068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/23/2020] [Accepted: 03/10/2020] [Indexed: 12/11/2022] Open
Abstract
Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.
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Affiliation(s)
- Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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Wen F, Wu X, Li T, Jia M, Liu X, Liao L. The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China. BMC Genomics 2021; 22:161. [PMID: 33676415 PMCID: PMC7937279 DOI: 10.1186/s12864-021-07484-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. RESULTS A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. CONCLUSIONS This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
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Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
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Blanco-Sánchez M, Moore MJ, Ramos-Muñoz M, Pías B, García-Fernández A, Prieto M, Plaza L, Isabel I, Escudero A, Matesanz S. Phylogeography of a gypsum endemic plant across its entire distribution range in the western Mediterranean. AMERICAN JOURNAL OF BOTANY 2021; 108:443-460. [PMID: 33740271 DOI: 10.1002/ajb2.1625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Gypsum soils in the Mediterranean Basin house large numbers of edaphic specialists that are adapted to stressful environments. The evolutionary history and standing genetic variation of these taxa have been influenced by the geological and paleoclimatic complexity of this area and the long-standing effect of human activities. However, little is known about the origin of Mediterranean gypsophiles and the factors affecting their genetic diversity and population structure. METHODS Using phylogenetic and phylogeographic approaches based on microsatellites and sequence data from nuclear and chloroplast regions, we evaluated the divergence time, genetic diversity, and population structure of 27 different populations of the widespread Iberian gypsophile Lepidium subulatum throughout its entire geographic range. RESULTS Lepidium subulatum diverged from its nearest relatives ~3 million years ago, and ITS and psbA/matK trees supported the monophyly of the species. These results suggest that both geological and climatic changes in the region around the Plio-Pleistocene promoted its origin, compared to other evolutionary processes. We found high genetic diversity in both nuclear and chloroplast markers, but a greater population structure in the chloroplast data. These results suggest that while seed dispersal is limited, pollen flow may be favored by the presence of numerous habitat patches that enhance the movement of pollinators. CONCLUSIONS Despite being an edaphic endemic, L. subulatum possesses high genetic diversity probably related to its relatively old age and high population sizes across its range. Our study highlights the value of using different markers to fully understand the phylogeographic history of plant species.
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Affiliation(s)
- Mario Blanco-Sánchez
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
| | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA
| | - Marina Ramos-Muñoz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
| | - Beatriz Pías
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, C/José Antonio Nováis 2, 28040, Madrid, Spain
| | - Alfredo García-Fernández
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
| | - María Prieto
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
| | - Lidia Plaza
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
| | - Ignacio Isabel
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos. C/ Tulipán s/n, 28933, Móstoles, Spain
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Shang S, Zhao L, Xu T, Li C, Shen R. The complete chloroplast genome of Lepidium latifolium linnaeus and phylogenetic analysis of brassicaceae. Mitochondrial DNA B Resour 2021; 6:178-179. [PMID: 33537434 PMCID: PMC7832579 DOI: 10.1080/23802359.2020.1860699] [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] [Indexed: 11/17/2022] Open
Abstract
The complete chloroplast genome sequence of Lepidium latifolium Linnaeus was assembled and characterized in the present study. The plastome is 153,989 bp in length, which is comprised of a large single-copy (LSC) region of 83,565 bp, a small single-copy (SSC) region of 17,526 bp, and two inverted repeat (IR) regions of 26,449 bp. The overall GC content of the plastome was 36.5%. The new sequence comprised 125 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 33 tRNA genes. Phylogenetic analysis showed that L. latifolium L. was close to Lepidium meyenii and Lepidium virginicum.
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Affiliation(s)
- Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Liping Zhao
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Tao Xu
- Shandong Fisheries Technology Extension Center, Jinan, China
| | - Caiyun Li
- Jinan Vocational College, Jinan, China
| | - Ruiting Shen
- CCCC Water Transportation Consultants Co., Ltd, Beijing, China
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Hu Y, Wu X, Jin G, Peng J, Leng R, Li L, Gui D, Fan C, Zhang C. Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications. FRONTIERS IN PLANT SCIENCE 2021; 12:772655. [PMID: 35058947 PMCID: PMC8764390 DOI: 10.3389/fpls.2021.772655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 05/21/2023]
Abstract
Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense's adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.
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Affiliation(s)
- Yanting Hu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaopei Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junchu Peng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Rong Leng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ling Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
- Chuanzhu Fan,
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Chengjun Zhang,
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Folk RA, Siniscalchi CM, Soltis DE. Angiosperms at the edge: Extremity, diversity, and phylogeny. PLANT, CELL & ENVIRONMENT 2020; 43:2871-2893. [PMID: 32926444 DOI: 10.1111/pce.13887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/21/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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Whittall JB, Butler TM, Dick C, Sandel B. Two cryptic species of California mustard within Caulanthus lasiophyllus. AMERICAN JOURNAL OF BOTANY 2020; 107:1815-1830. [PMID: 33370466 PMCID: PMC7839454 DOI: 10.1002/ajb2.1562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/03/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Cryptic species are evolutionarily distinct lineages lacking distinguishing morphological traits. Hidden diversity may be lurking in widespread species whose distributions cross phylogeographic barriers. This study investigates molecular and morphological variation in the widely distributed Caulanthus lasiophyllus (Brassicaceae) in comparison to its closest relatives. METHODS Fifty-two individuals of C. lasiophyllus from across the species' range were sequenced for the nuclear ribosomal internal transcribed spacer region (ITS) and the chloroplast trnL-F region. A subset of these samples were examined for the chloroplast ndhF gene. All 52 individuals were scored for 13 morphological traits, as well as monthly and annual climate conditions at the collection locality. Morphological and molecular results are compared with the closest relatives-C. anceps and C. flavescens-in the "Guillenia Clade." To test for polyploidy, genome size estimates were made for four populations. RESULTS Caulanthus lasiophyllus consists of two distinct lineages separated by eight ITS differences-eight times more variation than what distinguishes C. anceps and C. flavescens. Fewer variable sites were detected in trnL-F and ndhF regions, yet these data are consistent with the ITS results. The two lineages of C. lasiophyllus are geographically and climatically distinct; yet morphologically overlapping. Their genome sizes are not consistently different. CONCLUSIONS Two cryptic species within C. lasiophyllus are distinguished at the molecular, geographic, and climatic scales. They have similar genome sizes and are morphologically broadly overlapping, but an ephemeral basal leaf character may help distinguish the species.
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Affiliation(s)
- Justen B. Whittall
- Department of BiologySanta Clara University500 El Camino RealSanta ClaraCalifornia95053USA
| | - Timothy M. Butler
- Department of BiologySanta Clara University500 El Camino RealSanta ClaraCalifornia95053USA
| | - Cynthia Dick
- Department of BiologySanta Clara University500 El Camino RealSanta ClaraCalifornia95053USA
| | - Brody Sandel
- Department of BiologySanta Clara University500 El Camino RealSanta ClaraCalifornia95053USA
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