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Penin AA, Kasianov AS, Klepikova AV, Omelchenko DO, Makarenko MS, Logacheva MD. Origin and diversity of Capsella bursa-pastoris from the genomic point of view. BMC Biol 2024; 22:52. [PMID: 38439107 PMCID: PMC10913212 DOI: 10.1186/s12915-024-01832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. RESULTS We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance-both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. CONCLUSIONS C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella.
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Affiliation(s)
- Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
| | - Artem S Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Denis O Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maksim S Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Sha Y, Li Y, Zhang D, Lv R, Wang H, Wang R, Ji H, Li S, Gong L, Li N, Liu B. Genome shock in a synthetic allotetraploid wheat invokes subgenome-partitioned gene regulation, meiotic instability, and karyotype variation. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5547-5563. [PMID: 37379452 DOI: 10.1093/jxb/erad247] [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: 03/14/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
It is becoming increasingly evident that interspecific hybridization at the homoploid level or coupled with whole-genome duplication (i.e. allopolyploidization) has played a major role in biological evolution. However, the direct impacts of hybridization and allopolyploidization on genome structure and function, phenotype, and fitness remains to be fully understood. Synthetic hybrids and allopolyploids are trackable experimental systems that can be used to address this issue. In this study, we resynthesized a pair of reciprocal F1 hybrids and corresponding reciprocal allotetraploids using the two diploid progenitor species of bread wheat (Triticum aestivum, BBAADD), namely T. urartu (AA) and Aegilops tauschii (DD). By comparing phenotypes related to growth, development, and fitness, and by analysing genome expression in both hybrids and allotetraploids in relation to the parents, we found that the types and trends of karyotype variation in the immediately formed allotetraploids were correlated with both instability of meiosis and chromosome- and subgenome-biased expression. We determined clear advantages of allotetraploids over diploid F1 hybrids in several morphological traits including fitness that mirrored the tissue- and developmental stage-dependent subgenome-partitioning of the allotetraploids. The allotetraploids were meiotically unstable primarily due to homoeologous pairing that varied dramatically among the chromosomes. Nonetheless, the manifestation of organismal karyotype variation and the occurrence of meiotic irregularity were not concordant, suggesting a role of functional constraints probably imposed by subgenome- and chromosome-biased gene expression. Our results provide new insights into the direct impacts and consequences of hybridization and allopolyploidization that are relevant to evolution and likely to be informative for future crop improvement approaches using synthetic polyploids.
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Affiliation(s)
- Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Deshi Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Han Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Heyu Ji
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Shuhang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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3
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Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Farhat P, Mandáková T, Divíšek J, Kudoh H, German DA, Lysak MA. The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella. FRONTIERS IN PLANT SCIENCE 2023; 14:1165140. [PMID: 37223809 PMCID: PMC10200890 DOI: 10.3389/fpls.2023.1165140] [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: 02/13/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023]
Abstract
The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.
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Affiliation(s)
- Perla Farhat
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Divíšek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Russia
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
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5
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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6
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Wei ZZ, Zhou TQ, Xia ZM, Liu SF, Li M, Zhang GJ, Tian Y, Li B, Wang L. Four organosulfur compounds from the seeds of Capsella bursa-pastoris and their anti-inflammatory activities. Nat Prod Res 2022:1-9. [PMID: 36200729 DOI: 10.1080/14786419.2022.2130307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
Phytochemical investigation of the seeds of Capsella bursa-pastoris led to the isolation of four organosulfur compounds. There were two new compounds, 10-methylsulfinyl-decanamide (1) and 11-methylsulfinyl-undecanamide (2), along with two known compounds (3 - 4), which all have a sulfoxide group and an amide or a nitrile group. Their chemical structures were elucidated by analysing UV, IR, ESI-MS and NMR spectroscopy. In addition, compounds 1 - 4 were evaluated for their anti-inflammatory activities by using LPS-induced RAW 264.7 cells. Compounds 1 - 4 exhibited potential anti-inflammatory activities on NO release characterised by decreasing the mRNA expression levels of inducible NO synthase (iNOS), cytokines cyclooxygenase-2 (COX-2) and interleukin 6 (IL-6).
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Affiliation(s)
- Zhen-Zhen Wei
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China.,Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
| | - Ti-Qiang Zhou
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China.,Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China.,School of Life Science, Beijing Institute of Technology, Beijing, China.,Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China.,Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China.,Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing, China.,Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing, China
| | - Zi-Ming Xia
- Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
| | - Si-Fan Liu
- Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
| | - Min Li
- Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
| | - Guang-Jie Zhang
- Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
| | - Ying Tian
- Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
| | - Bin Li
- Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
| | - Lin Wang
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China.,Department of Pharmaceutical Science, Beijing Institute of Radiation Medicine, Beijing, China
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7
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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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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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9
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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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10
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Wang J, Dong S, Yang L, Harris A, Schneider H, Kang M. Allopolyploid Speciation Accompanied by Gene Flow in a Tree Fern. Mol Biol Evol 2021; 37:2487-2502. [PMID: 32302390 DOI: 10.1093/molbev/msaa097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid speciation as an evolutionary process in fern lineages remains poorly understood. Here, we employ flow cytometry, phylogeny, genomewide single nucleotide polymorphism data sets, and admixture and coalescent modeling to show that the scaly tree fern, Gymnosphaera metteniana is a naturally occurring allotetraploid species derived from hybridization between the diploids, G. denticulata and G. gigantea. Moreover, we detected ongoing gene flow between the hybrid species and its progenitors, and we found that G. gigantea and G. metteniana inhabit distinct niches, whereas climatic niches of G. denticulata and G. metteniana largely overlap. Taken together, these results suggest that either some degree of intrinsic genetic isolation between the hybrid species and its parental progenitors or ecological isolation over short distances may be playing an important role in the evolution of reproductive barriers. Historical climate change may have facilitated the origin of G. metteniana, with the timing of hybridization coinciding with a period of intensification of the East Asian monsoon during the Pliocene and Pleistocene periods in southern China. Our study of allotetraploid G. metteniana represents the first genomic-level documentation of hybrid speciation in scaly tree ferns and, thus, provides a new perspective on evolution in the lineage.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Shiyong Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Aj Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Department of Biology, Oberlin College, Oberlin, OH
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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11
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Wesse C, Welk E, Hurka H, Neuffer B. Geographical pattern of genetic diversity in Capsella bursa-pastoris (Brassicaceae)-A global perspective. Ecol Evol 2021; 11:199-213. [PMID: 33437423 PMCID: PMC7790636 DOI: 10.1002/ece3.7010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/06/2020] [Accepted: 10/16/2020] [Indexed: 12/15/2022] Open
Abstract
We analyzed the global genetic variation pattern of Capsella bursa-pastoris (Brassicaceae) as expressed in allozymic (within-locus) diversity and isozymic (between-locus) diversity. Results are based on a global sampling of more than 20,000 C. bursa-pastoris individuals randomly taken from 1,469 natural provenances in the native and introduced range, covering a broad spectrum of the species' geographic distribution. We evaluated data for population genetic parameters and F-statistics, and Mantel tests and AMOVA were performed. Geographical distribution patterns of alleles and multilocus genotypes are shown in maps and tables. Genetic diversity of introduced populations is only moderately reduced in comparison with native populations. Global population structure was analyzed with structure, and the obtained cluster affiliation was tested independently with classification approaches and macroclimatic data using species distribution modeling. Analyses revealed two main clusters: one distributed predominantly in warm arid to semiarid climate regions and the other predominantly in more temperate humid to semihumid climate regions. We observed admixture between the two lineages predominantly in regions with intermediate humidity in both the native and non-native ranges. The genetically derived clusters are strongly supported in macroclimatic data space. The worldwide distribution patterns of genetic variation in the range of C. bursa-pastoris can be explained by intensive intra- and intercontinental migration, but environmental filtering due to climate preadaption seems also involved. Multiple independent introductions of genotypes from different source regions are obvious. "Endemic" genotypes might be the outcome of admixture or of de novo mutation. We conclude that today's successfully established Capsella genotypes were preadapted and found matching niche conditions in the colonized range parts.
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Affiliation(s)
- Christina Wesse
- Department of BotanyUniversity of OsnabrueckOsnabrückGermany
| | - Erik Welk
- Institute for BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | - Herbert Hurka
- Department of BotanyUniversity of OsnabrueckOsnabrückGermany
| | - Barbara Neuffer
- Department of BotanyUniversity of OsnabrueckOsnabrückGermany
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12
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Wu Y, Lin F, Zhou Y, Wang J, Sun S, Wang B, Zhang Z, Li G, Lin X, Wang X, Sun Y, Dong Q, Xu C, Gong L, Wendel JF, Zhang Z, Liu B. Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids. Natl Sci Rev 2020; 8:nwaa277. [PMID: 34691642 PMCID: PMC8288387 DOI: 10.1093/nsr/nwaa277] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/01/2020] [Indexed: 01/03/2023] Open
Abstract
Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges (HEs) generate phenotypically variable progeny. However, the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the fourth selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole-genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.
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Affiliation(s)
- Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
- Department of Crop & Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Fan Lin
- Brightseed Inc., San Francisco, CA 94107, USA
| | - Yao Zhou
- Department of Crop & Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Qianli Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhiwu Zhang
- Department of Crop & Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
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13
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Zhang J, Yang F, Jiang Y, Guo Y, Wang Y, Zhu X, Li J, Wan H, Wang Q, Deng Z, Xuan P, Yang W. Preferential Subgenome Elimination and Chromosomal Structural Changes Occurring in Newly Formed Tetraploid Wheat- Aegilops ventricosa Amphiploid (AABBD vD vN vN v). Front Genet 2020; 11:330. [PMID: 32477398 PMCID: PMC7235383 DOI: 10.3389/fgene.2020.00330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/20/2020] [Indexed: 11/15/2022] Open
Abstract
Artificial allopolyploids derived from the genera Triticum and Aegilops have been used as genetic resources for wheat improvement and are a classic example of evolution via allopolyploidization. In this study, we investigated chromosomes and subgenome transmission behavior in the newly formed allopolyploid of wheat group via multicolor Fluorescence in situ hybridization (mc-FISH), using pSc119.2, pTa535, and (GAA)7 as probe combinations, to enabled us to precisely identify individual chromosomes in 381 S3 and S4 generations plants derived from reciprocal crosses between Ae. ventricosa (DvDvNvNv) and T. turgidum (AABB). A higher rate of aneuploidy, constituting 66.04–86.41% individuals, was observed in these two early generations. Of the four constituent subgenomes, Dv showed the highest frequency of elimination, followed by Nv and B, while A was the most stable. In addition, structural chromosomal changes occurred ubiquitously in the selfed progenies of allopolyploids. Among the constituent subgenomes, B showed the highest number of aberrations. In terms of chromosomal dynamics, there was no significant association between the chromosomal behavior model and the cytoplasm, with the exception of chromosomal loss in the Dv subgenome. The chromosome loss frequency in the Dv subgenome was significantly higher in the T. turgidum × Ae. ventricosa cross than in the Ae. ventricosa × T. turgidum cross. This result indicates that, although the D subgenome showed great instability, allopolyploids containing D subgenome could probably be maintained after a certain hybridization in which the D subgenome donor was used as the maternal parent at its onset stage. Our findings provide valuable information pertaining to the behavior patterns of subgenomes during allopolyploidization. Moreover, the allopolyploids developed here could be used as potential resources for the genetic improvement of wheat.
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Affiliation(s)
- Jie Zhang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China
| | - Fan Yang
- Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yuanlin Guo
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ying Wang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - XinGuo Zhu
- Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Li
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China.,Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China.,Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qin Wang
- Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ziyuan Deng
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Pu Xuan
- Institute of Agro-products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - WuYun Yang
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China.,Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
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14
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Omelchenko DO, Makarenko MS, Kasianov AS, Schelkunov MI, Logacheva MD, Penin AA. Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris. PLANTS (BASEL, SWITZERLAND) 2020; 9:E469. [PMID: 32276324 PMCID: PMC7238199 DOI: 10.3390/plants9040469] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/24/2020] [Accepted: 04/04/2020] [Indexed: 12/11/2022]
Abstract
Shepherd's purse (Capsella bursa-pastoris) is a cosmopolitan annual weed and a promising model plant for studying allopolyploidization in the evolution of angiosperms. Though plant mitochondrial genomes are a valuable source of genetic information, they are hard to assemble. At present, only the complete mitogenome of C. rubella is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of C. bursa-pastoris using high-precision PacBio SMRT third-generation sequencing technology. It is 287,799 bp long and contains 32 protein-coding genes, 3 rRNAs, 25 tRNAs corresponding to 15 amino acids, and 8 open reading frames (ORFs) supported by RNAseq data. Though many repeat regions have been found, none of them is longer than 1 kbp, and the most frequent structural variant originated from these repeats is present in only 4% of the mitogenome copies. The mitochondrial DNA sequence of C. bursa-pastoris differs from C. rubella, but not from C. orientalis, by two long inversions, suggesting that C. orientalis could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except cox1 and atp8 contain RNA editing sites, and most of them lead to non-synonymous changes of amino acids. Most of the identified RNA editing sites are identical to corresponding RNA editing sites in A. thaliana.
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Affiliation(s)
- Denis O. Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Maxim S. Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (A.S.K.); (M.I.S.); (M.D.L.); (A.A.P.)
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15
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Han TS, Zheng QJ, Onstein RE, Rojas-Andrés BM, Hauenschild F, Muellner-Riehl AN, Xing YW. Polyploidy promotes species diversification of Allium through ecological shifts. THE NEW PHYTOLOGIST 2020; 225:571-583. [PMID: 31394010 DOI: 10.1111/nph.16098] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/01/2019] [Indexed: 05/14/2023]
Abstract
Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.
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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
| | - 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
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
| | - Blanca M Rojas-Andrés
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Frank Hauenschild
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Alexandra N Muellner-Riehl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - 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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16
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Li J, Gao X, Li M, Fang F. Resistance evolution and mechanisms to ALS-inhibiting herbicides in Capsella bursa-pastoris populations from China. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 159:17-21. [PMID: 31400779 DOI: 10.1016/j.pestbp.2019.05.010] [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: 02/15/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 06/10/2023]
Abstract
Capsella bursa-pastoris is a serious broadleaf weed in winter wheat fields in China. It has evolved high levels of resistance to acetolactate synthase (ALS) inhibiting herbicides and has caused substantial losses of wheat yield in recent years. We monitored the herbicide resistance of Capsella bursa-pastoris collected from 18 regions of Shandong Province in 2009, 2013 and 2017, respectively. Compared with the 2009 populations, the number of populations resistant to florasulam had increased in 2013 and 2017. Resistance to tribenuron-methyl increased in 2013, but decreased in 2017. The 2009 and 2013 populations developed resistance only to tribenuron-methyl, but some 2017 populations developed cross-resistance to imazethapyr and florasulam as well. Mutations in ALS (Pro-197-Thr/Ser/His/Arg/Leu/Gln) were identified in the 2009 and 2013 populations; however, two ALS mutations (Pro197 and/or Trp574) were identified in 2017 plants. Meanwhile, plants containing both point mutations (Pro197 + Trp574) were identified in the 2017 populations. This study demonstrated that target site gene mutations were the main reason for Capsella bursa-pastoris resistance to ALS-inhibiting herbicides. Although target-site mutation is the reason for resistance to ALS-inhibiting herbicides in Capsella bursa-pastoris, the resistance patterns and mutations identified have changed over time.
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Affiliation(s)
- Jian Li
- Weed Science Department, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, PR China.
| | - Xingxiang Gao
- Weed Science Department, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, PR China
| | - Mei Li
- Weed Science Department, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, PR China.
| | - Feng Fang
- Weed Science Department, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, PR China
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17
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Li N, Xu C, Zhang A, Lv R, Meng X, Lin X, Gong L, Wendel JF, Liu B. DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. THE NEW PHYTOLOGIST 2019; 223:979-992. [PMID: 30919978 DOI: 10.1111/nph.15820] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/21/2019] [Indexed: 05/18/2023]
Abstract
Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome-wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome-wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome-wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.
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Affiliation(s)
- Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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18
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Gou X, Bian Y, Zhang A, Zhang H, Wang B, Lv R, Li J, Zhu B, Gong L, Liu B. Transgenerationally Precipitated Meiotic Chromosome Instability Fuels Rapid Karyotypic Evolution and Phenotypic Diversity in an Artificially Constructed Allotetraploid Wheat (AADD). Mol Biol Evol 2019; 35:1078-1091. [PMID: 29365173 PMCID: PMC5913668 DOI: 10.1093/molbev/msy009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although a distinct karyotype with defined chromosome number and structure characterizes each biological species, it is intrinsically labile. Polyploidy or whole-genome duplication has played a pervasive and ongoing role in the evolution of all eukaryotes, and is the most dramatic force known to cause rapid karyotypic reconfiguration, especially at the initial stage. However, issues concerning transgenerational propagation of karyotypic heterogeneity and its translation to phenotypic diversity in nascent allopolyploidy, at the population level, have yet to be studied in detail. Here, we report a large-scale examination of transgenerationally propagated karyotypic heterogeneity and its phenotypic manifestation in an artificially constructed allotetraploid with a genome composition of AADD, that is, involving two of the three progenitor genomes of polyploid wheat. Specifically, we show that 1) massive organismal karyotypic heterogeneity is precipitated after 12 consecutive generations of selfing from a single euploid founder individual, 2) there exist dramatic differences in aptitudes between subgenomes and among chromosomes for whole-chromosome gain and/or loss and structural variations, 3) majority of the numerical and structural chromosomal variations are concurrent due to mutual contingency and possible functional constraint, 4) purposed and continuous selection and propagation for euploidy over generations did not result in enhanced karyotype stabilization, and 5) extent of karyotypic variation correlates with variability of phenotypic manifestation. Together, our results document that allopolyploidization catalyzes rampant and transgenerationally heritable organismal karyotypic heterogeneity that drives population-level phenotypic diversification, which lends fresh empirical support to the still contentious notion that whole-genome duplication enhances organismal evolvability.
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Affiliation(s)
- Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Yao Bian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bo Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
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Molina-Henao YF, Hopkins R. Autopolyploid lineage shows climatic niche expansion but not divergence in Arabidopsis arenosa. AMERICAN JOURNAL OF BOTANY 2019; 106:61-70. [PMID: 30609009 DOI: 10.1002/ajb2.1212] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/24/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Successful establishment of neopolyploids, and therefore polyploid speciation, is thought to be contingent on environmental niche shifts from their progenitors. We explore this niche shift hypothesis in the obligate outcrosser Arabidopsis arenosa complex, which includes diploid and recently formed autotetraploid populations. METHODS To characterize the climatic niches for both cytotypes in Arabidopsis arenosa, we first gathered climatic data from localities with known ploidy types. We then estimated the climatic niches for diploids and autotetraploids and calculated niche overlap. Using this niche overlap statistic, we tested for niche equivalency and similarity. We explored differences in niches by estimating and comparing niche optimum and breadth and then calculated indices of niche expansion and unfilling. KEY RESULTS Climatic niche overlap between diploids and autotetraploids is substantial. Although the two niche models are not significantly divergent, they are not identical as they differ in both optimum and breadth along two environmental gradients. Autotetraploids fill nearly the entire niche space of diploids and have expanded into novel environments. CONCLUSIONS We find climatic niche expansion but not divergence, together with a moderate change in the niche optimum, in the autotetraploid lineage of Arabidopsis arenosa. These results indicate that the climatic niche shift hypothesis alone cannot explain the coexistence of tetraploid and diploid cytotypes.
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Affiliation(s)
- Y Franchesco Molina-Henao
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
- Departamento de Biología, Universidad del Valle, Cali, Valle, 760032, Colombia
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
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20
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Levin DA, Soltis DE. Factors promoting polyploid persistence and diversification and limiting diploid speciation during the K-Pg interlude. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:1-7. [PMID: 29107221 DOI: 10.1016/j.pbi.2017.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 05/14/2023]
Abstract
The large wave of polyploidization following the Cretaceous-Paleogene (K-Pg) mass extinction has been explained by enhanced polyploid persistence arising from adaptive properties of the polyploids themselves, as well as an increase in unreduced gamete production and diploid hybridization. We propose that the demise of diploids afforded opportunities for polyploid establishment and expansion into novel habitats. Augmented polyploid gene pools from diploid and polyploid relatives, in association with their multiple and independent origins (of both autopolyploids and allopolyploids), facilitated their subsequent diversification. Their ability to recruit genetic variation from their diploid relatives or from products of recurrent origins sharing their genome(s) ostensibly contributed to polyploid persistence. Concomitantly, we propose that the number of congeneric diploid species dramatically contracted disproportionally to polyploids during the K-Pg interval (i.e. a diploid trough), resulting in a reduction in the rate of diploid speciation. Accordingly, the preponderance of neopolyploids was likely autopolyploids.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA
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21
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Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol 2017; 18:239. [PMID: 29284515 PMCID: PMC5745794 DOI: 10.1186/s13059-017-1378-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
Background Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. Results We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping. Conclusions A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1378-9) contains supplementary material, which is available to authorized users.
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22
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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23
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Wu Q, Han TS, Chen X, Chen JF, Zou YP, Li ZW, Xu YC, Guo YL. Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives. Genome Biol 2017; 18:217. [PMID: 29141655 PMCID: PMC5686891 DOI: 10.1186/s13059-017-1342-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/16/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adaptation in diverse organisms. However, which genes, genome-wide, are under balancing selection and the extent to which these genes are involved in adaptation are largely unknown. RESULTS We performed a genome-wide scan for genes under balancing selection across two plant species, Arabidopsis thaliana and its relative Capsella rubella, which diverged about 8 million generations ago. Among hundreds of genes with shared coding-region polymorphisms, we find evidence for long-term balancing selection in five genes: AT1G35220, AT2G16570, AT4G29360, AT5G38460, and AT5G44000. These genes are involved in the response to biotic and abiotic stress and other fundamental biochemical processes. More intriguingly, for these genes, we detected significant ecological diversification between the two haplotype groups, suggesting that balancing selection has been very important for adaptation. CONCLUSIONS Our results indicate that beyond the well-known S-locus genes and resistance genes, many loci are under balancing selection. These genes are mostly correlated with resistance to stress or other fundamental functions and likely play a more important role in adaptation to diverse habitats than previously thought.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ting-Shen Han
- 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
| | - Xi 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
| | - Jia-Fu 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
| | - Yu-Pan Zou
- 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
| | - Zi-Wen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yong-Chao Xu
- 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
| | - Ya-Long Guo
- 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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24
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Kasianov AS, Klepikova AV, Kulakovskiy IV, Gerasimov ES, Fedotova AV, Besedina EG, Kondrashov AS, Logacheva MD, Penin AA. High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:278-291. [PMID: 28387959 DOI: 10.1111/tpj.13563] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/01/2017] [Accepted: 03/31/2017] [Indexed: 05/22/2023]
Abstract
Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range.
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Affiliation(s)
- Artem S Kasianov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
| | - Anna V Klepikova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Ivan V Kulakovskiy
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russia
| | - Evgeny S Gerasimov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna V Fedotova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Elizaveta G Besedina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Ecology and Evolution, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, MI, USA
| | - Maria D Logacheva
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlevskaya str, Kazan, 420008, Russia
| | - Aleksey A Penin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Qian C, Yin H, Shi Y, Zhao J, Yin C, Luo W, Dong Z, Chen G, Yan X, Wang XR, Ma XF. Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change. Sci Rep 2016; 6:26613. [PMID: 27210568 PMCID: PMC4876407 DOI: 10.1038/srep26613] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/04/2016] [Indexed: 12/02/2022] Open
Abstract
Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.
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Affiliation(s)
- Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hengxia Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Shi
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiecai Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengliang Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyin Luo
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Zhibao Dong
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Xia Yan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- Key Laboratory of Eco-hydrology and of Inland River Basin, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå 90187, Sweden
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
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26
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Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA. Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers. Mol Ecol 2016; 25:2413-26. [PMID: 27065091 PMCID: PMC4999052 DOI: 10.1111/mec.13644] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 04/05/2016] [Accepted: 04/08/2016] [Indexed: 01/02/2023]
Abstract
Hybridization may lead to introgression of genes among species. Introgression may be bidirectional or unidirectional, depending on factors such as the demography of the hybridizing species, or the nature of reproductive barriers between them. Previous microsatellite studies suggested bidirectional introgression between diploid Betula nana (dwarf birch) and tetraploid B. pubescens (downy birch) and also between B. pubescens and diploid B. pendula (silver birch) in Britain. Here, we analyse introgression among these species using 51 237 variants in restriction site‐associated (RAD) markers in 194 individuals, called with allele dosages in the tetraploids. In contrast to the microsatellite study, we found unidirectional introgression into B. pubescens from both of the diploid species. This pattern fits better with the expected nature of the reproductive barrier between diploids and tetraploids. As in the microsatellite study, introgression into B. pubescens showed clear clines with increasing introgression from B. nana in the north and from B. pendula in the south. Unlike B. pendula alleles, introgression of B. nana alleles was found far from the current area of sympatry or allopatry between B. nana and B. pubescens. This pattern fits a shifting zone of hybridization due to Holocene reduction in the range of B. nana and expansion in the range of B. pubescens.
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Affiliation(s)
- Jasmin Zohren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Nian Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Igor Kardailsky
- QIAGEN Aarhus A/S, Silkeborgvej 2, Prismet, Aarhus C, 8000, Denmark
| | - James S Borrell
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Anika Joecker
- QIAGEN Aarhus A/S, Silkeborgvej 2, Prismet, Aarhus C, 8000, Denmark
| | - Richard A Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
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27
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Cotrim H, Monteiro F, Sousa E, Pinto MJ, Fay MF. Marked hybridization and introgression in Ophrys sect. Pseudophrys in the western Iberian Peninsula. AMERICAN JOURNAL OF BOTANY 2016; 103:677-691. [PMID: 27056929 DOI: 10.3732/ajb.1500252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Orchids in the genus Ophrys represent extraordinary cases of tight coevolution between plants and their pollinators, and as a result, they present opportunities for studying hybridization, or a lack thereof, during speciation. However, few studies assess the real effect of hybridization in diversification. The three most representative species of section Pseudophrys in the western Iberian Peninsula-O. dyris, O. fusca, and O. lutea-were chosen to study evolutionary relationships and examine speciation. METHODS Using eight specific nuclear microsatellite loci, 357 individuals from 28 locations were studied; 142 of these samples were also studied with four plastid microsatellite loci. Data were analyzed using Bayesian cluster analysis, a median-joint network, and multivariate analysis. KEY RESULTS Many O. dyris and O. fusca specimens had three or four alleles and were therefore treated as tetraploid. Ophrys dyris is poorly genetically separated from O. fusca, and pure populations are rare. Ophrys fusca and O. lutea are distinct, but hybrids/introgressed individuals were detected in most of the populations and supported by plastid haplotypes. Ophrys fusca is subdivided into three well-delimited genetic lineages with a strict geographic correspondence confirmed by plastid haplotypes. CONCLUSIONS Because postzygotic barriers are weak, leakage in this highly specialized orchid-pollinator system contributes to hybridization and introgression. These leakages may have occurred during periods of past climate change, promoting homogenization and the potential for generations of new biodiversity via production of novel genotypes/phenotypes interacting with pollinators.
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Affiliation(s)
- Helena Cotrim
- Centre for Ecology, Evolution and Environmental Change (CE3C), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal Botanic Garden, National Museum of Natural History and Science, University of Lisbon, 1250-102 Lisbon, Portugal Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, United Kingdom
| | - Filipa Monteiro
- Biosystems and Integrative Sciences Institute (BIOISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Eva Sousa
- Biosystems and Integrative Sciences Institute (BIOISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Manuel J Pinto
- Botanic Garden, National Museum of Natural History and Science, University of Lisbon, 1250-102 Lisbon, Portugal
| | - Michael F Fay
- Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, United Kingdom
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28
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Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright SI, Lascoux M. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris). Mol Ecol 2016; 25:616-29. [PMID: 26607306 DOI: 10.1111/mec.13491] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/29/2022]
Abstract
Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.
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Affiliation(s)
- A Cornille
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - A Salcedo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - D Kryvokhyzha
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - K Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
| | - S I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M6R 1M3, Canada
| | - M Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for life Laboratory, Uppsala University, Uppsala 75236, Sweden
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Wu Z, Ma Q. Limited variation across two chloroplast genomes with finishing chloroplast genome of Capsella grandiflora. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3460-1. [PMID: 26186303 DOI: 10.3109/19401736.2015.1066347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast genome of Capsella grandiflora is finished in this study, which consists of 154 638 base pairs (bp) in size containing a pair of inverted repeats (IRa and IRb) of 26 462 bp each and a small and large single-copies (SSC and LSC) of 17 835 and 83 879 bp, respectively. The overall GC content is 36.54% and the GC contents of LSC, IRs, and SSC are 34.34%, 42.38%, and 29.61% separately. The gene contents and numbers are the same with other two published species in genus Capsella with 112 annotated unique genes including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among these, 16 are duplicated in the inverted repeat regions, 15 genes contained one intron, and three genes (rps12, clpP, and ycf3) comprising two introns. Based on the whole genome comparison, only 28 SNPs and 16 Indels (insertion and deletion) are detected between two closed relatives' chloroplast genomes.
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Affiliation(s)
- Zhiqiang Wu
- a Department of Biological Sciences , Texas Tech University , Lubbock , TX , USA and
| | - Qiumao Ma
- b Department of Computer Science , Iowa State University , Ames , IA , USA
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