51
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Liu Y, Wang S, Li L, Yang T, Dong S, Wei T, Wu S, Liu Y, Gong Y, Feng X, Ma J, Chang G, Huang J, Yang Y, Wang H, Liu M, Xu Y, Liang H, Yu J, Cai Y, Zhang Z, Fan Y, Mu W, Sahu SK, Liu S, Lang X, Yang L, Li N, Habib S, Yang Y, Lindstrom AJ, Liang P, Goffinet B, Zaman S, Wegrzyn JL, Li D, Liu J, Cui J, Sonnenschein EC, Wang X, Ruan J, Xue JY, Shao ZQ, Song C, Fan G, Li Z, Zhang L, Liu J, Liu ZJ, Jiao Y, Wang XQ, Wu H, Wang E, Lisby M, Yang H, Wang J, Liu X, Xu X, Li N, Soltis PS, Van de Peer Y, Soltis DE, Gong X, Liu H, Zhang S. The Cycas genome and the early evolution of seed plants. NATURE PLANTS 2022; 8:389-401. [PMID: 35437001 PMCID: PMC9023351 DOI: 10.1038/s41477-022-01129-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/10/2022] [Indexed: 05/05/2023]
Abstract
Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ting Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shengdan Wu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jianchao Ma
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Guanxiao Chang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Yong Yang
- College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Liang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jin Yu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuqing Cai
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaowu Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yannan Fan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shuchun Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoan Lang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Nanning Botanical Garden, Nanning, China
| | - Leilei Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Na Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Sadaf Habib
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yongqiong Yang
- Sichuan Cycas panzhihuaensis National Nature Reserve, Panzhihua, China
| | | | - Pei Liang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Dexiang Li
- Nanning Botanical Garden, Nanning, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Xiaobo Wang
- Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jue Ruan
- Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chi Song
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guangyi Fan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB UGent Center for Plant Systems Biology, Gent, Belgium
| | - Liangsheng Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Jianquan Liu
- The College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhong-Jian Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Nan Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB UGent Center for Plant Systems Biology, Gent, Belgium.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
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Ma X, Yu L, Fatima M, Wadlington WH, Hulse-Kemp AM, Zhang X, Zhang S, Xu X, Wang J, Huang H, Lin J, Deng B, Liao Z, Yang Z, Ma Y, Tang H, Van Deynze A, Ming R. The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species. Genome Biol 2022; 23:75. [PMID: 35255946 PMCID: PMC8902716 DOI: 10.1186/s13059-022-02633-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
Background Spinach (Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y chromosome has not been fully characterized. Our knowledge about the history of its domestication and improvement remains limited. Results A high-quality YY genome of spinach is assembled into 952 Mb in six pseudo-chromosomes. By a combination of genetic mapping, Genome-Wide Association Studies, and genomic analysis, we characterize a 17.42-Mb sex determination region (SDR) on chromosome 1. The sex chromosomes of spinach evolved when an insertion containing sex determination genes occurred, followed by a large genomic inversion about 1.98 Mya. A subsequent burst of SDR-specific repeats (0.1–0.15 Mya) explains the large size of this SDR. We identify a Y-specific gene, NRT1/PTR 6.4 which resides in this insertion, as a strong candidate for the sex determination or differentiation factor. Resequencing of 112 spinach genomes reveals a severe domestication bottleneck approximately 10.87 Kya, which dates the domestication of spinach 7000 years earlier than the archeological record. We demonstrate that a strong selection signal associated with internode elongation and leaf area expansion is associated with domestication of edibility traits in spinach. We find that several strong genomic introgressions from the wild species Spinacia turkestanica and Spinacia tetrandra harbor desirable alleles of genes related to downy mildew resistance, frost resistance, leaf morphology, and flowering-time shift, which likely contribute to spinach improvement. Conclusions Analysis of the YY genome uncovers evolutionary forces shaping nascent sex chromosome evolution in spinach. Our findings provide novel insights about the domestication and improvement of spinach. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02633-x.
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Affiliation(s)
- Xiaokai Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li'ang Yu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mahpara Fatima
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - William H Wadlington
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Amanda M Hulse-Kemp
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.,USDA-ARS, Genomics and Bioinformatics Research Unit, North Carolina, 27695, Raleigh, USA
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shengcheng Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xindan Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jingjing Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huaxing Huang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ban Deng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenyang Liao
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenhui Yang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanhong Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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53
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Yu L, Ma X, Wadlington W, Ming R. Identification of structural variation and polymorphisms of a sex co-segregating scaffold in spinach. PLANT REPRODUCTION 2022; 35:19-30. [PMID: 34319458 DOI: 10.1007/s00497-021-00424-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Spinach is a common vegetable, and dioecy is maintained by a pair of XY sex chromosomes. Due to limited genomic resources and its highly repetitive genome, limited studies were conducted to investigate the genomic landscape of the region near sex-determining loci. In this study, we screened the structure variations (SVs) between Y-linked contigs and a 1.78-Mb X scaffold (Super_scaffold 66), which enabled the development of 12 sex co-segregating DNA markers. These markers were tested in one F1 mapping population and 40 spinach accessions, which comprised 692 individual plants with the strong sex linkage pattern. In addition, we found that Super_scaffold 66 was highly repetitive along with the enriched LTR-RTs insertions and decreased microsatellite distribution compared with the rest genome, which matches extremely low gene density featured by only nine annotated genes. Synteny analysis between Y contigs and Superscaffold_66 revealed a 340-Kb accumulative Y contig (non-continuous) and a 500-Kb X counterpart along with SVs and wide-spread tandem duplications. Among the nine genes, one ABC transporter gene revealed noticeable SVs between Y contig and X counterpart, as an approximate 5-Kb recent Gypsy LTR-RT insertion in the Y-linked allele, but not the X allele. The gene paucity, SVs, and sex-linked polymorphisms attributed to the recombination suppression. We proposed that Super_scaffold 66 is part of the non-recombining region containing the sex determination genes. The spread of 12 sex co-segregating markers from this 1.78 Mb genomic region indicated the existence and expansion of sex determination region during progression of the Y chromosome.
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Affiliation(s)
- Li'ang Yu
- Department of Plant Biology, University of Illinois At Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL, 61801-3838, USA
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - William Wadlington
- Department of Plant Biology, University of Illinois At Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL, 61801-3838, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois At Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL, 61801-3838, USA.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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54
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Käfer J, Bewick A, Andres-Robin A, Lapetoule G, Harkess A, Caïus J, Fogliani B, Gâteblé G, Ralph P, dePamphilis CW, Picard F, Scutt C, Marais GAB, Leebens-Mack J. A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants. THE NEW PHYTOLOGIST 2022; 233:1636-1642. [PMID: 34342006 DOI: 10.1111/nph.17662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
The genetic basis and evolution of sex determination in dioecious plants is emerging as an active area of research with exciting advances in genome sequencing and analysis technologies. As the sole species within the sister lineage to all other extant flowering plants, Amborella trichopoda is an important model for understanding the evolution and development of flowers. Plants typically produce only male or female flowers, but sex determination mechanisms are unknown for the species. Sequence data derived from plants of natural origin and an F1 mapping population were used to identify sex-linked genes and the nonrecombining region. Amborella trichopoda has a ZW sex determination system. Analysis of genes in a 4 Mb nonrecombining sex-determination region reveals recent divergence of Z and W gametologs, and few Z- and W-specific genes. The sex chromosomes of A. trichopoda evolved less than 16.5 Myr ago, long after the divergence of the extant angiosperms.
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Affiliation(s)
- Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
| | - Adam Bewick
- Department of Plant Biology, University of Georgia, Athens, GA, 30602-7271, USA
- Bayer Crop Science, Chesterfield, MO, 63017, USA
| | - Amélie Andres-Robin
- Laboratoire Reproduction et Développement des plantes, UMR 5667, Ecole Normale Supérieure de Lyon, CNRS, Lyon, F-69364, France
| | - Garance Lapetoule
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - José Caïus
- Institute of Plant Sciences, Plateforme transcriptOmique de l'IPS2 (POPS), Université de Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Bruno Fogliani
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, Païta, 98890, New Caledonia
- Institute of Exact and Applied Sciences (ISEA), Université de la Nouvelle-Calédonie, BP R4, Nouméa Cedex, 98851, New Caledonia
| | - Gildas Gâteblé
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, Païta, 98890, New Caledonia
| | - Paula Ralph
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
| | - Charlie Scutt
- Laboratoire Reproduction et Développement des plantes, UMR 5667, Ecole Normale Supérieure de Lyon, CNRS, Lyon, F-69364, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, F-69622, France
- LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, 1349-017, Portugal
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602-7271, USA
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55
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Zhou P, Zhang X, Ma X, Yue J, Liao Z, Ming R. Methylation related genes affect sex differentiation in dioecious and gynodioecious papaya. HORTICULTURE RESEARCH 2022; 9:uhab065. [PMID: 35048102 PMCID: PMC8935930 DOI: 10.1093/hr/uhab065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Morphological, genic and epigenetic differences often exist in separate sexes of dioecious and trioecious plants. However, the connections and relationships among them in different breeding systems are still unclear. Papaya has three sex types, which is genetically determined and epigenetically regulated, and was chosen as a model to study sex differentiation. Bisulfite sequencing of genomic DNA extracted from early-stage flowers revealed sex-specific genomic methylation landscapes and seasonally methylome reprogramming processes in dioecious and gynodioecious papaya grown in spring and summer. Extensive methylation of sex-determining region (SDR) was the distinguishing epigenetic characteristics of nascent XY sex chromosomes in papaya. Seasonal methylome reprogramming of early-stage flowers in both dioecy and gynodioecy systems were detected, resulting from transcriptional expression pattern alterations of methylation-modification-related and chromatin-remodeling-related genes, particularly from those genes involved in active demethylation. Genes involved in phytohormone signal transduction pathway in male flowers have played an important role in the formation of male-specific characteristics. These findings enhanced the understanding of the genetic and epigenetic contributions to sex differentiation and the complexity of sex chromosome evolution in trioecious plants.
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Affiliation(s)
- Ping Zhou
- Fruit Research Institute,Fujian Academy of Agricultural Sciences,Fuzhou 350013,Fujian, China
| | - Xiaodan Zhang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xinyi Ma
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jingjing Yue
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhenyang Liao
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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56
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Jabbour F, Espinosa F, Dejonghe Q, Le Péchon T. Development and Evolution of Unisexual Flowers: A Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020155. [PMID: 35050043 PMCID: PMC8780417 DOI: 10.3390/plants11020155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 06/12/2023]
Abstract
The development of unisexual flowers has been described in a large number of taxa, sampling the diversity of floral phenotypes and sexual systems observed in extant angiosperms, in studies focusing on floral ontogeny, on the evo-devo of unisexuality, or on the genetic and chromosomal bases of unisexuality. We review here such developmental studies, aiming at characterizing the diversity of ontogenic pathways leading to functionally unisexual flowers. In addition, we present for the first time and in a two-dimensional morphospace a quantitative description of the developmental rate of the sexual organs in functionally unisexual flowers, in a non-exhaustive sampling of angiosperms with contrasted floral morphologies. Eventually, recommendations are provided to help plant evo-devo researchers and botanists addressing macroevolutionary and ecological issues to more precisely select the taxa, the biological material, or the developmental stages to be investigated.
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Affiliation(s)
- Florian Jabbour
- Institut de Systématique Évolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, 75005 Paris, France;
| | - Felipe Espinosa
- Independent Researcher, Carrera 13 # 113-24, Bogotá 110111, Colombia;
| | - Quentin Dejonghe
- Institut de Systématique Évolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, 75005 Paris, France;
| | - Timothée Le Péchon
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium;
- Fédération Wallonie-Bruxelles, Service Général de l’Enseignement Supérieur et de la Recherche Scientifique, Rue A. Lavalée, 1, 1080 Brussels, Belgium
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Gene regulation network analyses of pistil development in papaya. BMC Genomics 2022; 23:8. [PMID: 34983382 PMCID: PMC8729085 DOI: 10.1186/s12864-021-08197-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The pistil is an essential part of flowers that functions in the differentiation of the sexes and reproduction in plants. The stigma on the pistil can accept pollen to allow fertilization and seed development. Papaya (Carica papaya L.) is a dioecious plant, where female flowers exhibit normal pistil, while the male flowers exhibit aborted pistil at a late stage of pistil development. RESULTS The developmental stages of papaya pistil were analyzed after first dividing it into slices representing the primordium stage 1 (S1), the pre-meiotic stages S2, post-meiotic stage S3, and the mitotic stage S4. The SS scoring algorithm analysis of genes preferentially expressed at different stages revealed differentially expressed genes between male and female flowers. A transcription factor regulatory network for each stage based on the genes that are differentially expressed between male and female flowers was constructed. Some transcription factors related to pistil development were revealed based on the analysis of regulatory networks such as CpAGL11, CpHEC2, and CpSUPL. Based on the specific expression of genes, constructed a gene regulatory subnetwork with CpAGL11-CpSUPL-CpHEC2 functioning as the core. Analysis of the functionally enriched terms in this network reveals several differentially expressed genes related to auxin/ brassinosteroid signal transduction in the plant hormone signal transduction pathway. At the same time, significant differences in the expression of auxin and brassinosteroid synthesis-related genes between male and female flowers at different developmental stages were detected. CONCLUSIONS The pistil abortion of papaya might be caused by the lack of expression or decreased expression of some transcription factors and hormone-related genes, affecting hormone signal transduction or hormone biosynthesis. Analysis of aborted and normally developing pistil in papaya provided new insights into the molecular mechanism of pistil development and sex differentiation in dioecious papaya.
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Rosselló JA, Maravilla AJ, Rosato M. The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:788911. [PMID: 35283933 PMCID: PMC8908318 DOI: 10.3389/fpls.2022.788911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/27/2022] [Indexed: 05/04/2023]
Abstract
The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.
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Transcriptomic Analysis of Sex-Associated DEGs in Female and Male Flowers of Kiwifruit (Actinidia deliciosa [A. Chev] C. F. Liang & A. R. Ferguson). HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Kiwifruit (Actinidia deliciosa [A. Chev.], C.V. Liang & A. R. Ferguson, 1984) is a perennial plant, with morphologically hermaphroditic and functionally dioecious flowers. Fruits of this species are berries of great commercial and nutritional importance. Nevertheless, few studies have analyzed the molecular mechanisms involved in sexual differentiation in this species. To determine these mechanisms, we performed RNA-seq in floral tissue at stage 60 on the BBCH scale in cultivar ‘Hayward’ (H, female) and a seedling from ‘Green Light’ × ‘Tomuri’ (G × T, male). From these analyses, we obtained expression profiles of 24,888 (H) and 27,027 (G × T) genes, of which 6413 showed differential transcript abundance. Genetic ontology (GO) and KEGG analysis revealed activation of pathways associated with the translation of hormonal signals, plant-pathogen interaction, metabolism of hormones, sugars, and nucleotides. The analysis of the protein-protein interaction network showed that the genes ERL1, AG, AGL8, LFY, WUS, AP2, WRKY, and CO, are crucial elements in the regulation of the hormonal response for the formation and development of anatomical reproductive structures and gametophytes. On the other hand, genes encoding four Putative S-adenosyl-L-methionine-dependent methyltransferases (Achn201401, Achn281971, Achn047771 and Achn231981) were identified, which were up-regulated mainly in the male flowers. Moreover, the expression profiles of 15 selected genes through RT-qPCR were consistent with the results of RNA-seq. Finally, this work provides gene expression-based interactions between transcription factors and effector genes from hormonal signaling pathways, development of floral organs, biological and metabolic processes or even epigenetic mechanisms which could be involved in the kiwi sex-determination. Thus, in order to decode the nature of these interactions, it could be helpful to propose new models of flower development and sex determination in the Actinidia genus.
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Potential of Impedance Flow Cytometry to Assess the Viability and Quantity of Cannabis sativa L. Pollen. PLANTS 2021; 10:plants10122739. [PMID: 34961212 PMCID: PMC8704011 DOI: 10.3390/plants10122739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022]
Abstract
Over the last decade, efforts to breed new Cannabis sativa L. cultivars with high Cannabidiol (CBD) and other non-psychoactive cannabinoids with low tetrahydrocannabinol (THC) levels have increased. In this context, the identification of the viability and quantity of pollen, which represents the fitness of male gametophytes, to accomplish successful pollination is of high importance. The present study aims to evaluate the potential of impedance flow cytometry (IFC) for the assessment of pollen viability (PV) and total number of pollen cells (TPC) in two phytocannabinoid-rich cannabis genotypes, KANADA (KAN) and A4 treated with two different chemical solutions, silver thiosulfate solution (STS) and gibberellic acid (GA3). Pollen was collected over a period of 8 to 24 days after flowering (DAF) in a greenhouse experiment. Impedance flow cytometry (IFC) technology was used with Cannabis sativa to assess the viability and quantity of pollen. The results showed that the number of flowers per plant was highest at 24 DAF for both genotypes, A4 (317.78) and KAN (189.74). TPC induced by STS was significantly higher compared to GA3 over the collection period of 8 to 24 DAF with the highest mean TPC of 1.54 × 105 at 14 DAF. STS showed significantly higher viability of pollen compared to GA3 in genotype KAN, with the highest PV of 78.18% 11 DAF. Genotype A4 also showed significantly higher PV with STS at 8 (45.66%), 14 (77.88%), 18 (79.37%), and 24 (51.92%) DAF compared to GA3. Furthermore, counting the numbers of flowers did not provide insights into the quality and quantity of pollen; the results showed that PV was highest at 18 DAF with A4; however, the number of flowers per plant was 150.33 at 18 DAF and was thus not the maximum of produced flowers within the experiment. IFC technology successfully estimated the TPC and differentiated between viable and non-viable cells over a period of 8 to 24 DAF in tested genotypes of Cannabis sativa. IFC seems to be an efficient and reliable method to estimate PV, opening new chances for plant breeding and plant production processes in cannabis.
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Aamir M, Karmakar P, Singh VK, Kashyap SP, Pandey S, Singh BK, Singh PM, Singh J. A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). PHYSIOLOGIA PLANTARUM 2021; 173:1729-1764. [PMID: 33547804 DOI: 10.1111/ppl.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.
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Affiliation(s)
- Mohd Aamir
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Pradip Karmakar
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Sudhakar Pandey
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Binod Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Jagdish Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
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Wang X, Song M, Flaishman MA, Chen S, Ma H. AGAMOUS Gene as a New Sex-Identification Marker in Fig ( Ficus carica L.) Is More Efficient Than RAN1. FRONTIERS IN PLANT SCIENCE 2021; 12:755358. [PMID: 34745187 PMCID: PMC8564383 DOI: 10.3389/fpls.2021.755358] [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: 08/08/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Fig is an ancient gynodioecious fruit tree with females for commercial fruit production and hermaphrodites (males) sometimes used as pollen providers. An early sex-identification method would improve breeding efficiency. Three AGAMOUS (AG) genes were recruited from the Ficus carica genome using AG sequences from Ficus microcarpa and Ficus hispida. FcAG was 5230 bp in length, with 7 exons and 6 introns, and a 744-bp coding sequence. The gene was present in both female and male fig genomes, with a 15-bp deletion in the 7th exon. The other two AG genes (FcAG2-Gall_Stamen and FcAG3-Gall_Stamen) were male-specific, without the 15-bp deletion (759-bp coding sequence), and were only expressed in the gall and stamen of the male fig fruit. Using the deletion as the forward primer (AG-Marker), male plants were very efficiently identified by the presence of a 146-bp PCR product. The previously reported fig male and female polymorphism gene RESPONSIVE-TO-ANTAGONIST1 (RAN1) was also cloned and compared between male and female plants. Fifteen SNPs were found in the 3015-bp protein-coding sequence. Among them, 12 SNPs were identified as having sex-differentiating capacity by checking the sequences of 27 known male and 24 known female cultivars. A RAN1-Marker of 608 bp, including 6 SNPs, was designed, and a PCR and sequencing-based method was verified with 352 fig seedlings from two hybrid populations. Our results confirmed that the newly established AG-Marker is as accurate as the RAN1-Marker, and provide new clues to understanding Ficus sex determination.
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Affiliation(s)
- Xu Wang
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, China
| | - Miaoyu Song
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, China
| | - Moshe A. Flaishman
- Department of Fruit Tree Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Shangwu Chen
- College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, China
| | - Huiqin Ma
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, China
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Borin M, Palumbo F, Vannozzi A, Scariolo F, Sacilotto GB, Gazzola M, Barcaccia G. Developing and Testing Molecular Markers in Cannabis sativa (Hemp) for Their Use in Variety and Dioecy Assessments. PLANTS 2021; 10:plants10102174. [PMID: 34685983 PMCID: PMC8540786 DOI: 10.3390/plants10102174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
Cannabis sativa (2n = 2x = 20) is a popular species belonging to the Cannabaceae family. Despite its use for medical, recreational, and industrial purposes as well as its long history, the genetic research on this species is in its infancy due to the legal implications and the prohibition campaigns. The recent legalization of Cannabis in many countries along with the use of genomics boosted the approaches aimed at marker-assisted selection, germplasm management, genetic discrimination, and authentication of cultivars. Nonetheless, the exploitation of molecular markers for the development of commercial varieties through marker-assisted breeding schemes is still rare. The present study aimed to develop an informative panel of simple sequence repeat markers to be used for the genotyping of high breeding value C. sativa lines. Starting from 41 nuclear SSR designated by in silico analyses, we selected 20 highly polymorphic and discriminant loci that were tested in 104 individuals belonging to 11 distinct hemp varieties. The selected markers were successful in accessing homozygosity, genetic uniformity, and genetic variation within and among varieties. Population structure analysis identified eight genetic groups, clustering individuals based on sexual behaviors (dioecious and monoecious) and geographical origins. Overall, this study provides important tools for the genetic characterization, authentication, conservation of biodiversity, genetic improvement and traceability of this increasingly important plant species.
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Affiliation(s)
- Marcello Borin
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37034 Verona, Italy;
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
| | - Francesco Scariolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
| | - Gio Batta Sacilotto
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Marco Gazzola
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
- Correspondence:
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Dioecious hemp (Cannabis sativa L.) plants do not express significant sexually dimorphic morphology in the seedling stage. Sci Rep 2021; 11:16825. [PMID: 34413374 PMCID: PMC8376874 DOI: 10.1038/s41598-021-96311-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 07/30/2021] [Indexed: 11/19/2022] Open
Abstract
Some economically important crop species are dioecious, producing pollen and ovules on distinct, unisexual, individuals. On-the-spot diagnosis of sex is important to breeders and farmers for crop improvement and maximizing yield, yet diagnostic tools at the seedling stage are understudied and lack a scientific basis. Understanding sexual dimorphism in juvenile plants may provide key ecological, evolutionary and economic insights into dioecious plant species in addition to improving the process of crop cultivation. To address this gap in the literature, we asked: can we reliably differentiate males, females, and co-sexual individuals based on seedling morphology in Cannabis sativa, and do the traits used to distinguish sex at this stage vary between genotypes? To answer these questions, we collected data on phenotypic traits of 112 C. sativa plants (50 female, 52 male, 10 co-sexuals) from two hemp cultivars (CFX-1, CFX-2) during the second week of vegetative growth and used ANOVAs to compare morphology among sexes. We found males grew significantly longer hypocotyls than females by week 2, but this difference depended on the cultivar investigated. Preliminary evidence suggests that co-sexual plants may be distinguished from male and female plants using short hypocotyl length and seedling height, although this relationship requires more study since sample sizes of co-sexual plants were small. In one of the cultivars, two-week old male plants tend to produce longer hypocotyls than other plants, which may help to identify these plants prior to anthesis. We call for increased research effort on co-sexual plants, given their heavy economic cost in industrial contexts and rare mention in the literature. Our preliminary data suggests that short hypocotyl length may be an indicator of co-sexuality. These results are the first steps towards developing diagnostic tools for predicting sex using vegetative morphology in dioecious species and understanding how sexual dimorphism influences phenotype preceding sexual maturity.
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Prentout D, Stajner N, Cerenak A, Tricou T, Brochier-Armanet C, Jakse J, Käfer J, Marais GAB. Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes. THE NEW PHYTOLOGIST 2021; 231:1599-1611. [PMID: 33978992 DOI: 10.1111/nph.17456] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
We recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants (12-28 Myr old). Based on the estimated age, we predicted that it should be shared by its sister genus Humulus, which is known also to possess XY chromosomes. Here, we used transcriptome sequencing of an F1 family of H. lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector. We identified 265 sex-linked genes in H. lupulus, which preferentially mapped to the C. sativa X chromosome. Using phylogenies of sex-linked genes, we showed that a region of the sex chromosomes had already stopped recombining in an ancestor of both species. Furthermore, as in C. sativa, Y-linked gene expression reduction is correlated to the position on the X chromosome, and highly Y degenerated genes showed dosage compensation. We report, for the first time in Angiosperms, a sex chromosome system that is shared by two different genera. Thus, recombination suppression started at least 21-25 Myr ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes (c. 70%), leading to a degenerated Y chromosome.
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Affiliation(s)
- Djivan Prentout
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Natasa Stajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Andreja Cerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Zalskega Tabora 2, Zalec, SI-3310, Slovenia
| | - Theo Tricou
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Celine Brochier-Armanet
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
- LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, 1349-017, Portugal
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Zhang J, Li Y, Luo S, Cao M, Zhang L, Li X. Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica. BMC PLANT BIOLOGY 2021; 21:335. [PMID: 34261451 PMCID: PMC8278619 DOI: 10.1186/s12870-021-03117-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND In brown algae, dioicy is the prevalent sexual system, and phenotypic differences between male and female gametophytes have been found in many dioicous species. Saccharina japonica show remarkable sexual dimorphism in gametophytes before gametogenesis. A higher level of phenotypic differentiation was also found in female and male gametes after gametogenesis. However, the patterns of differential gene expression throughout gametophyte development and how these changes might relate to sex-specific fitness at the gamete stage in S. japonica are not well known. RESULTS In this study, differences in gene expression between male and female gametophytes in different developmental stages were investigated using comparative transcriptome analysis. Among the 20,151 genes expressed in the haploid gametophyte generation, 37.53% were sex-biased. The abundance of sex-biased genes in mature gametophytes was much higher than that in immature gametophytes, and more male-biased than female-biased genes were observed in the mature stage. The predicted functions of most sex-biased genes were closely related to the sex-specific characteristics of gametes, including cell wall biosynthesis, sperm motility, and sperm and egg recognition. In addition, 51 genes were specifically expressed in males in both stages, showing great potential as candidate male sex-determining region (SDR) genes. CONCLUSIONS This study describes a thorough investigation into differential gene expression between male and female gametophytes in the dioicous kelp S. japonica. A large number of sex-biased genes in mature gametophytes may be associated with the divergence of phenotypic traits and physiological functions between female gametes (eggs) and male gametes (sperm) during sexual differentiation. These genes may mainly come from new sex-biased genes that have recently evolved in the S. japonica lineage. The duplication of sex-biased genes was detected, which may increase the number of sex-biased genes after gametogenesis in S. japonica to some extent. The excess of male-biased genes over female-biased genes in the mature stage may reflect the different levels of sexual selection across sexes. This study deepens our understanding of the regulation of sex development and differentiation in the dioicous kelp S. japonica.
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Affiliation(s)
- Jiaxun Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yan Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Shiju Luo
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Linan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
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Masuda K, Yamamoto E, Shirasawa K, Onoue N, Kono A, Ushijima K, Kubo Y, Tao R, Henry IM, Akagi T. Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon. DNA Res 2021; 27:5858979. [PMID: 32761076 PMCID: PMC7406971 DOI: 10.1093/dnares/dsaa012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/10/2020] [Indexed: 11/17/2022] Open
Abstract
Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Eiji Yamamoto
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Noriyuki Onoue
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Atsushi Kono
- Institute of Fruit Tree and Tea Science, NARO, Hiroshima 739-2494, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
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68
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Chae T, Harkess A, Moore RC. Sex-linked gene expression and the emergence of hermaphrodites in Carica papaya. AMERICAN JOURNAL OF BOTANY 2021; 108:1029-1041. [PMID: 34156700 DOI: 10.1002/ajb2.1689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/08/2021] [Indexed: 06/13/2023]
Abstract
PREMISE One evolutionary path from hermaphroditism to dioecy is via a gynodioecious intermediate. The evolution of dioecy may also coincide with the formation of sex chromosomes that possess sex-determining loci that are physically linked in a region of suppressed recombination. Dioecious papaya (Carica papaya) has an XY chromosome system, where the presence of a Y chromosome determines maleness. However, in cultivation, papaya is gynodioecious, due to the conversion of the male Y chromosome to a hermaphroditic Yh chromosome during its domestication. METHODS We investigated gene expression linked to the X, Y, and Yh chromosomes at different floral developmental stages to identify differentially expressed genes that may be involved in the sexual transition of males to hermaphrodites. RESULTS We identified 309 sex-biased genes found on the sex chromosomes, most of which are found in the pseudoautosomal regions. Female (XX) expression in the sex-determining region was almost double that of X-linked expression in males (XY) and hermaphrodites (XYh ), which rules out dosage compensation for most sex-linked genes; although, an analysis of hemizygous X-linked loci found evidence of partial dosage compensation. Furthermore, we identified a candidate gene associated with sex determination and the transition to hermaphroditism, a homolog of the MADS-box protein SHORT VEGETATIVE PHASE. CONCLUSIONS We identified a pattern of partial dosage compensation for hemizygous genes located in the papaya sex-determining region. Furthermore, we propose that loss-of-expression of the Y-linked SHORT VEGETATIVE PHASE homolog facilitated the transition from males to hermaphrodites in papaya.
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Affiliation(s)
- Taylor Chae
- Department of Biology, Miami University, Oxford, OH
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
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69
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Coelho FF, Damasceno AG, Fávaro A, Teodoro GS, Langsdorff LP. Size-dependent sex allocation in Solanum lycocarpum St. Hil. (Solanaceae). BRAZ J BIOL 2021; 82:e237575. [PMID: 33978077 DOI: 10.1590/1519-6984.237575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022] Open
Abstract
Resource allocation to reproduction can change depending on size, as predicted by the size-dependent sex allocation. This theory is based on the fact that small individuals will invest in the allocation of sex with lower cost of production, usually male gender. In plants, there are some andromonoecy species, presence of hermaphrodite and male flowers in the same individual. Andromonoecy provides a strategy to optimally allocate resources to male and female function, evolving a reproductive energy-saving strategy. Thus, our objective was to investigate the size-dependent sex allocation in Solanum lycocarpum St. Hil. We tested the hypothesis that plants with larger size will invest in the production of hermaphrodite flowers, because higher individuals have greater availability of resources to invest in more complex structures involving greater energy expenditure. The studied species was S. lycocarpum, an andromonoecious species. From June 2016 to March 2017 the data were collected in 38 individuals, divided in two groups: the larger plant group (n=18; height=3-5 m) and the smaller plant group (n=20; height=1-2 m).Our data show that there was effect of plant size on the flower production and the sexual gender allocation. The larger plants showed more flowers and higher production of hermaphrodite flowers. Furthermore, in the flower scale, we observed allometric relationship among the flower's traits with proportional investments in biomass, anther size and gynoecium size. Our results are in agreement with size-dependent sex allocation theory and andromonoecy hypothesis related to mechanisms for optimal resource allocation to male and female function.
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Affiliation(s)
- F F Coelho
- Universidade Federal de Lavras - UFLA, Departamento de Biologia, Setor de Botânica, Lavras, MG, Brasil
| | - A G Damasceno
- Universidade Federal de Lavras - UFLA, Departamento de Biologia, Programa de Pós-graduação em Genética, Lavras, MG, Brasil
| | - A Fávaro
- Universidade Federal de Lavras - UFLA, Departamento de Biologia, Programa de Pós-graduação em Ecologia Aplicada, Lavras, MG, Brasil
| | - G S Teodoro
- Universidade Federal do Pará - UFPA, Instituto de Ciências Biológicas, Belém, PA, Brasil
| | - L P Langsdorff
- Universidade Federal de Lavras - UFLA, Departamento de Biologia, Programa de Pós-graduação em Botânica Aplicada, Lavras, MG, Brasil
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70
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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71
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Abstract
We studied the grape sex-determining region (SDR) in 12 Vitis genomes and demonstrated its conservation across 556 genotypes including 193 accessions from 47 world-wide wild grapevine species and 363 accessions of cultivated grapevine. Although the grape SDR is recombination free in all wild species, we found two distinct hermaphrodite (H) haplotypes (H1 and H2) among the cultivated grapevines, both chimeras of male (M) and female (f) haplotypes. The two independent recombinations carry different genetic signatures which long predate the domestication of grapevine, suggesting independent evolutions of this trait in wild European grapevine gene pools prior to human domestication. Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.
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72
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Renner SS, Müller NA. Plant sex chromosomes defy evolutionary models of expanding recombination suppression and genetic degeneration. NATURE PLANTS 2021; 7:392-402. [PMID: 33782581 DOI: 10.1038/s41477-021-00884-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/18/2021] [Indexed: 05/17/2023]
Abstract
Hundreds of land plant lineages have independently evolved separate sexes in either gametophytes (dioicy) or sporophytes (dioecy), but 43% of all dioecious angiosperms are found in just 34 entirely dioecious clades, suggesting that their mode of sex determination evolved a long time ago. Here, we review recent insights on the molecular mechanisms that underlie the evolutionary change from individuals that each produce male and female gametes to individuals specializing in the production of just one type of gamete. The canonical model of sex chromosome evolution in plants predicts that two sex-determining genes will become linked in a sex-determining region (SDR), followed by expanding recombination suppression, chromosome differentiation and, ultimately, degeneration. Experimental work, however, is showing that single genes function as master regulators in model systems, such as the liverwort Marchantia and the angiosperms Diospyros and Populus. In Populus, this type of regulatory function has been demonstrated by genome editing. In other systems, including Actinidia, Asparagus and Vitis, two coinherited factors appear to independently regulate female and male function, yet sex chromosome differentiation has remained low. We discuss the best-understood systems and evolutionary pathways to dioecy, and present a meta-analysis of the sizes and ages of SDRs. We propose that limited sexual conflict explains why most SDRs are small and sex chromosomes remain homomorphic. It appears that models of increasing recombination suppression with age do not apply because selection favours mechanisms in which sex determination depends on minimal differences, keeping it surgically precise.
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Affiliation(s)
- Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany.
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
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73
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Ma WJ, Veltsos P. The Diversity and Evolution of Sex Chromosomes in Frogs. Genes (Basel) 2021; 12:483. [PMID: 33810524 PMCID: PMC8067296 DOI: 10.3390/genes12040483] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/30/2022] Open
Abstract
Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.
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Affiliation(s)
- Wen-Juan Ma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Paris Veltsos
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA;
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74
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Pan J, Wen H, Chen G, Lin WH, Du H, Chen Y, Zhang L, Lian H, Wang G, Cai R, Pan J. A Positive Feedback Loop Mediated by CsERF31 Initiates Female Cucumber Flower Development: ETHYLENE RESPONSE FACTOR31 mediates a positive feedback loop that initiates female cucumber flower development. PLANT PHYSIOLOGY 2021; 186:kiab141. [PMID: 33744968 PMCID: PMC8195516 DOI: 10.1093/plphys/kiab141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/05/2021] [Indexed: 05/24/2023]
Abstract
Sex determination is a crucially important developmental event that is pervasive throughout nature and enhances the adaptation of species. Among plants, cucumber (Cucumis sativus L.) can generate both unisexual and bisexual flowers, and the sex type is mainly controlled by several 1-aminocyclopropane-1-carboxylic acid (ACC) synthases. However, the regulatory mechanism of these synthases remains elusive. Here, we used gene expression analysis, protein-DNA interaction assays and transgenic plants to study the function of a gynoecium-specific gene, ETHYLENE RESPONSE FACTOR31 (CsERF31), in female flower differentiation. We found that in a predetermined female flower, ethylene signalling activates CsERF31 by CsEIN3, and then CsERF31 stimulates CsACS2, which triggers a positive feedback loop to ensure female rather than bisexual flower development. A similar interplay is functionally conserved in melon (Cucumis melo L.). Knockdown of CsERF31 by RNAi causes defective bisexual flowers to replace female flowers. Ectopic expression of CsERF31 suppresses stamen development and promotes pistil development in male flowers, demonstrating that CsERF31 functions as a sex switch. Taken together, our data confirm that CsERF31 represents the molecular link between female-male determination and female-bisexual determination, and provide mechanistic insight into how ethylene promotes female flowers, rather than bisexual flowers, in cucumber sex determination.
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Affiliation(s)
- Jian Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Haifan Wen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guanqun Chen
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Wen-Hui Lin
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Leyu Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongli Lian
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Junsong Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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75
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He L, Jia KH, Zhang RG, Wang Y, Shi TL, Li ZC, Zeng SW, Cai XJ, Wagner ND, Hörandl E, Muyle A, Yang K, Charlesworth D, Mao JF. Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. Mol Ecol Resour 2021; 21:1966-1982. [PMID: 33609314 PMCID: PMC8359994 DOI: 10.1111/1755-0998.13362] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022]
Abstract
Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.
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Affiliation(s)
- Li He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ren-Gang Zhang
- Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, China
| | - Yuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Si-Wen Zeng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin-Jie Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Ke Yang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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76
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Transcriptional regulation of dosage compensation in Carica papaya. Sci Rep 2021; 11:5854. [PMID: 33712672 PMCID: PMC7971000 DOI: 10.1038/s41598-021-85480-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Sex chromosome evolution results in the disparity in gene content between heterogametic sex chromosomes and creates the need for dosage compensation to counteract the effects of gene dose imbalance of sex chromosomes in males and females. It is not known at which stage of sex chromosome evolution dosage compensation would evolve. We used global gene expression profiling in male and female papayas to assess gene expression patterns of sex-linked genes on the papaya sex chromosomes. By analyzing expression ratios of sex-linked genes to autosomal genes and sex-linked genes in males relative to females, our results showed that dosage compensation was regulated on a gene-by-gene level rather than whole sex-linked region in papaya. Seven genes on the papaya X chromosome exhibited dosage compensation. We further compared gene expression ratios in the two evolutionary strata. Y alleles in the older evolutionary stratum showed reduced expression compared to X alleles, while Y alleles in the younger evolutionary stratum showed elevated expression compared to X alleles. Reduced expression of Y alleles in the older evolutionary stratum might be caused by accumulation of deleterious mutations in regulatory regions or transposable element-mediated methylation spreading. Most X-hemizygous genes exhibited either no or very low expression, suggesting that gene silencing might play a role in maintaining transcriptional balance between females and males.
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77
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Yang W, Wang D, Li Y, Zhang Z, Tong S, Li M, Zhang X, Zhang L, Ren L, Ma X, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, Liu J, DiFazio SP, Olson M, Ma T. A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae. Mol Biol Evol 2021; 38:968-980. [PMID: 33027519 PMCID: PMC7947767 DOI: 10.1093/molbev/msaa261] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.
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Affiliation(s)
- Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhiyang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Liwen Ren
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin—Madison, Madison, WI
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | | | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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78
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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79
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Hill P, Shams F, Burridge CP, Wapstra E, Ezaz T. Differences in Homomorphic Sex Chromosomes Are Associated with Population Divergence in Sex Determination in Carinascincus ocellatus (Scincidae: Lygosominae). Cells 2021; 10:291. [PMID: 33535518 PMCID: PMC7912723 DOI: 10.3390/cells10020291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 01/09/2023] Open
Abstract
Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains elusive. Here we explore the links between mechanisms of transitions in sex determination and sex chromosome evolution at both recent and deeper temporal scales (<1 Myr; ~79 Myr). We studied a rare example of a species with intraspecific variation in sex determination, Carinascincus ocellatus, and a relative, Liopholis whitii, using c-banding and mapping of repeat motifs and a custom Y chromosome probe set to identify the sex chromosomes. We identified both unique and conserved regions of the Y chromosome among C. ocellatus populations differing in sex determination. There was no evidence for homology of sex chromosomes between C. ocellatus and L. whitii, suggesting independent evolutionary origins. We discuss sex chromosome homology between members of the subfamily Lygosominae and propose links between sex chromosome evolution, sex determination transitions, and karyotype evolution.
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Affiliation(s)
- Peta Hill
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia; (F.S.); (T.E.)
| | - Christopher P. Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Erik Wapstra
- Discipline of Biological Sciences, University of Tasmania, Private Bag 5, Sandy Bay, TAS 7000, Australia; (C.P.B.); (E.W.)
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia; (F.S.); (T.E.)
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80
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Leite Montalvão AP, Kersten B, Fladung M, Müller NA. The Diversity and Dynamics of Sex Determination in Dioecious Plants. FRONTIERS IN PLANT SCIENCE 2021; 11:580488. [PMID: 33519840 PMCID: PMC7843427 DOI: 10.3389/fpls.2020.580488] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/23/2020] [Indexed: 05/03/2023]
Abstract
The diversity of inflorescences among flowering plants is captivating. Such charm is not only due to the variety of sizes, shapes, colors, and flowers displayed, but also to the range of reproductive systems. For instance, hermaphrodites occur abundantly throughout the plant kingdom with both stamens and carpels within the same flower. Nevertheless, 10% of flowering plants have separate unisexual flowers, either in different locations of the same individual (monoecy) or on different individuals (dioecy). Despite their rarity, dioecious plants provide an excellent opportunity to investigate the mechanisms involved in sex expression and the evolution of sex-determining regions (SDRs) and sex chromosomes. The SDRs and the evolution of dioecy have been studied in many species ranging from Ginkgo to important fruit crops. Some of these studies, for example in asparagus or kiwifruit, identified two sex-determining genes within the non-recombining SDR and may thus be consistent with the classical model for the evolution of dioecy from hermaphroditism via gynodioecy, that predicts two successive mutations, the first one affecting male and the second one female function, becoming linked in a region of suppressed recombination. On the other hand, aided by genome sequencing and gene editing, single factor sex determination has emerged in other species, such as persimmon or poplar. Despite the diversity of sex-determining mechanisms, a tentative comparative analysis of the known sex-determining genes and candidates in different species suggests that similar genes and pathways may be employed repeatedly for the evolution of dioecy. The cytokinin signaling pathway appears important for sex determination in several species regardless of the underlying genetic system. Additionally, tapetum-related genes often seem to act as male-promoting factors when sex is determined via two genes. We present a unified model that synthesizes the genetic networks of sex determination in monoecious and dioecious plants and will support the generation of hypothesis regarding candidate sex determinants in future studies.
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Affiliation(s)
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, Großhansdorf, Germany
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81
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Feller AF, Ogi V, Seehausen O, Meier JI. Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages. HYDROBIOLOGIA 2021; 848:3727-3745. [PMID: 34720170 PMCID: PMC8550731 DOI: 10.1007/s10750-021-04560-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 05/02/2023]
Abstract
UNLABELLED Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10750-021-04560-7.
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Affiliation(s)
- Anna F. Feller
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Vera Ogi
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Joana I. Meier
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
- St John’s College, University of Cambridge, St John’s Street, Cambridge, CB2 1TP UK
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82
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Jesionek W, Bodláková M, Kubát Z, Čegan R, Vyskot B, Vrána J, Šafář J, Puterova J, Hobza R. Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa. ANNALS OF BOTANY 2021; 127:33-47. [PMID: 32902599 PMCID: PMC7750719 DOI: 10.1093/aob/mcaa160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes. METHODS We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons. KEY RESULTS We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes. CONCLUSIONS The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.
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Affiliation(s)
- Wojciech Jesionek
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
- For correspondence. E-mail: or
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Janka Puterova
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Brno University of Technology, Faculty of Information Technology, Centre of Excellence IT4Innovations, Bozetechova, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- For correspondence. E-mail: or
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83
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Neves CJ, Matzrafi M, Thiele M, Lorant A, Mesgaran MB, Stetter MG. Male Linked Genomic Region Determines Sex in Dioecious Amaranthus palmeri. J Hered 2020; 111:606-612. [PMID: 33340320 PMCID: PMC7846199 DOI: 10.1093/jhered/esaa047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/15/2020] [Indexed: 12/27/2022] Open
Abstract
Dioecy, the separation of reproductive organs on different individuals, has evolved repeatedly in different plant families. Several evolutionary paths to dioecy have been suggested, but the mechanisms behind sex determination is not well understood. The diploid dioecious Amaranthus palmeri represents a well-suited model system to study sex determination in plants. Despite the agricultural importance of the species, the genetic control and evolutionary state of dioecy in A. palmeri is currently unknown. Early cytogenetic experiments did not identify heteromorphic chromosomes. Here, we used whole-genome sequencing of male and female pools from 2 independent populations to elucidate the genetic control of dioecy in A. palmeri. Read alignment to a close monoecious relative and allele frequency comparisons between male and female pools did not reveal significant sex-linked genes. Consequently, we employed an alignment-free k-mer comparison which enabled us to identify a large number of male-specific k-mers. We assembled male-specific contigs comprising a total of almost 2 Mb sequence, proposing a XY sex-determination system in the species. We were able to identify the potential Y chromosome in the A. palmeri draft genome sequence as 90% of our male-specific sequence aligned to a single scaffold. Based on our findings, we suggest an intermediate evolutionary state of dioecy with a young Y chromosome in A. palmeri. Our findings give insight into the evolution of sex chromosomes in plants and may help to develop sustainable strategies for weed management.
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Affiliation(s)
- Cátia José Neves
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Maor Matzrafi
- Department of Plant Sciences, University of California, Davis, Davis, CA.,Department of Plant Pathology and Weed Research, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, Israel
| | - Meik Thiele
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, CA
| | - Mohsen B Mesgaran
- Department of Plant Sciences, University of California, Davis, Davis, CA
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
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84
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Liao Q, Du R, Gou J, Guo L, Shen H, Liu H, Nguyen JK, Ming R, Yin T, Huang S, Yan J. The genomic architecture of the sex-determining region and sex-related metabolic variation in Ginkgobiloba. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1399-1409. [PMID: 33015884 DOI: 10.1111/tpj.15009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/14/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Sex differences and evolutionary differences are critical biological issues. Ginkgo is an ancient lineage of dioecious gymnosperms with special value for studying the mechanism of sex determination in plants. However, the major genetic basic underlying sex chromosomes remains to be uncovered. In this study, we identify the sex-determining region of Ginkgo and locate it to the area from megabases 48 to 75 on chromosome 2. We find that the male sex-determining region of Ginkgo contains more than 200 genes, including four MADS-box genes, demonstrating that the Ginkgo sex determination system is of the XY type. We also find that genetic sex differences result in specialized flavonoid metabolism and regulation in each sex. These findings establish a foundation for revealing the molecular mechanism of sexual dimorphism and promoting the development of the Ginkgo industry.
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Affiliation(s)
- Qinggang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Junbo Gou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Lvjun Guo
- Center for Synthetic and Systems Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - He Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hailin Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Julie K Nguyen
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tongming Yin
- Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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85
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Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol Genet Genomics 2020; 296:41-53. [DOI: 10.1007/s00438-020-01723-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022]
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86
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Baránková S, Pascual-Díaz JP, Sultana N, Alonso-Lifante MP, Balant M, Barros K, D'Ambrosio U, Malinská H, Peska V, Pérez Lorenzo I, Kovařík A, Vyskot B, Janoušek B, Garcia S. Sex-chrom, a database on plant sex chromosomes. THE NEW PHYTOLOGIST 2020; 227:1594-1604. [PMID: 32357248 DOI: 10.1111/nph.16635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/25/2020] [Indexed: 05/15/2023]
Affiliation(s)
- Simona Baránková
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Joan Pere Pascual-Díaz
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Nusrat Sultana
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Department of Botany, Faculty of Life and Earth Sciences, Jagannath University, Dhaka, 1100, Bangladesh
| | - Maria Pilar Alonso-Lifante
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Manica Balant
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Karina Barros
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Ugo D'Ambrosio
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Hana Malinská
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Department of Biology, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, 400 96, Ústí nad Labem, Czech Republic
| | - Vratislav Peska
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Iván Pérez Lorenzo
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Boris Vyskot
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Bohuslav Janoušek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
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87
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Liu J, Ali M, Zhou Q. Establishment and evolution of heterochromatin. Ann N Y Acad Sci 2020; 1476:59-77. [PMID: 32017156 PMCID: PMC7586837 DOI: 10.1111/nyas.14303] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome is packaged into transcriptionally active euchromatin and silent heterochromatin, with most studies focused on the former encompassing the majority of protein-coding genes. The recent development of various sequencing techniques has refined this classic dichromatic partition and has better illuminated the composition, establishment, and evolution of this genomic and epigenomic "dark matter" in the context of topologically associated domains and phase-separated droplets. Heterochromatin includes genomic regions that can be densely stained by chemical dyes, which have been shown to be enriched for repetitive elements and epigenetic marks, including H3K9me2/3 and H3K27me3. Heterochromatin is usually replicated late, concentrated at the nuclear periphery or around nucleoli, and usually lacks highly expressed genes; and now it is considered to be as neither genetically inert nor developmentally static. Heterochromatin guards genome integrity against transposon activities and exerts important regulatory functions by targeting beyond its contained genes. Both its nucleotide sequences and regulatory proteins exhibit rapid coevolution between species. In addition, there are dynamic transitions between euchromatin and heterochromatin during developmental and evolutionary processes. We summarize here the ever-changing characteristics of heterochromatin and propose models and principles for the evolutionary transitions of heterochromatin that have been mainly learned from studies of Drosophila and yeast. Finally, we highlight the role of sex chromosomes in studying heterochromatin evolution.
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Affiliation(s)
- Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Mujahid Ali
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
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88
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Hörandl E, Hadacek F. Oxygen, life forms, and the evolution of sexes in multicellular eukaryotes. Heredity (Edinb) 2020; 125:1-14. [PMID: 32415185 PMCID: PMC7413252 DOI: 10.1038/s41437-020-0317-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/26/2020] [Accepted: 04/26/2020] [Indexed: 12/27/2022] Open
Abstract
The evolutionary advantage of different sexual systems in multicellular eukaryotes is still not well understood, because the differentiation into male and female individuals halves offspring production compared with asexuality. Here we propose that various physiological adaptations to oxidative stress could have forged sessility versus motility, and consequently the evolution of sexual systems in multicellular animals, plants, and fungi. Photosynthesis causes substantial amounts of oxidative stress in photoautotrophic plants and, likewise, oxidative chemistry of polymer breakdown, cellulose and lignin, for saprotrophic fungi. In both cases, its extent precludes motility, an additional source of oxidative stress. Sessile life form and the lack of neuronal systems, however, limit options for mate recognition and adult sexual selection, resulting in inefficient mate-searching systems. Hence, sessility requires that all individuals can produce offspring, which is achieved by hermaphroditism in plants and/or by multiple mating types in fungi. In animals, motility requires neuronal systems, and muscle activity, both of which are highly sensitive to oxidative damage. As a consequence, motility has evolved in animals as heterotrophic organisms that (1) are not photosynthetically active, and (2) are not primary decomposers. Adaptations to motility provide prerequisites for an active mating behavior and efficient mate-searching systems. These benefits compensate for the "cost of males", and may explain the early evolution of sex chromosomes in metazoans. We conclude that different sexual systems evolved under the indirect physiological constraints of lifestyles.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Goettingen, Göttingen, Germany.
| | - Franz Hadacek
- Department of Plant Biochemistry, University of Goettingen, Göttingen, Germany
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89
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Fruchard C, Badouin H, Latrasse D, Devani RS, Muyle A, Rhoné B, Renner SS, Banerjee AK, Bendahmane A, Marais GAB. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes (Basel) 2020; 11:E787. [PMID: 32668777 PMCID: PMC7397054 DOI: 10.3390/genes11070787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 01/17/2023] Open
Abstract
About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped, and the transmission patterns of SNPs were then analyzed. In the >1300 sex-linked genes studied, maximum X-Y divergence was 0.13-0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.
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Affiliation(s)
- Cécile Fruchard
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - Hélène Badouin
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Ravi S. Devani
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA;
| | - Bénédicte Rhoné
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
- Institut de Recherche pour le Développement (IRD), Université Montpellier, DIADE, F-34394 Montpellier, France
| | - Susanne S. Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany;
| | - Anjan K. Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Gabriel A. B. Marais
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
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90
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020; 18:78. [PMID: 32605573 PMCID: PMC7329446 DOI: 10.1186/s12915-020-00808-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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91
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020. [PMID: 32605573 DOI: 10.1101/589804v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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92
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Punja ZK, Holmes JE. Hermaphroditism in Marijuana ( Cannabis sativa L.) Inflorescences - Impact on Floral Morphology, Seed Formation, Progeny Sex Ratios, and Genetic Variation. FRONTIERS IN PLANT SCIENCE 2020; 11:718. [PMID: 32670310 PMCID: PMC7329997 DOI: 10.3389/fpls.2020.00718] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/06/2020] [Indexed: 05/26/2023]
Abstract
Cannabis sativa L. (hemp, marijuana) produces male and female inflorescences on different plants (dioecious) and therefore the plants are obligatory out-crossers. In commercial production, marijuana plants are all genetically female; male plants are destroyed as seed formation reduces flower quality. Spontaneously occurring hermaphroditic inflorescences, in which pistillate flowers are accompanied by formation of anthers, leads to undesired seed formation; the mechanism for this is poorly understood. We studied hermaphroditism in several marijuana strains with three objectives: (i) to compare the morphological features of this unique phenotype with normal male flowers; (ii) to assess pollen and seed viability from hermaphroditic flowers; and (iii) to assess the effect of hermaphroditism on progeny male:female (sex) ratios and on genetic variation using molecular methods. The morphological features of anthers, pollen production and germination in hermaphroditic flowers and in staminate inflorescences on male plants were compared using light and scanning electron microscopy. Seeds produced on hermaphroditic plants and seeds derived from cross-fertilization were germinated and seedlings were compared for gender ratios using a PCR-based assay as well as for the extent of genetic variation using six ISSR primers. Nei's index of gene diversity and Shannon's Information index were compared for these two populations. The morphology of anthers and pollen formation in hermaphroditic inflorescences was similar to that in staminate flowers. Seedlings from hermaphroditic seeds, and anther tissues, showed a female genetic composition while seedlings derived from cross-fertilized seeds showed a 1:1 male:female sex expression ratio. Uniquely, hermaphroditic inflorescences produced seeds which gave rise only to genetically female plants. In PCR assays, a 540 bp size fragment was present in male and female plants, while a 390 bp band was uniquely associated with male plants. Sequence analysis of these fragments revealed the presence of Copia-like retrotransposons within the C. sativa genome which may be associated with the expression of male or female phenotype. In ISSR analysis, the percentage of polymorphic loci ranged from 44 to 72% in hermaphroditic and cross-fertilized populations. Nei's index of gene diversity and Shannon's Information index were not statistically different for both populations. The extent of genetic variation after one generation of selfing in the progeny from hermaphroditic seed is similar to that in progeny from cross-fertilized seeds.
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93
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Molecular Sex Identification in the Hardy Rubber Tree ( Eucommia ulmoides Oliver) via ddRAD Markers. Int J Genomics 2020; 2020:2420976. [PMID: 32509842 PMCID: PMC7246395 DOI: 10.1155/2020/2420976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/03/2020] [Indexed: 11/18/2022] Open
Abstract
Eucommia ulmoides, also known as the industrially and medicinally important hardy rubber tree, is the sole species of Eucommiaceae. Nevertheless, its dioecious property hinders sex recognition by traditional morphological observation at very early developmental stages, thus inhibiting breeding and economic cropping. In this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) was applied to screen sex-linked molecular markers for sex identification and investigation of the sex determination system in 20 male and female E. ulmoides individual plants, respectively. In consequence, five candidate male-specific loci but no female-specific loci were predicated among the 183,752 male and 147,122 female catalogue loci by bioinformatics analysis. Subsequent PCR (polymerase chain reaction) amplification and Sanger sequencing examinations were performed on another 24 individuals, 12 for each sex, from a separate population. One ideal sex-linked locus, MSL4, was identified among the five putative male-specific loci that were found using ddRAD data. MSL4 is 479 bp in length and highly conserved in all the male individuals, suggesting its feature of being stable and repeatable. Our results also indicated that the sex of E. ulmoides is likely determined genetically. In short, this study provides a consistent and reproducible ddRAD marker (MSL4) that is able to discriminate male from female seedlings in E. ulmoides, which will be valuable for rapid breeding practice and better commercial production of this economically important tree.
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94
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Zhou P, Zhang X, Fatima M, Ma X, Fang H, Yan H, Ming R. DNA methylome and transcriptome landscapes revealed differential characteristics of dioecious flowers in papaya. HORTICULTURE RESEARCH 2020; 7:81. [PMID: 32528693 PMCID: PMC7261803 DOI: 10.1038/s41438-020-0298-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 05/21/2023]
Abstract
Separate sexes in dioecious plants display different morphology and physiological characteristics. The differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype, which is genetically determined and epigenetically modified. In dioecious papaya (Carica papaya L.), global comparisons of epigenetic DNA methylation and gene expressions were still limited. We conducted bisulfite sequencing of early-stage flowers grown in three seasons (spring, summer and winter) and compared their methylome and transcriptome profiles to investigate the differential characteristics of male and female in papaya. Methylation variances between female and male papaya were conserved among three different seasons. However, combined genome-scale transcriptomic evidence revealed that most methylation variances did not have influence on the expression profiles of neighboring genes, and the differentially expressed genes were most overrepresented in phytohormone signal transduction pathways. Further analyses showed diverse stress-responsive methylation alteration in male and female flowers. Male flower methylation was more responsive to stress whereas female flower methylation varied less under stress. Early flowering of male papaya in spring might be associated with the variation in the transcription of CpSVP and CpAP1 coinciding with their gene-specific hypomethylation. These findings provide insights into the sex-specific DNA methylation and gene expression landscapes of dioecious papaya and a foundation to investigate the correlation between differentiated floral characteristics and their candidate genes.
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Affiliation(s)
- Ping Zhou
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, 350013 Fuzhou, Fujian China
| | - Xiaodan Zhang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Xinyi Ma
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Hongkun Fang
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Hansong Yan
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
| | - Ray Ming
- College of Life Sciences, FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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95
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Aliferis KA, Bernard-Perron D. Cannabinomics: Application of Metabolomics in Cannabis ( Cannabis sativa L.) Research and Development. FRONTIERS IN PLANT SCIENCE 2020; 11:554. [PMID: 32457786 PMCID: PMC7225349 DOI: 10.3389/fpls.2020.00554] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/14/2020] [Indexed: 05/18/2023]
Abstract
Cannabis (Cannabis sativa L.) is a complex, polymorphic plant species, which produces a vast array of bioactive metabolites, the two major chemical groups being cannabinoids and terpenoids. Nonetheless, the psychoactive cannabinoid tetrahydrocannabinol (Δ 9 -THC) and the non-psychoactive cannabidiol (CBD), are the two major cannabinoids that have monopolized the research interest. Currently, more than 600 Cannabis varieties are commercially available, providing access to a multitude of potent extracts with complex compositions, whose genetics are largely inconclusive. Recently introduced legislation on Cannabis cultivation in many countries represents a great opportunity, but at the same time, a great challenge for Cannabis research and development (R&D) toward applications in the pharmaceutical, food, cosmetics, and agrochemical industries. Based on its versatility and unique capabilities in the deconvolution of the metabolite composition of complex matrices, metabolomics represents an ideal bioanalytical tool that could greatly assist and accelerate Cannabis R&D. Among others, Cannabis metabolomics or cannabinomics can be applied in the taxonomy of Cannabis varieties in chemovars, the research on the discovery and assessment of new Cannabis-based sources of bioactivity in medicine, the development of new food products, and the optimization of its cultivation, aiming for improvements in yield and potency. Although Cannabis research is still in its infancy, it is highly foreseen that the employment of advanced metabolomics will provide insights that could assist the sector to face the aforementioned challenges. Within this context, here, the current state-of-the-art and conceptual aspects of cannabinomics are presented.
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Affiliation(s)
- Konstantinos A. Aliferis
- Laboratory of Pesticide Science, Agricultural University of Athens, Athens, Greece
- Department of Plant Science, McGill University, Montreal, QC, Canada
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96
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Gao S, Wang B, Xie S, Xu X, Zhang J, Pei L, Yu Y, Yang W, Zhang Y. A high-quality reference genome of wild Cannabis sativa. HORTICULTURE RESEARCH 2020; 7:73. [PMID: 32377363 PMCID: PMC7195422 DOI: 10.1038/s41438-020-0295-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 05/02/2023]
Abstract
Cannabis sativa is a well-known plant species that has great economic and ecological significance. An incomplete genome of cloned C. sativa was obtained by using SOAPdenovo software in 2011. To further explore the utilization of this plant resource, we generated an updated draft genome sequence for wild-type varieties of C. sativa in China using PacBio single-molecule sequencing and Hi-C technology. Our assembled genome is approximately 808 Mb, with scaffold and contig N50 sizes of 83.00 Mb and 513.57 kb, respectively. Repetitive elements account for 74.75% of the genome. A total of 38,828 protein-coding genes were annotated, 98.20% of which were functionally annotated. We provide the first comprehensive de novo genome of wild-type varieties of C. sativa distributed in Tibet, China. Due to long-term growth in the wild environment, these varieties exhibit higher heterozygosity and contain more genetic information. This genetic resource is of great value for future investigations of cannabinoid metabolic pathways and will aid in promoting the commercial production of C. sativa and the effective utilization of cannabinoids. The assembled genome is also a valuable resource for intensively and effectively investigating the C. sativa genome further in the future.
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Affiliation(s)
- Shan Gao
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, Beijing, 100038 China
| | - Baishi Wang
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, Beijing, 100038 China
| | - Shanshan Xie
- Beijing Century Legend Bioscience Co., Ltd., Beijing, 102300 China
| | - Xiaoyu Xu
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, Beijing, 100038 China
| | - Jin Zhang
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, Beijing, 100038 China
| | - Li Pei
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, Beijing, 100038 China
| | - Yongyi Yu
- Beijing Century Legend Bioscience Co., Ltd., Beijing, 102300 China
| | - Weifei Yang
- Beijing Century Legend Bioscience Co., Ltd., Beijing, 102300 China
| | - Ying Zhang
- Institute of Forensic Science, Ministry of Public Security, No. 17 South Muxidi Lane, Xicheng District, Beijing, 100038 China
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97
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Li W, Wu H, Li X, Chen Y, Yin T. Fine mapping of the sex locus in Salix triandra confirms a consistent sex determination mechanism in genus Salix. HORTICULTURE RESEARCH 2020; 7:64. [PMID: 32377355 PMCID: PMC7193568 DOI: 10.1038/s41438-020-0289-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 05/19/2023]
Abstract
Salix triandra belongs to section Amygdalinae in genus Salix, which is in a different section from the willow species in which sex determination has been well studied. Studying sex determination in distantly related willow species will help to clarify whether the sexes of different willows arise through a common sex determination system. For this purpose, we generated an intraspecific full-sib F1 population for S. triandra and constructed high-density genetic linkage maps for the crossing parents using restriction site-associated DNA sequencing and following a two-way pseudo-testcross strategy. With the established maps, the sex locus was positioned in linkage group XV only in the maternal map, and no sex linkage was detected in the paternal map. Consistent with previous findings in other willow species, our study showed that chromosome XV was the incipient sex chromosome and that females were the heterogametic sex in S. triandra. Therefore, sex in this willow species is also determined through a ZW sex determination system. We further performed fine mapping in the vicinity of the sex locus with SSR markers. By comparing the physical and genetic distances for the target interval encompassing the sex determination gene confined by SSRs, severe recombination repression was revealed in the sex determination region in the female map. The recombination rate in the confined interval encompassing the sex locus was approximately eight-fold lower than the genome-wide average. This study provides critical information relevant to sex determination in S. triandra.
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Affiliation(s)
- Wei Li
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Huaitong Wu
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Xiaoping Li
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Yingnan Chen
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Tongming Yin
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
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98
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Kovalchuk I, Pellino M, Rigault P, van Velzen R, Ebersbach J, Ashnest JR, Mau M, Schranz ME, Alcorn J, Laprairie RB, McKay JK, Burbridge C, Schneider D, Vergara D, Kane NC, Sharbel TF. The Genomics of Cannabis and Its Close Relatives. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:713-739. [PMID: 32155342 DOI: 10.1146/annurev-arplant-081519-040203] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10-25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.
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Affiliation(s)
- I Kovalchuk
- Department of Biology, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - M Pellino
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - P Rigault
- Gydle Inc., Québec, Québec G1S 1E7, Canada
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - R van Velzen
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
- Bedrocan International, 9640 CA Veendam, The Netherlands
| | - J Ebersbach
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - J R Ashnest
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M Mau
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M E Schranz
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
| | - J Alcorn
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - R B Laprairie
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
- Department of Pharmacology, College of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - J K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - C Burbridge
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Schneider
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Vergara
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - N C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - T F Sharbel
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
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99
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Exposito-Alonso M, Drost HG, Burbano HA, Weigel D. The Earth BioGenome project: opportunities and challenges for plant genomics and conservation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:222-229. [PMID: 31788877 DOI: 10.1111/tpj.14631] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/03/2019] [Accepted: 11/18/2019] [Indexed: 05/28/2023]
Abstract
Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome project (Proceedings of the National Academy of Sciences of the United States of America, 115, 4325-4333), which aims to produce reference genomes for all eukaryotic species within the next decade. In this perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300 000 species. For this, we highlight four key points: (i) the unique biological insights that could be gained from studying plants, (ii) their apparent underrepresentation in sequencing efforts given the number of threatened species, (iii) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (iv) the accounting for within-species genetic diversity and the historical aspect of conservation genetics.
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Affiliation(s)
| | - Hajk-Georg Drost
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, CB2 1LR, Cambridge, UK
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, London, WC1H 0AG, UK
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
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100
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Feng G, Sanderson BJ, Keefover-Ring K, Liu J, Ma T, Yin T, Smart LB, DiFazio SP, Olson MS. Pathways to sex determination in plants: how many roads lead to Rome? CURRENT OPINION IN PLANT BIOLOGY 2020; 54:61-68. [PMID: 32106015 DOI: 10.1016/j.pbi.2020.01.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 05/20/2023]
Abstract
The presence of thousands of independent origins of dioecy in angiosperms provides a unique opportunity to address the parallel evolution of the molecular pathways underlying unisexual flowers. Recent progress towards identifying sex determination genes has identified hormone response pathways, mainly associated with cytokinin and ethylene response pathways, as having been recruited multiple times independently to control unisexuality. Moreover, transcriptomics has begun to identify commonalities among intermediate sections of signal transduction pathways. These recent advances set the stage for development of a comparative evolutionary development research program to identify the shared and unique aspects of the genetic pathways of unisexual flower development in angiosperms.
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Affiliation(s)
- Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin Madison, Madison, WI 53795, USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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