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Iwasaki M, Kajiwara T, Yasui Y, Yoshitake Y, Miyazaki M, Kawamura S, Suetsugu N, Nishihama R, Yamaoka S, Wanke D, Hashimoto K, Kuchitsu K, Montgomery SA, Singh S, Tanizawa Y, Yagura M, Mochizuki T, Sakamoto M, Nakamura Y, Liu C, Berger F, Yamato KT, Bowman JL, Kohchi T. Identification of the sex-determining factor in the liverwort Marchantia polymorpha reveals unique evolution of sex chromosomes in a haploid system. Curr Biol 2021; 31:5522-5532.e7. [PMID: 34735792 PMCID: PMC8699743 DOI: 10.1016/j.cub.2021.10.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/02/2021] [Accepted: 10/08/2021] [Indexed: 12/18/2022]
Abstract
Sex determination is a central process for sexual reproduction and is often regulated by a sex determinant encoded on a sex chromosome. Rules that govern the evolution of sex chromosomes via specialization and degeneration following the evolution of a sex determinant have been well studied in diploid organisms. However, distinct predictions apply to sex chromosomes in organisms where sex is determined in the haploid phase of the life cycle: both sex chromosomes, female U and male V, are expected to maintain their gene functions, even though both are non-recombining. This is in contrast to the X-Y (or Z-W) asymmetry and Y (W) chromosome degeneration in XY (ZW) systems of diploids. Here, we provide evidence that sex chromosomes diverged early during the evolution of haploid liverworts and identify the sex determinant on the Marchantia polymorpha U chromosome. This gene, Feminizer, encodes a member of the plant-specific BASIC PENTACYSTEINE transcription factor family. It triggers female differentiation via regulation of the autosomal sex-determining locus of FEMALE GAMETOPHYTE MYB and SUPPRESSOR OF FEMINIZATION. Phylogenetic analyses of Feminizer and other sex chromosome genes indicate dimorphic sex chromosomes had already been established 430 mya in the ancestral liverwort. Feminizer also plays a role in reproductive induction that is shared with its gametolog on the V chromosome, suggesting an ancestral function, distinct from sex determination, was retained by the gametologs. This implies ancestral functions can be preserved after the acquisition of a sex determination mechanism during the evolution of a dominant haploid sex chromosome system.
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Affiliation(s)
- Miyuki Iwasaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Tomoaki Kajiwara
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yukiko Yasui
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Motoki Miyazaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shogo Kawamura
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Dierk Wanke
- Department Biologie I, Ludwig-Maximilians-University (LMU), München 80638, Germany
| | - Kenji Hashimoto
- Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Kazuyuki Kuchitsu
- Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Shilpi Singh
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Yasuhiro Tanizawa
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Masaru Yagura
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Takako Mochizuki
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart 70599, Germany
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology (BOST), Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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Al‐Dossary O, Alsubaie B, Kharabian‐Masouleh A, Al‐Mssallem I, Furtado A, Henry RJ. The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1283-1294. [PMID: 34570389 PMCID: PMC9293028 DOI: 10.1111/tpj.15509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Most flowering plants are hermaphrodites, but around 6% of species are dioecious, having separate male and female plants. Sex chromosomes and some sex-specific genes have been reported in plants, but the genome sequences have not been compared. We now report the genome sequence of male and female jojoba (Simmondsia chinensis) plants, revealing a very large difference in the sex chromosomes. The male genome assembly was 832 Mb and the female 822 Mb. This was explained by the large size differences in the Y chromosome (37.6 Mb) compared with the X chromosome (26.9 Mb). Relative to the X chromosome, the Y chromosome had two large insertions each of more than 5 Mb containing more than 400 genes. Many of the genes in the chromosome-specific regions were novel. These male-specific regions included many flowering-related and stress response genes. Smaller insertions found only in the X chromosome totalled 877 kb. The wide divergence of the sex chromosomes suggests a long period of adaptation to diverging sex-specific roles. Male and female plants may have evolved to accommodate factors such as differing reproductive resource allocation requirements under the stress of the desert environment in which the plants are found. The sex-determining regions accumulate genes beneficial to each sex. This has required the evolution of many more novel sex-specific genes than has been reported for other organisms. This suggest that dioecious plants provide a novel source of genes for manipulation of reproductive performance and environmental adaptation in crops.
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Affiliation(s)
- Othman Al‐Dossary
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | - Bader Alsubaie
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | | | - Ibrahim Al‐Mssallem
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureUniversity of QueenslandBrisbane4072Australia
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VviPLATZ1 is a major factor that controls female flower morphology determination in grapevine. Nat Commun 2021; 12:6995. [PMID: 34848714 PMCID: PMC8632994 DOI: 10.1038/s41467-021-27259-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/10/2021] [Indexed: 12/26/2022] Open
Abstract
Plant genetic sex determinants that mediate the transition to dioecy are predicted to be diverse, as this type of mating system independently evolved multiple times in angiosperms. Wild Vitis species are dioecious with individuals producing morphologically distinct female or male flowers; whereas, modern domesticated Vitis vinifera cultivars form hermaphrodite flowers capable of self-pollination. Here, we identify the VviPLATZ1 transcription factor as a key candidate female flower morphology factor that localizes to the Vitis SEX-DETERMINING REGION. The expression pattern of this gene correlates with the formation reflex stamens, a prominent morphological phenotype of female flowers. After generating CRISPR/Cas9 gene-edited alleles in a hermaphrodite genotype, phenotype analysis shows that individual homozygous lines produce flowers with reflex stamens. Taken together, our results demonstrate that loss of VviPLATZ1 function is a major factor that controls female flower morphology in Vitis. Unlike wild Vitis species, which produce either female or male flowers, modern grapevine cultivars form hermaphrodite flowers for self-pollination. Here, the authors report that the VviPLATZ1 (plant AT-rich sequence-and zinc-binding protein1) transcription factor functions in controlling female flower morphology determination.
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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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55
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Li SF, Lv CC, Lan LN, Jiang KL, Zhang YL, Li N, Deng CL, Gao WJ. DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus. HORTICULTURE RESEARCH 2021; 8:198. [PMID: 34465747 PMCID: PMC8408194 DOI: 10.1038/s41438-021-00633-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 05/04/2023]
Abstract
DNA methylation is a crucial regulatory mechanism in many biological processes. However, limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants. In this study, we investigated the variances in methylation and transcriptional patterns of male and female flowers of garden asparagus. Compared with male flowers, female flowers at the same stages showed higher levels of DNA methylation. Both male and female flowers gained DNA methylation globally from the premeiotic to meiotic stages. Detailed analysis revealed that the increased DNA methylation was largely due to increased CHH methylation. Correlation analysis of differentially expressed genes and differentially methylated regions suggested that DNA methylation might not have contributed to the expression variation of the sex-determining genes SOFF and TDF1 but probably played important roles in sexual differentiation and flower development of garden asparagus. The upregulated genes AoMS1, AoLAP3, AoAMS, and AoLAP5 with varied methylated CHH regions might have been involved in sexual differentiation and flower development of garden asparagus. Plant hormone signaling genes and transcription factor genes also participated in sexual differentiation and flower development with potential epigenetic regulation. In addition, the CG and CHG methylation levels in the Y chromosome were notably higher than those in the X chromosome, implying that DNA methylation might have been involved in Y chromosome evolution. These data provide insights into the epigenetic modification of sexual differentiation and flower development and improve our understanding of sex chromosome evolution in garden asparagus.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Can-Can Lv
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Kai-Lu Jiang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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56
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Hyden B, Carlson CH, Gouker FE, Schmutz J, Barry K, Lipzen A, Sharma A, Sandor L, Tuskan GA, Feng G, Olson MS, DiFazio SP, Smart LB. Integrative genomics reveals paths to sex dimorphism in Salix purpurea L. HORTICULTURE RESEARCH 2021; 8:170. [PMID: 34333534 PMCID: PMC8325687 DOI: 10.1038/s41438-021-00606-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 05/16/2023]
Abstract
Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Anna Lipzen
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Aditi Sharma
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Guanqiao Feng
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Matthew S Olson
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA.
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Charlesworth D. The timing of genetic degeneration of sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200093. [PMID: 34247501 DOI: 10.1098/rstb.2020.0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genetic degeneration is an extraordinary feature of sex chromosomes, with the loss of functions of Y-linked genes in species with XY systems, and W-linked genes in ZW systems, eventually affecting almost all genes. Although degeneration is familiar to most biologists, important aspects are not yet well understood, including how quickly a Y or W chromosome can become completely degenerated. I review the current understanding of the time-course of degeneration. Degeneration starts after crossing over between the sex chromosome pair stops, and theoretical models predict an initially fast degeneration rate and a later much slower one. It has become possible to estimate the two quantities that the models suggest are the most important in determining degeneration rates-the size of the sex-linked region, and the time when recombination became suppressed (which can be estimated using Y-X or W-Z sequence divergence). However, quantifying degeneration is still difficult. I review evidence on gene losses (based on coverage analysis) or loss of function (by classifying coding sequences into functional alleles and pseudogenes). I also review evidence about whether small genome regions degenerate, or only large ones, whether selective constraints on the genes in a sex-linked region also strongly affect degeneration rates, and about how long it takes before all (or almost all) genes are lost. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
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Kohchi T, Yamato KT, Ishizaki K, Yamaoka S, Nishihama R. Development and Molecular Genetics of Marchantia polymorpha. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:677-702. [PMID: 33684298 DOI: 10.1146/annurev-arplant-082520-094256] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.
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Affiliation(s)
- Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa 649-6493, Japan;
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; , ,
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Vekemans X, Castric V, Hipperson H, Müller NA, Westerdahl H, Cronk Q. Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility. Mol Ecol 2021; 30:6072-6086. [PMID: 34137092 PMCID: PMC9290700 DOI: 10.1111/mec.16020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 11/27/2022]
Abstract
Whole‐genome sequencing of non‐model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data‐handling. Three such regions are the major histocompatibility complex (MHC), sex‐determining regions (SDRs) and the plant self‐incompatibility locus (S‐locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short‐read sequences against multiple alternative references improves genotyping comprehensiveness at the S‐locus thereby contributing to more accurate assessments of allelic frequencies. Long‐read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S‐locus haplotypes. These advances are adding value to short‐read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.
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Affiliation(s)
| | | | - Helen Hipperson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Helena Westerdahl
- Molecular Ecology and Evolution Laboratory, Department of Biology, Lund University, Lund, Sweden
| | - Quentin Cronk
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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60
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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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61
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Abstract
Y and W chromosomes start degenerating after they evolve a non-recombining region that is always heterozygous in males (Y) or females (W), sometimes losing almost all genes that were originally present on their X or Z counterparts. A new model for such degeneration involves evolutionary change in regulatory sequences.
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62
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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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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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64
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Charlesworth D. When and how do sex-linked regions become sex chromosomes? Evolution 2021; 75:569-581. [PMID: 33592115 DOI: 10.1111/evo.14196] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022]
Abstract
The attention given to heteromorphism and genetic degeneration of "classical sex chromosomes" (Y chromosomes in XY systems, and the W in ZW systems that were studied first and are best described) has perhaps created the impression that the absence of recombination between sex chromosomes is inevitable. I here argue that continued recombination is often to be expected, that absence of recombination is surprising and demands further study, and that the involvement of selection in reduced recombination is not yet well understood. Despite a long history of investigations of sex chromosome pairs, there is a need for more quantitative approaches to studying sex-linked regions. I describe a scheme to help understand the relationships between different properties of sex-linked regions. Specifically, I focus on their sizes (differentiating between small regions and extensive fully sex-linked ones), the times when they evolved, and their differentiation, and review studies using DNA sequencing in nonmodel organisms that are providing information about the processes causing these properties.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
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Wright SI. Deborah Charlesworth, winner of the society for the study of evolution's inaugural lifetime achievement award: Evolutionary biology for the genomics era. Evolution 2021; 75:566-568. [PMID: 33592116 DOI: 10.1111/evo.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
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66
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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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67
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Montgomery JS, Giacomini DA, Weigel D, Tranel PJ. Male-specific Y-chromosomal regions in waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri). THE NEW PHYTOLOGIST 2021; 229:3522-3533. [PMID: 33301599 DOI: 10.1111/nph.17108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/13/2020] [Indexed: 05/16/2023]
Abstract
Amaranthus tuberculatus and Amaranthus palmeri are agronomically important weed species, both with stable dioecious reproductive systems. An understanding of the genetic basis of sex determination may lead to new methods of managing these troublesome weeds. Previous research identified genomic sequences associated with maleness in each species. Male-specific sequences were used to identify genomic regions in both species that are believed to contain sex-determining genes, i.e. the male-specific Y (MSY) region. These regions were compared to understand if sex determination is controlled via the same physiological pathway and if dioecy evolved independently. A contiguously assembled candidate MSY region identified in Amaranthus palmeri is approximately 1.3 Mb with 121 predicted gene models. In Amaranthus tuberculatus, several contigs, with combined length of 4.6 Mb and with 147 gene models, were identified as belonging to the MSY region. Synteny was not detected between the two species' candidate MSY regions but they shared two predicted genes. With lists of candidate genes for sex determination containing fewer than 200 in each species, future research can address whether sex determination is controlled via similar physiological pathways and whether dioecy has indeed evolved independently in these species.
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Affiliation(s)
- Jacob S Montgomery
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Darci A Giacomini
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
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68
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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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69
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Li N, Meng Z, Tao M, Wang Y, Zhang Y, Li S, Gao W, Deng C. Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L. BMC Genomics 2020; 21:850. [PMID: 33256615 PMCID: PMC7708156 DOI: 10.1186/s12864-020-07277-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/24/2020] [Indexed: 12/30/2022] Open
Abstract
Background Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, comparative transcriptome analysis of male and female flowers were performed to explore the sex differentiation mechanism in spinach. Results Compared with published genome of spinach, 10,800 transcripts were newly annotated; alternative splicing, alternative polyadenylation and lncRNA were analyzed for the first time, increasing the diversity of spinach transcriptome. A total of 2965 differentially expressed genes were identified between female and male flowers at three early development stages. The differential expression of RNA splicing-related genes, polyadenylation-related genes and lncRNAs suggested the involvement of alternative splicing, alternative polyadenylation and lncRNA in sex differentiation. Moreover, 1946 male-biased genes and 961 female-biased genes were found and several candidate genes related to gender development were identified, providing new clues to reveal the mechanism of sex differentiation. In addition, weighted gene co-expression network analysis showed that auxin and gibberellin were the common crucial factors in regulating female or male flower development; however, the closely co-expressed genes of these two factors were different between male and female flower, which may result in spinach sex differentiation. Conclusions In this study, 10,800 transcripts were newly annotated, and the alternative splicing, alternative polyadenylation and long-noncoding RNA were comprehensively analyzed for the first time in spinach, providing valuable information for functional genome study. Moreover, candidate genes related to gender development were identified, shedding new insight on studying the mechanism of sex determination and differentiation in plant. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07277-4.
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Affiliation(s)
- Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Ziwei Meng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Minjie Tao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yueyuan Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yulan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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70
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Han M, Yang Y, Zhang M, Wang K. Considerations regarding centromere assembly in plant whole-genome sequencing. Methods 2020; 187:54-56. [PMID: 32920129 DOI: 10.1016/j.ymeth.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/19/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
The assembly of centromeric regions has become one of the most intractable tasks in whole-genome sequencing due to the enrichment of highly repetitive DNA sequences in most eukaryotic centromeres. Here, we describe a method used to identify centromeric DNAs through chromatin immunoprecipitation and sequencing (ChIP-seq). By mapping ChIP-seq reads, centromeric regions can be indicated in genome assemblies. We demonstrated that the assembly quality of centromeres obtained using ChIP-seq mapping can reflect and indicate the quality of a whole-genome assembly. We discuss an expected 'high-quality' centromere assembly obtained via centromere ChIP-seq mapping.
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Affiliation(s)
- Miaomiao Han
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yae Yang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | - Kai Wang
- Guangxi Key Laboratory of Sugarcane Biology & Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, China.
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71
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Müller NA, Kersten B, Leite Montalvão AP, Mähler N, Bernhardsson C, Bräutigam K, Carracedo Lorenzo Z, Hoenicka H, Kumar V, Mader M, Pakull B, Robinson KM, Sabatti M, Vettori C, Ingvarsson PK, Cronk Q, Street NR, Fladung M. A single gene underlies the dynamic evolution of poplar sex determination. NATURE PLANTS 2020; 6:630-637. [PMID: 32483326 DOI: 10.1038/s41477-020-0672-9] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive1. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR-Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.
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Affiliation(s)
- Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | | | - Niklas Mähler
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå, Sweden
| | - Carolina Bernhardsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Katharina Bräutigam
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vikash Kumar
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå, Sweden
| | - Malte Mader
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Birte Pakull
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | | | - Maurizio Sabatti
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Cristina Vettori
- Institute of Biosciences and BioResources, Division of Florence, National Research Council, Sesto Fiorentino, Italy
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Quentin Cronk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Cronk Q, Müller NA. Default Sex and Single Gene Sex Determination in Dioecious Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:1162. [PMID: 32849717 PMCID: PMC7403218 DOI: 10.3389/fpls.2020.01162] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/16/2020] [Indexed: 05/20/2023]
Abstract
A well-established hypothesis for the evolution of dioecy involves two genes linked at a sex-determining region (SDR). Recently there has been increased interest in possible single gene sex determination. Work in Populus has finally provided direct experimental evidence for single gene sex determination in plants using CRISPR-Cas9 to knock out a single gene and convert individuals from female to male. In poplar, the feminizing factor popARR17 acts as a "master regulator", analogous to the mammalian masculinizing factor SRY. The production of fully functional males from females by a simple single gene knockout is experimental evidence that an antagonistic male-determining factor does not exist in Populus. Mammals have a "default sex" (female), as do poplar trees (Populus), although the default sex in poplars is male. The occurrence of single gene sex determination with a default sex may be much commoner in plants than hitherto expected, especially when dioecy evolved via monoecy. The master regulator does not even need to be at the SDR (although it may be). In most poplars the feminizing factor popARR17 is not at the SDR, but instead a negative regulator of it. So far there is little information on how high-level regulators are connected to floral phenotype. A model is presented of how sex-determining genes could lead to different floral morphologies via MADS-box floral developmental genes.
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Affiliation(s)
- Quentin Cronk
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Quentin Cronk,
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