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Wang Y, Zhang RG, Hörandl E, Zhang ZX, Charlesworth D, He L. Evolution of Sex-linked Genes and the Role of Pericentromeric Regions in Sex Chromosomes: Insights from Diploid Willows. Mol Biol Evol 2024; 41:msae235. [PMID: 39530333 PMCID: PMC11580687 DOI: 10.1093/molbev/msae235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 10/25/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024] Open
Abstract
The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S. triandra (15XY system), a basal species in the Vetrix clade, and the Salix clade species S. mesnyi (7XY system). Combining these with other available genome assemblies, we found inversions within the sex-linked regions, which are likely to be pericentromeric and probably recombined rarely in the ancestral species, before sex-linkage evolved. The Y-linked regions in all 15XY and 7XY species include partial duplicates containing exon 1 of an ARR17-like gene similar to male-determining factors in other Salicaceae species. We also found duplicates of a Y-specific gene, which we named MSF. The derived Salix clade 7XY chromosome systems appear to have evolved when these two genes transposed from the 15Y to the 7Y. Additionally, the 7Y chromosomes in S. dunnii and S. chaenomeloides probably evolved from the ancestral 7X of the Salix clade, involving a similar transposition, and loss of the ancestral 7Y. We suggest that pericentromeric regions that recombine infrequently may facilitate the evolution of sex linkage.
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Affiliation(s)
- Yi Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100091, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen 37073, Germany
| | - Zhi-Xiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100091, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
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2
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Kato Y, Konishi M. A mature liquid fertilizer derived from cattle urine promotes Arabidopsis thaliana growth via hormone-like responses. Biosci Biotechnol Biochem 2024; 88:1007-1018. [PMID: 38849314 DOI: 10.1093/bbb/zbae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/01/2024] [Indexed: 06/09/2024]
Abstract
To understand the fertilization effects of liquid fertilizer (LF) produced by aerobic microbial processing of cattle urine, we investigated the influence of LF on growth and shoot genetic responses of the model plant Arabidopsis thaliana. LF significantly enhanced both shoot and root growth under aseptic conditions. Although filtrate from ultrafiltration (molecular weight cutoff: 10 000) also promoted shoot growth and root elongation, the concentrate only promoted root growth. Multiple growth-promoting factors were therefore associated with the growth promotion. Transcriptome analysis of shoots following LF addition identified 353 upregulated and 512 downregulated genes. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, signal transduction of a phytohormone cytokinin was influenced by LF addition. Cytochrome P450 induction triggered the related signal transitions, and would introduce the growth promotion for shoot. Primary auxin responses and abscisic acid signaling responses were also observed in the presence of LF. Ethylene signaling seemed to be insensitive.
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Affiliation(s)
- Yuta Kato
- Kankyo Daizen Co., Ltd, Hokkaido, Japan
- Cold Regions, Environmental and Energy Engineering Course, Graduate School of Engineering, Kitami Institute of Technology, Hokkaido, Japan
| | - Masaaki Konishi
- Department of Applied Chemistry, Kitami Institute of Technology, Hokkaido, Japan
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He L, Wang Y, Wang Y, Zhang RG, Wang Y, Hörandl E, Ma T, Mao YF, Mank JE, Ming R. Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes. Nat Commun 2024; 15:6893. [PMID: 39134553 PMCID: PMC11319354 DOI: 10.1038/s41467-024-51158-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Yuàn Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuán Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
| | - Tao Ma
- Key Laboratory for Bio‑Resource and Eco‑Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yan-Fei Mao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Ray Ming
- Centre 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 Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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4
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Cheng JL, Wei XP, Chen Y, Qi YD, Zhang BG, Liu HT. Comparative transcriptome analysis reveals candidate genes related to the sex differentiation of Schisandra chinensis. Funct Integr Genomics 2023; 23:344. [PMID: 37991590 DOI: 10.1007/s10142-023-01264-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/23/2023]
Abstract
Schisandra chinensis is a monoecious plant with unisex flowers. The fruit of S. chinensis is of high medical with economic value. The yield of S. chinensis fruit is related to the ratio of its female and male flowers. However, there is little research on its floral development and sex differentiation. To elucidate the possible mechanism for the sex differentiation of S. chinensis, we collected 18 samples of female and male flowers from three developmental stages and performed a comparative RNA-seq analysis aimed at identifying differentially expressed genes (DEGs) that may be related to sex differentiation. The results showed 936, 7179, and 6890 differentially expressed genes between female and male flowers at three developmental stages, respectively, and 466 candidate genes may play roles in sex differentiation. KEGG analysis showed genes involved in the flavonoid biosynthesis pathway and DNA replication pathway were essential for the development of female flowers. 51 MADS-box genes and 10 YABBY genes were identified in S. chinensis. The DEGs analysis indicated that MADS-box and YABBY genes were strongly related to the sex determination of S. chinensis. RT-qPCR confirmed the RNA-seq results of 20 differentially expressed genes, including three male-biased genes and 17 female-biased genes. A possible regulatory model of sex differentiation in S. chinensis was proposed according to our results. This study helps reveal the sex-differentiation mechanism of S. chinensis and lays the foundation for regulating the male-female ratio of S. chinensis in the future.
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Affiliation(s)
- Ji-Long Cheng
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue-Ping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yu Chen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yao-Dong Qi
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ben-Gang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Tao Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Tradition Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Hu N, Sanderson BJ, Guo M, Feng G, Gambhir D, Hale H, Wang D, Hyden B, Liu J, Smart LB, DiFazio SP, Ma T, Olson MS. Evolution of a ZW sex chromosome system in willows. Nat Commun 2023; 14:7144. [PMID: 37932261 PMCID: PMC10628195 DOI: 10.1038/s41467-023-42880-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
Transitions in the heterogamety of sex chromosomes (e.g., XY to ZW or vice versa) fundamentally alter the genetic basis of sex determination, however the details of these changes have been studied in only a few cases. In an XY to ZW transition, the X is likely to give rise to the W because they both carry feminizing genes and the X is expected to harbour less genetic load than the Y. Here, using a new reference genome for Salix exigua, we trace the X, Y, Z, and W sex determination regions during the homologous transition from an XY system to a ZW system in willow (Salix). We show that both the W and the Z arose from the Y chromosome. We find that the new Z chromosome shares multiple homologous putative masculinizing factors with the ancestral Y, whereas the new W lost these masculinizing factors and gained feminizing factors. The origination of both the W and Z from the Y was permitted by an unexpectedly low genetic load on the Y and this indicates that the origins of sex chromosomes during homologous transitions may be more flexible than previously considered.
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Affiliation(s)
- Nan Hu
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Brian J Sanderson
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Minghao Guo
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Diksha Gambhir
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Haley Hale
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, USA
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
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6
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Liao LY, He ZQ, Zhang L. Cloning and Functional Analysis of the VfRR17 Gene from tung tree ( Vernicia fordii). PLANTS (BASEL, SWITZERLAND) 2023; 12:2474. [PMID: 37447035 DOI: 10.3390/plants12132474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Tung tree (Vernicia fordii) is one of the four major woody oilseed species in China. However, its fruit yield is severely hampered by the low number of female flowers and the imbalanced male-to-female flower ratio, which is a problem that restricts the development of the oilseed industry. Previous research has demonstrated that the exogenous application of cytokinins can significantly augment the number of female flowers, although the underlying regulatory mechanism remains elusive. To elucidate the involvement of VfRR17, a member of the A-type ARRs family, in the exogenous cytokinin regulation of flower sexual differentiation in tung tree, this study conducted a comprehensive bioinformatic analysis of the physicochemical properties, structural characteristics, and evolutionary relationships of the protein encoded by VfRR17. Additionally, gene function analysis was performed using subcellular localization, qRT-PCR, and genetic transformation techniques. The findings revealed that the VfRR17 gene's coding region spanned 471 bp, encoding an unstable protein of 156 amino acids with a relative molecular mass of 17.4 kDa. Phylogenetic analysis demonstrated a higher similarity between VfRR17 of the tung tree and the RR17 gene of Jatropha curcas, Ricinus communis, Hevea brasiliensis, and other species within the Euphorbiaceae family compared to other species, with the greatest similarity of 86% observed with the RR17 gene of Jatropha curcas. The qRT-PCR analysis indicated that VfRR17 exhibited high expression levels during the early stage of tung tree inflorescence buds following 6-BA treatment, peaking at 24 h and displaying a 3.47-fold increase compared to that at 0 h. In female and male flowers of the tung tree, the expression in female flowers during the 1 DBF period was significantly higher than in male flowers, exhibiting a difference of approximately 47.91-fold. Furthermore, notable differential expression was observed in the root, leaf, and petiole segments of the tung tree under low-temperature stress at the 12-h time point. In transgenic Arabidopsis, the VfRR17 lines and wild-type lines exhibited significantly different flowering times under an exogenous 6-BA treatment at a concentration of 2 mg/L, with the VfRR17 lines experiencing an 11-day delay compared to the wild-type lines. Additionally, the number of fruit pods in VfRR17 transgenic Arabidopsis lines was significantly reduced by 28 compared to the wild-type lines at a 6-BA concentration of 3 mg/L. These findings suggest that VfRR17 likely plays a critical role in regulating flower development in response to exogenous 6-BA, providing valuable insights into the mechanisms underlying exogenous 6-BA-mediated regulation of female flower development in the tung tree.
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Affiliation(s)
- Li-Yu Liao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Lab of Non-Wood Forest Products of State Forestry and Grassland Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhang-Qi He
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Lab of Non-Wood Forest Products of State Forestry and Grassland Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
- Key Lab of Non-Wood Forest Products of State Forestry and Grassland Administration, Central South University of Forestry and Technology, Changsha 410004, China
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Bobadilla LK, Baek Y, Tranel PJ. Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus. BMC PLANT BIOLOGY 2023; 23:339. [PMID: 37365527 DOI: 10.1186/s12870-023-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are two dioecious and important weed species in the world that can rapidly evolve herbicide-resistance traits. Understanding these two species' dioecious and sex-determination mechanisms could open opportunities for new tools to control them. This study aims to identify the differential expression patterns between males and females in A. tuberculatus and A. palmeri. Multiple analyses, including differential expression, co-expression, and promoter analyses, used RNA-seq data from multiple tissue types to identify putative essential genes for sex determination in both dioecious species. RESULTS Genes were identified as potential key players for sex determination in A. palmeri. Genes PPR247, WEX, and ACD6 were differentially expressed between the sexes and located at scaffold 20 within or near the male-specific Y (MSY) region. Multiple genes involved with flower development were co-expressed with these three genes. For A. tuberculatus, no differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were identified as differentially expressed and possible candidate genes. CONCLUSIONS This is the first study comparing the global expression profile between males and females in dioecious weedy Amaranthus species. Results narrow down putative essential genes for sex-determination in A. palmeri and A. tuberculatus and also strengthen the hypothesis of two different evolutionary events for dioecy within the genus.
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Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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Hyden B, Zou J, Wilkerson DG, Carlson CH, Robles AR, DiFazio SP, Smart LB. Structural variation of a sex-linked region confers monoecy and implicates GATA15 as a master regulator of sex in Salix purpurea. THE NEW PHYTOLOGIST 2023; 238:2512-2523. [PMID: 36866707 DOI: 10.1111/nph.18853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/21/2023] [Indexed: 05/19/2023]
Abstract
The Salicaceae, including Populus and Salix, are dioecious perennials that utilize different sex determination systems. This family provides a useful system to better understand the evolution of dioecy and sex chromosomes. Here, a rare monoecious genotype of Salix purpurea, 94003, was self- and cross-pollinated and progeny sex ratios were used to test hypotheses on possible mechanisms of sex determination. To delimit genomic regions associated with monoecious expression, the 94003 genome sequence was assembled and DNA- and RNA-Seq of progeny inflorescences was performed. Based on alignments of progeny shotgun DNA sequences to the haplotype-resolved monoecious 94003 genome assembly and reference male and female genomes, a 1.15 Mb sex-linked region on Chr15W was confirmed to be absent in monecious plants. Inheritance of this structural variation is responsible for the loss of a male-suppressing function in what would otherwise be genetic females (ZW), resulting in monoecy (ZWH or WWH ), or lethality, if homozygous (WH WH ). We present a refined, two-gene sex determination model for Salix purpurea, mediated by ARR17 and GATA15 that is different from the single-gene ARR17-mediated system in the related genus Populus.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Junzhu Zou
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Research Institute of Forestry, Chinese Academy of Forestry, Dongxiaofu No. 1, Haidian District, Beijing, 100091, China
| | - Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Ayiana Rivera Robles
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
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Masuda K, Akagi T. Evolution of sex in crops: recurrent scrap and rebuild. BREEDING SCIENCE 2023; 73:95-107. [PMID: 37404348 PMCID: PMC10316312 DOI: 10.1270/jsbbs.22082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 07/06/2023]
Abstract
Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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Raiyemo DA, Bobadilla LK, Tranel PJ. Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes. BMC Biol 2023; 21:37. [PMID: 36804015 PMCID: PMC9940365 DOI: 10.1186/s12915-023-01539-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/08/2023] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Amaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions. RESULTS We provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination. CONCLUSIONS The results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.
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Affiliation(s)
- Damilola A Raiyemo
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
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Zhang X, Wang X, Pan L, Guo W, Li Y, Wang W. Genome-wide identification and expression analysis of MADS-box transcription factors reveal their involvement in sex determination of hardy rubber tree ( Eucommia ulmoides oliv.). Front Genet 2023; 14:1138703. [PMID: 36896236 PMCID: PMC9988917 DOI: 10.3389/fgene.2023.1138703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Eucommia ulmoides is a famous rubber-producing and medicinal tree species that produces unisexual flowers on separate individuals from the earliest stage of stamen/pistil primordium formation. To explore the genetic regulation pathway of sex in E. ulmoides, comprehensive genome-wide analyses and tissue-/sex-specific transcriptome comparisons of MADS-box transcription factors were performed for the first time in this work. Quantitative real-time PCR technique was employed to further validate the expression of genes that are assigned to floral organ ABCDE model. A total of 66 non-redundant E. ulmoides MADS-box (EuMADS) genes were identified, they were classified into Type I (M-type, 17 genes) and Type II (MIKC, 49 genes). Complex protein-motif composition, exon-intron structure and phytohormone-response cis-elements were detected in MIKC-EuMADS genes. Furthermore, 24 differentially-expressed EuMADS genes (DEGs) between male and female flowers, and two DEGs between male and female leaves were revealed. Amongst the 14 floral organ ABCDE model-related genes, there were 6 (A/B/C/E-class) and 5 (A/D/E-class) genes displayed male- and female-biased expression respectively. In particular, one B-class gene EuMADS39 and one A-class gene EuMADS65 were almost exclusively expressed in male trees, no matter in flower or leaf tissues. Collectively, these results suggested a critical role of MADS-box transcription factors in sex determination of E. ulmoides, which is conducive to decoding the molecular regulation mechanism of sex in E. ulmoides.
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Affiliation(s)
- Xianzhi Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xinyi Wang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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Tang N, Cao Z, Wu P, Zhang X, Lou J, Liu Y, Wang Q, Hu Y, Si S, Sun X, Chen Z. Genome-wide identification, interaction of the MADS-box proteins in Zanthoxylum armatum and functional characterization of ZaMADS80 in floral development. FRONTIERS IN PLANT SCIENCE 2022; 13:1038828. [PMID: 36507394 PMCID: PMC9732391 DOI: 10.3389/fpls.2022.1038828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
As a typical dioecious species, Zanthoxylum armatum establishes apomictic reproduction, hence only female trees are cultivated. However, male and hermaphrodite flowers have recently appeared in female plants, resulting in a dramatic yield reduction. To date, the genetic basis underlying sex determination and apomixis in Z. armatum has been largely unknown. Here, we observed abortion of the stamen or carpel prior to primordium initiation, thus corroborating the potential regulation of MADS-box in sex determination. In Z. armatum, a total of 105 MADS-box genes were identified, harboring 86 MIKC-type MADSs with lack of FLC orthologues. Transcriptome analysis revealed candidate MADSs involved in floral organ identity, including ten male-biased MADSs, represented by ZaMADS92/81/75(AP3/PI-like), and twenty-six female-specified, represented by ZaMADS80/49 (STK/AGL11-like) and ZaMADS42 (AG-like). Overexpressing ZaMADS92 resulted in earlier flowering, while ZaMADS80 overexpression triggered precocious fruit set and parthenocarpy as well as dramatic modifications in floral organs. To characterize their regulatory mechanisms, a comprehensive protein-protein interaction network of the represented MADSs was constructed based on yeast two-hybrid and bimolecular fluorescence complementation assays. Compared with model plants, the protein interaction patterns in Z. armatum exhibited both conservation and divergence. ZaMADS70 (SEP3-like) interacted with ZaMADS42 and ZaMADS48 (AP3-like) but not ZaMADS40 (AP1-like), facilitating the loss of petals in Z. armatum. The ZaMADS92/ZaMADS40 heterodimer could be responsible for accelerating flowering in ZaMADS92-OX lines. Moreover, the interactions between ZaMADS80 and ZaMADS67(AGL32-like) might contribute to apomixis. This work provides new insight into the molecular mechanisms of MADS-boxes in sex organ identity in Z. armatum.
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Affiliation(s)
- Ning Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Zhengyan Cao
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Peiyin Wu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, China
| | - Xian Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Juan Lou
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yanni Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
- College of Biology and Food Engineering, Chongqing Three Georges University, Chongqing, China
| | - Qiyao Wang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yang Hu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Shuo Si
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xiaofan Sun
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Zexiong Chen
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, China
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Zhang S, Wu Z, Ma D, Zhai J, Han X, Jiang Z, Liu S, Xu J, Jiao P, Li Z. Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism. Commun Biol 2022; 5:1186. [PMCID: PMC9636151 DOI: 10.1038/s42003-022-04145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Reference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus. Reference-quality genomes of both sexes of the dioecious tree species, Populus euphratica, provide further insight into the evolution of Populus sex chromosomes and highlight male-specific fusion genes that may contribute to sexual dimorphism.
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Affiliation(s)
- Shanhe Zhang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhihua Wu
- grid.453534.00000 0001 2219 2654College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 China
| | - De Ma
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Juntuan Zhai
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Xiaoli Han
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhenbo Jiang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Jingdong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Peipei Jiao
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhijun Li
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
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Zhang X, Pan L, Guo W, Li Y, Wang W. A convergent mechanism of sex determination in dioecious plants: Distinct sex-determining genes display converged regulation on floral B-class genes. FRONTIERS IN PLANT SCIENCE 2022; 13:953445. [PMID: 36092432 PMCID: PMC9459113 DOI: 10.3389/fpls.2022.953445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 06/12/2023]
Abstract
Sex determination in dioecious plants has been broadly and progressively studied with the blooming of genome sequencing and editing techniques. This provides us with a great opportunity to explore the evolution and genetic mechanisms underlining the sex-determining system in dioecious plants. In this study, comprehensively reviewing advances in sex-chromosomes, sex-determining genes, and floral MADS-box genes in dioecious plants, we proposed a convergent model that governs plant dioecy across divergent species using a cascade regulation pathway connecting sex-determining genes and MADS-box genes e.g., B-class genes. We believe that this convergent mechanism of sex determination in dioecious plants will shed light on our understanding of gene regulation and evolution of plant dioecy. Perspectives concerning the evolutionary pathway of plant dioecy are also suggested.
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Affiliation(s)
- Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Department of Molecular of Biology, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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Renner SS, Müller NA. Sex determination and sex chromosome evolution in land plants. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210210. [PMID: 35306895 PMCID: PMC8935313 DOI: 10.1098/rstb.2021.0210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/19/2022] [Indexed: 01/02/2023] Open
Abstract
Linnaeus's very first opus, written when he was 22 years old, dealt with the analogy that exists between plants and animals in how they 'propagate their species', and a revised version with a plate depicting the union of male and female Mercurialis annua plants became a foundational text on the sexuality of plants. The question how systems with separate males and females have evolved in sedentary organisms that appear ancestrally bisexual has fascinated biologists ever since. The phenomenon, termed dioecy, has important consequences for plant reproductive success and is of commercial interest since it affects seed quality and fruit production. This theme issue presents a series of articles that synthesize and challenge the current understanding of how plants achieve dioecy. The articles deal with a broad set of taxa, including Coccinia, Ginkgo, Mercurialis, Populus, Rumex and Silene, as well as overarching topics, such as the field's terminology, analogies with animal sex determination systems, evolutionary pathways to dioecy, dosage compensation, and the longevity of the two sexes. In this introduction, we focus on four topics, each addressed by several articles from different angles and with different conclusions. Our highlighting of unclear or controversial issues may help future studies to build on the current understanding and to ask new questions that will expand our knowledge of plant sexual systems. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Susanne S. Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Niels A. Müller
- Thünen-Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
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