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Borkhert EV, Pushkova EN, Nasimovich YA, Kostina MV, Vasilieva NV, Murataev RA, Novakovskiy RO, Dvorianinova EM, Povkhova LV, Zhernova DA, Turba AA, Sigova EA, Snezhkina AV, Kudryavtseva AV, Bolsheva NL, Krasnov GS, Dmitriev AA, Melnikova NV. Sex-determining region complements traditionally used in phylogenetic studies nuclear and chloroplast sequences in investigation of Aigeiros Duby and Tacamahaca Spach poplars (genus Populus L., Salicaceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1204899. [PMID: 37860260 PMCID: PMC10582643 DOI: 10.3389/fpls.2023.1204899] [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: 04/12/2023] [Accepted: 08/07/2023] [Indexed: 10/21/2023]
Abstract
Members of the genus Populus L. play an important role in the formation of forests in the northern hemisphere and are used in urban landscaping and timber production. Populus species of closely related sections show extensive hybridization. Therefore, the systematics of the genus is rather complicated, especially for poplars of hybrid origin. We aimed to assess the efficiency of application of the sex-determining region (SDR) in addition to the nuclear and chloroplast genome loci traditionally used in phylogenetic studies of poplars to investigate relationships in sections Aigeiros Duby and Tacamahaca Spach. Targeted deep sequencing of NTS 5S rDNA, ITS, DSH 2, DSH 5, DSH 8, DSH 12, DSH 29, 6, 15, 16, X18, trnG-psbK-psbI, rps2-rpoC2, rpoC2-rpoC1, as well as SDR and ARR17 gene was performed for 379 poplars. The SDR and ARR17 gene together with traditionally used multicopy and single-copy loci of nuclear and chloroplast DNA allowed us to obtain a clustering that is most consistent with poplar systematics based on morphological data and to shed light on several controversial hypotheses about the origin of the studied taxa (for example, the inexpediency of separating P. koreana, P. maximowiczii, and P. suaveolens into different species). We present a scheme of relationships between species and hybrids of sections Aigeiros and Tacamahaca based on molecular genetic, morphological, and geographical data. The geographical proximity of species and, therefore, the possibility of hybridization between them appear to be more important than the affiliation of species to the same section. We speculate that sections Aigeiros and Tacamahaca are distinguished primarily on an ecological principle (plain and mountain poplars) rather than on a genetic basis. Joint analysis of sequencing data for the SDR and chloroplast genome loci allowed us to determine the ancestors of P. × petrovskoe - P. laurifolia (female tree) × P. × canadensis (male tree), and P. × rasumovskoe - P. nigra (female tree) × P. suaveolens (male tree). Thus, the efficiency of using the SDR for the study of poplars of sections Aigeiros and Tacamahaca and the prospects of its use for the investigation of species of the genus Populus were shown.
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Affiliation(s)
- Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri A. Nasimovich
- State Environmental Protection Budgetary Institution of Moscow “Mospriroda”, Moscow, Russia
| | - Marina V. Kostina
- Institute of Biology and Chemistry, Moscow Pedagogical State University, Moscow, Russia
| | | | - Ramil A. Murataev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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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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Zhao Y, Liu G, Wang Z, Ning Y, Ni R, Xi M. Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly. Int J Mol Sci 2023; 24:9950. [PMID: 37373099 DOI: 10.3390/ijms24129950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Poplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of Populus simonii which is a Chinese native species with many excellent traits. This karyotype was anchored by oligonucleotide (oligo)-based chromosome specific painting probes, a centromere-specific repeat (Ps34), ribosomal DNA, and telomeric DNA. We updated the known karyotype formula for P. simonii to 2n = 2x = 38 = 26m + 8st + 4t and the karyotype was 2C. The fluorescence in situ hybridization (FISH) results revealed some errors in the current P. simonii genome assembly. The 45S rDNA loci were located at the end of the short arm of chromosomes 8 and 14 by FISH. However, they were assembled on pseudochromosomes 8 and 15. In addition, the Ps34 loci were distributed in every centromere of the P. simonii chromosome in the FISH results, but they were only found to be present in pseudochromosomes 1, 3, 6, 10, 16, 17, 18, and 19. Our results reveal that pachytene chromosomes oligo-FISH is a powerful tool for constructing high-resolution karyotypes and improving the quality of genome assembly.
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Affiliation(s)
- Yilian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Guangxin Liu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Ziyue Wang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yihang Ning
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Runxin Ni
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Mengli Xi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
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Li Y, Wang D, Wang W, Yang W, Gao J, Zhang W, Shan L, Kang M, Chen Y, Ma T. A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination. Mol Ecol 2023; 32:1366-1380. [PMID: 35712997 DOI: 10.1111/mec.16566] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/24/2022] [Accepted: 06/10/2022] [Indexed: 01/17/2023]
Abstract
Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.
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Affiliation(s)
- Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Weiwei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jinwen Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenyan Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lanxing Shan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China
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Wang Y, Cai X, Zhang Y, Hörandl E, Zhang Z, He L. The male-heterogametic sex determination system on chromosome 15 of Salix triandra and Salix arbutifolia reveals ancestral male heterogamety and subsequent turnover events in the genus Salix. Heredity (Edinb) 2023; 130:122-134. [PMID: 36593355 PMCID: PMC9981616 DOI: 10.1038/s41437-022-00586-2] [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: 09/14/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/03/2023] Open
Abstract
Dioecious Salix evolved more than 45 million years ago, but have homomorphic sex chromosomes, suggesting that turnover event(s) prevented major differentiation. Sex chromosome turnover events have been inferred in the sister genus Populus. The genus Salix includes two main clades, Salix and Vetrix, with several previously studied Vetrix clade species having female-heterogametic (ZW) or male-heterogametic (XY) sex-determining systems (SDSs) on chromosome 15, while three Salix clade species have XY SDSs on chromosome 7. We here studied two basal taxa of the Vetrix clade, S. arbutifolia and S. triandra using S. purpurea as the reference genome. Analyses of whole genome resequencing data for genome-wide associations (GWAS) with the sexes and genetic differentiation between the sexes (FST values) showed that both species have male heterogamety with a sex-determining locus on chromosome 15, suggesting an early turnover event within the Vetrix clade, perhaps promoted by sexually antagonistic or (and) sex-ratio selection. Changepoint analysis based on FST values identified small sex-linked regions of ~3.33 Mb and ~2.80 Mb in S. arbutifolia and S. triandra, respectively. The SDS of S. arbutifolia was consistent with recent results that used its own genome as reference. Ancestral state reconstruction of SDS suggests that at least two turnover events occurred in Salix.
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Affiliation(s)
- Yi Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xinjie Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yue Zhang
- Shenyang Arboretum, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
| | - Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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Leite Montalvão AP, Kersten B, Kim G, Fladung M, Müller NA. ARR17 controls dioecy in Populus by repressing B-class MADS-box gene expression. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210217. [PMID: 35306887 PMCID: PMC8935312 DOI: 10.1098/rstb.2021.0217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The number of dioecious species for which the genetic basis of sex determination has been resolved is rapidly increasing. Nevertheless, the molecular mechanisms downstream of the sex determinants remain largely elusive. Here, by RNA-sequencing early-flowering isogenic aspen (Populus tremula) lines differing exclusively for the sex switch gene ARR17, we show that a narrowly defined genetic network controls differential development of female and male flowers. Although ARR17 encodes a type-A response regulator supposedly involved in cytokinin (CK) hormone signalling, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated arr17 knockout only affected the expression of a strikingly small number of genes, indicating a specific role in the regulation of floral development rather than a generic function in hormone signalling. Notably, the UNUSUAL FLORAL ORGANS (UFO) gene, encoding an F-box protein acting as a transcriptional cofactor with LEAFY (LFY) to activate B-class MADS-box gene expression, and the B-class gene PISTILLATA (PI), necessary for male floral organ development, were strongly de-repressed in the arr17 CRISPR mutants. Our data highlight a CK-independent role of the poplar response regulator ARR17 and further emphasize the minimal differences between female and male individuals. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Ana P Leite Montalvão
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Gihwan Kim
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
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Hallingbäck HR, Pucholt P, Ingvarsson PK, Rönnberg-Wästljung AC, Berlin S. Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis. BMC Genomics 2021; 22:710. [PMID: 34600471 PMCID: PMC8487499 DOI: 10.1186/s12864-021-08021-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/14/2021] [Indexed: 01/24/2023] Open
Abstract
Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher’s exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08021-2.
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Affiliation(s)
- Henrik R Hallingbäck
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden.,Present Address: Skogforsk (The Forestry Research Institute of Sweden), Uppsala Science Park, SE-751 83, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
| | - Ann Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden.
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
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Melnikova NV, Pushkova EN, Dvorianinova EM, Beniaminov AD, Novakovskiy RO, Povkhova LV, Bolsheva NL, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Dmitriev AA. Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica. FRONTIERS IN PLANT SCIENCE 2021; 12:625416. [PMID: 34567016 PMCID: PMC8455832 DOI: 10.3389/fpls.2021.625416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.
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Affiliation(s)
- Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Artemy D. Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Pushkova EN, Krasnov GS, Lakunina VA, Novakovskiy RO, Povkhova LV, Dvorianinova EM, Beniaminov AD, Fedorova MS, Snezhkina AV, Kudryavtseva AV, Dmitriev AA, Melnikova NV. Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene. Front Genet 2021; 12:676935. [PMID: 34456967 PMCID: PMC8385651 DOI: 10.3389/fgene.2021.676935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/28/2021] [Indexed: 12/04/2022] Open
Abstract
Transcriptome sequencing of leaves, catkin axes, and flowers from male and female trees of Populus × sibirica and genome sequencing of the same plants were performed for the first time. The availability of both genome and transcriptome sequencing data enabled the identification of allele-specific expression. Such an analysis was performed for genes from the sex-determining region (SDR). P. × sibirica is an intersectional hybrid between species from sections Aigeiros (Populus nigra) and Tacamahaca (Populus laurifolia, Populus suaveolens, or Populus × moskoviensis); therefore, a significant number of heterozygous polymorphisms were identified in the SDR that allowed us to distinguish between alleles. In the SDR, both allelic variants of the TCP (T-complex protein 1 subunit gamma), CLC (Chloride channel protein CLC-c), and MET1 (DNA-methyltransferase 1) genes were expressed in females, while in males, two allelic variants were expressed for TCP and MET1 but only one allelic variant prevailed for CLC. Targeted sequencing of TCP, CLC, and MET1 regions on a representative set of trees confirmed the sex-associated allele-specific expression of the CLC gene in generative and vegetative tissues of P. × sibirica. Our study brings new knowledge on sex-associated differences in Populus species.
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Affiliation(s)
- Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Valentina A Lakunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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10
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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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11
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Yang W, Wang D, Li Y, Zhang Z, Tong S, Li M, Zhang X, Zhang L, Ren L, Ma X, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, Liu J, DiFazio SP, Olson M, Ma T. A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae. Mol Biol Evol 2021; 38:968-980. [PMID: 33027519 PMCID: PMC7947767 DOI: 10.1093/molbev/msaa261] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.
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Affiliation(s)
- Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhiyang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Liwen Ren
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin—Madison, Madison, WI
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | | | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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12
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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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13
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Xue L, Wu H, Chen Y, Li X, Hou J, Lu J, Wei S, Dai X, Olson MS, Liu J, Wang M, Charlesworth D, Yin T. Evidences for a role of two Y-specific genes in sex determination in Populus deltoides. Nat Commun 2020; 11:5893. [PMID: 33208755 PMCID: PMC7674411 DOI: 10.1038/s41467-020-19559-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Almost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene's expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera.
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Affiliation(s)
- Liangjiao Xue
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Huaitong Wu
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Yingnan Chen
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Xiaoping Li
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Jing Hou
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Jing Lu
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Suyun Wei
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Xiaogang Dai
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Mingxiu Wang
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.
| | - Tongming Yin
- The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, 200137, Nanjing, China.
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14
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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: 98] [Impact Index Per Article: 24.5] [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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15
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Li W, Wu H, Li X, Chen Y, Yin T. Fine mapping of the sex locus in Salix triandra confirms a consistent sex determination mechanism in genus Salix. HORTICULTURE RESEARCH 2020; 7:64. [PMID: 32377355 PMCID: PMC7193568 DOI: 10.1038/s41438-020-0289-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 05/19/2023]
Abstract
Salix triandra belongs to section Amygdalinae in genus Salix, which is in a different section from the willow species in which sex determination has been well studied. Studying sex determination in distantly related willow species will help to clarify whether the sexes of different willows arise through a common sex determination system. For this purpose, we generated an intraspecific full-sib F1 population for S. triandra and constructed high-density genetic linkage maps for the crossing parents using restriction site-associated DNA sequencing and following a two-way pseudo-testcross strategy. With the established maps, the sex locus was positioned in linkage group XV only in the maternal map, and no sex linkage was detected in the paternal map. Consistent with previous findings in other willow species, our study showed that chromosome XV was the incipient sex chromosome and that females were the heterogametic sex in S. triandra. Therefore, sex in this willow species is also determined through a ZW sex determination system. We further performed fine mapping in the vicinity of the sex locus with SSR markers. By comparing the physical and genetic distances for the target interval encompassing the sex determination gene confined by SSRs, severe recombination repression was revealed in the sex determination region in the female map. The recombination rate in the confined interval encompassing the sex locus was approximately eight-fold lower than the genome-wide average. This study provides critical information relevant to sex determination in S. triandra.
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Affiliation(s)
- Wei Li
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Huaitong Wu
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Xiaoping Li
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Yingnan Chen
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Tongming Yin
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
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16
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Sabatti M, Gaudet M, Müller NA, Kersten B, Gaudiano C, Scarascia Mugnozza G, Fladung M, Beritognolo I. Long-term study of a subdioecious Populus ×canescens family reveals sex lability of females and reproduction behaviour of cosexual plants. PLANT REPRODUCTION 2020; 33:1-17. [PMID: 31650409 DOI: 10.1007/s00497-019-00378-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Cosexual Populus ×canescens plants are inconstant females with life course plasticity of sex phenotype and can reproduce by selfing. Populus species are dioecious, but deviations from dioecy are reported in some cases. The objectives of this study were to investigate the phenotypic expression and the inheritance of subdioecy in a Populus ×canescens pedigree. The F1 progeny was monitored for sex during 14 years. Thirty per cent of individuals expressed deviations from dioecy and long-term plasticity of sex. Some plants started flowering as male, then became cosexual, and finally turned female. Two cosexual individuals were self-pollinated and generated a selfed progeny markedly impaired by inbreeding depression, but able to reproduce by outcrossing. Sex segregation of the F1 progeny statistically fitted the expected ratio 1:2:1 (female:male:cosexual). By analysis of DNA markers, the cosexual individuals were genetically clustered with the females. The segregation ratio and the genetic profile indicated that cosexual plants were female with altered sex phenotype. Linkage analysis identified a putative sex-determining region with suppressed recombination on chromosome 19 of the male Populus tremula parent. The male sex trait was linked to the pericentromeric region of the P. tremula chromosome 19, whereas the cosexual trait was linked to chromosome 19 of the female Populus alba parent. A genetic model is proposed to explain inheritance and phenotypic expression of sex.
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Affiliation(s)
- Maurizio Sabatti
- Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy.
| | - Muriel Gaudet
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Porano, TR, Italy
| | - Niels A Müller
- Thünen-Institute of Forest Genetics, Sieker Landstr.2, 22927, Grosshansdorf, Germany
| | - Birgit Kersten
- Thünen-Institute of Forest Genetics, Sieker Landstr.2, 22927, Grosshansdorf, Germany
| | - Cosimo Gaudiano
- Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Giuseppe Scarascia Mugnozza
- Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Matthias Fladung
- Thünen-Institute of Forest Genetics, Sieker Landstr.2, 22927, Grosshansdorf, Germany
| | - Isacco Beritognolo
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Porano, TR, Italy
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17
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Li MM, Wang DY, Zhang L, Kang MH, Lu ZQ, Zhu RB, Mao XX, Xi ZX, Tao M. Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics. Int J Mol Sci 2019; 20:ijms20153788. [PMID: 31382526 PMCID: PMC6696080 DOI: 10.3390/ijms20153788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022] Open
Abstract
Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.
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Affiliation(s)
- Meng-Meng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - De-Yan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ming-Hui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhi-Qiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Ren-Bin Zhu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Xing-Xing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhen-Xiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ma Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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18
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Lu H, Klocko AL, Brunner AM, Ma C, Magnuson AC, Howe GT, An X, Strauss SH. RNA interference suppression of AGAMOUS and SEEDSTICK alters floral organ identity and impairs floral organ determinacy, ovule differentiation, and seed-hair development in Populus. THE NEW PHYTOLOGIST 2019; 222:923-937. [PMID: 30565259 PMCID: PMC6590139 DOI: 10.1111/nph.15648] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/09/2018] [Indexed: 05/24/2023]
Abstract
The role of the floral homeotic gene AGAMOUS (AG) and its close homologues in development of anemophilous, unisexual catkins has not previously been studied. We transformed two RNA interference (RNAi) constructs, PTG and its matrix-attachment-region flanked version MPG, into the early-flowering female poplar clone 6K10 (Populus alba) to suppress the expression of its two duplicate AG orthologues. By early 2018, six out of 22 flowering PTG events and 11 out of 12 flowering MPG events showed modified floral phenotypes in a field trial in Oregon, USA. Flowers in catkins from modified events had 'carpel-inside-carpel' phenotypes. Complete disruption of seed production was observed in seven events, and sterile anther-like organs in 10 events. Events with strong co-suppression of both the two AG and two SEEDSTICK (STK) paralogues lacked both seeds and associated seed hairs. Alterations in all of the modified floral phenotypes were stable over 4 yr of study. Trees from floral-modified events did not differ significantly (P < 0.05) from nonmodified transgenic or nontransgenic controls in biomass growth or leaf morphology. AG and STK genes show strong conservation of gene function during poplar catkin development and are promising targets for genetic containment of exotic or genetically engineered trees.
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Affiliation(s)
- Haiwei Lu
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Amy L. Klocko
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
- Department of BiologyUniversity of Colorado Colorado SpringsColorado SpringsCO80918USA
| | - Amy M. Brunner
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVA24061USA
| | - Cathleen Ma
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Anna C. Magnuson
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Glenn T. Howe
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
| | - Xinmin An
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and BiotechnologyBeijing Forestry UniversityBeijing100083China
| | - Steven H. Strauss
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOR97331USA
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19
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Melnikova NV, Kudryavtseva AV, Borkhert EV, Pushkova EN, Fedorova MS, Snezhkina AV, Krasnov GS, Dmitriev AA. Sex-specific polymorphism of MET1 and ARR17 genes in Populus × sibirica. Biochimie 2019; 162:26-32. [PMID: 30935960 DOI: 10.1016/j.biochi.2019.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/27/2019] [Indexed: 01/25/2023]
Abstract
The genus Populus is an effective model in tree genetics. This genus includes dioecious species and, recently, whole genome resequencing of P. trichocarpa and P. balsamifera enabled the identification of sex-linked regions and sex-associated single nucleotide polymorphisms (SNPs). These results created new opportunities to study sex determination in poplars. In the present work, we performed deep sequencing of genes encoding METHYLTRANSFERASE1 (MET1) and homolog of ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17), which are localized in a sex-linked region of Populus genome and contain a number of sex-associated SNPs. Amplicon libraries for 38 samples of P. × sibirica (19 males and 19 females) were sequenced on MiSeq Illumina (300 nt paired-end reads) and approximately 4000× coverage was obtained for each sample. In total, from 80 to 179 SNPs were detected in poplar individuals for MET1, and from 16 to 49 SNPs were detected for ARR17. We identified 17 sex-specific SNPs (11 in MET1 and 6 in ARR17) - they were present in all males but absent in all females. For identified sex-specific SNP sites, females were homozygous, while males were heterozygous. Moreover, colocation of sex-specific SNPs confirming the XY sex-determination system of poplars was revealed: in one allelic variant, males had the same nucleotides as females, while in the other, sex-specific SNPs were present. Based on the data obtained, we developed and successfully applied a high-resolution melting-based approach for sex identification in poplars. The developed molecular markers are useful for distinguishing between male and female poplars in scientific research and can also be applied to select male-only genotypes for use in city landscaping and production of paper, pulp, and biofuel.
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Affiliation(s)
- Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
| | - Elena V Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
| | - Maria S Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
| | - Anastasiya V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
| | - George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
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20
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Sanderson BJ, Wang L, Tiffin P, Wu Z, Olson MS. Sex-biased gene expression in flowers, but not leaves, reveals secondary sexual dimorphism in Populus balsamifera. THE NEW PHYTOLOGIST 2019; 221:527-539. [PMID: 30252135 DOI: 10.1111/nph.15421] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 06/29/2018] [Indexed: 05/11/2023]
Abstract
Because sexual dimorphism in plants is often less morphologically conspicuous than in animals, studies of sex-biased gene expression may provide a quantitative metric to better address their commonality, molecular pathways, consistency across tissues and taxa, and evolution. The presence of sex-biased gene expression in tissues other than the androecium or gynoecium, termed secondary sexual characters, suggests that these traits arose after the initial evolution of dioecy. Patterns of sequence evolution may provide evidence of positive selection that drove sexual specialization. We compared gene expression in male and female flowers and leaves of Populus balsamifera to assess the extent of sex-biased expression, and tested whether sex-biased genes exhibit elevated rates of protein evolution. Sex-biased expression was pervasive in floral tissue, but nearly absent in leaf tissue. Female-biased genes in flowers were associated with photosynthesis, whereas male-biased genes were associated with mitochondrial function. Sex-biased genes did not exhibit elevated rates of protein evolution, contrary to results from other studies in animals and plants. Our results suggest that the ecological and physiological constraints associated with the energetics of flowering, rather than sexual conflict, have probably shaped the differences in male and female gene expression in P. balsamifera.
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Affiliation(s)
- Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
| | - Li Wang
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Zhiqiang Wu
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
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21
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Hobza R, Hudzieczek V, Kubat Z, Cegan R, Vyskot B, Kejnovsky E, Janousek B. Sex and the flower - developmental aspects of sex chromosome evolution. ANNALS OF BOTANY 2018; 122:1085-1101. [PMID: 30032185 PMCID: PMC6324748 DOI: 10.1093/aob/mcy130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/13/2018] [Indexed: 05/07/2023]
Abstract
Background The evolution of dioecious plants is occasionally accompanied by the establishment of sex chromosomes: both XY and ZW systems have been found in plants. Structural studies of sex chromosomes are now being followed up by functional studies that are gradually shedding light on the specific genetic and epigenetic processes that shape the development of separate sexes in plants. Scope This review describes sex determination diversity in plants and the genetic background of dioecy, summarizes recent progress in the investigation of both classical and emerging model dioecious plants and discusses novel findings. The advantages of interspecies hybrids in studies focused on sex determination and the role of epigenetic processes in sexual development are also overviewed. Conclusions We integrate the genic, genomic and epigenetic levels of sex determination and stress the impact of sex chromosome evolution on structural and functional aspects of plant sexual development. We also discuss the impact of dioecy and sex chromosomes on genome structure and expression.
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Affiliation(s)
- Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Vojtech Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Radim Cegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Bohuslav Janousek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
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22
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Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proc Natl Acad Sci U S A 2018; 115:E10970-E10978. [PMID: 30373829 PMCID: PMC6243237 DOI: 10.1073/pnas.1801437115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We performed de novo, full-genome sequence analysis of two Populus species, North American quaking and Eurasian trembling aspen, that contain striking levels of genetic variation. Our results showed that positive and negative selection broadly affects patterns of genomic variation, but to varying degrees across coding and noncoding regions. The strength of selection and rates of sequence divergence were strongly related to differences in gene expression and coexpression network connectivity. These results highlight the importance of both positive and negative selection in shaping genome-wide levels of genetic variation in an obligately outcrossing, perennial plant. The resources we present establish aspens as a powerful study system enabling future studies for understanding the genomic determinants of adaptive evolution. The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).
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23
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Zhang L, Xi Z, Wang M, Guo X, Ma T. Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows. Ecol Evol 2018; 8:7817-7823. [PMID: 30250665 PMCID: PMC6145263 DOI: 10.1002/ece3.4261] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/27/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022] Open
Abstract
Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well-resolved phylogeny from the perspective of the plastomes.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Zhenxiang Xi
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Mingcheng Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Xinyi Guo
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
| | - Tao Ma
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuanChina
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24
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Zhou R, Macaya-Sanz D, Rodgers-Melnick E, Carlson CH, Gouker FE, Evans LM, Schmutz J, Jenkins JW, Yan J, Tuskan GA, Smart LB, DiFazio SP. Characterization of a large sex determination region in Salix purpurea L. (Salicaceae). Mol Genet Genomics 2018; 293:1437-1452. [PMID: 30022352 DOI: 10.1007/s00438-018-1473-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022]
Abstract
Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region. We demonstrate that Salix purpurea also has a ZW system on chromosome 15. The sex determination region has reduced recombination, high structural polymorphism, an abundance of transposable elements, and contains genes that are involved in sex expression in other plants. We also show that chromosome 19 contains sex-associated markers in this S. purpurea assembly, along with other autosomes. This raises the intriguing possibility of a translocation of the sex determination region within the Salicaceae lineage, suggesting a common evolutionary origin of the Populus and Salix sex determination loci.
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Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Luke M Evans
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA.,Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Juying Yan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.,Biosciences Division, Oak Ridge National Lab, Oak Ridge, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA.
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25
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Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 2018. [PMID: 29520650 DOI: 10.1007/s00412-018-0664-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dioecious species accounted for 6% of all plant species, including a number of crops and economically important species, such as poplar. However, sex determination and sex chromosome evolution have been studied only in few dioecious species. In poplar, the sex-determining locus was mapped to chromosome 19. Interestingly, this locus was mapped to either a peritelomeric or a centromeric region among different poplar species. We developed an oligonucleotide (oligo)-based chromosome painting probe based on the sequence of chromosome 19 from Populus trichocarpa. We performed chromosome painting in P. tomentosa and P. deltoides. Surprisingly, the distal end on the short arm of chromosome 19, which corresponds to the location of the sex-determining locus reported in several species, was not painted in both species. Thus, the DNA sequences associated with this region have not been anchored to the current chromosome 19 pseudomolecule, which was confirmed by painting of somatic metaphase chromosome 19 of P. trichocarpa. Interestingly, the unpainted distal ends of the two chromosome 19 did not pair at the pachytene stage in 22-24% of the meiotic cells in the two species, suggest that these regions from the sex chromosomes have structurally diverged from each other, resulting in the reduced pairing frequency. These results shed light on divergence of a pair of young sex chromosomes in poplar.
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26
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Pucholt P, Wright AE, Conze LL, Mank JE, Berlin S. Recent Sex Chromosome Divergence despite Ancient Dioecy in the Willow Salix viminalis. Mol Biol Evol 2018; 34:1991-2001. [PMID: 28453634 PMCID: PMC5850815 DOI: 10.1093/molbev/msx144] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Sex chromosomes can evolve when recombination is halted between a pair of chromosomes, and this can lead to degeneration of the sex-limited chromosome. In the early stages of differentiation sex chromosomes are homomorphic, and even though homomorphic sex chromosomes are very common throughout animals and plants, we know little about the evolutionary forces shaping these types of sex chromosomes. We used DNA- and RNA-Seq data from females and males to explore the sex chromosomes in the female heterogametic willow, Salix viminalis, a species with ancient dioecy but with homomorphic sex chromosomes. We detected no major sex differences in read coverage in the sex determination (SD) region, indicating that the W region has not significantly degenerated. However, single nucleotide polymorphism densities in the SD region are higher in females compared with males, indicating very recent recombination suppression, followed by the accumulation of sex-specific single nucleotide polymorphisms. Interestingly, we identified two female-specific scaffolds that likely represent W-chromosome-specific sequence. We show that genes located in the SD region display a mild excess of male-biased expression in sex-specific tissue, and we use allele-specific gene expression analysis to show that this is the result of masculinization of expression on the Z chromosome rather than degeneration of female-expression on the W chromosome. Together, our results demonstrate that insertion of small DNA fragments and accumulation of sex-biased gene expression can occur before the detectable decay of the sex-limited chromosome.
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Affiliation(s)
- Pascal Pucholt
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alison E Wright
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Lei Liu Conze
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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27
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Reisser CMO, Fasel D, Hürlimann E, Dukic M, Haag-Liautard C, Thuillier V, Galimov Y, Haag CR. Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome. Mol Biol Evol 2017; 34:575-588. [PMID: 28007974 DOI: 10.1093/molbev/msw251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species of Daphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations of D. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, including transformer2 and sox9. Taken together, the region determining the genetic females shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes. D. magna is a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.
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Affiliation(s)
- Céline M O Reisser
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, CNRS Université de Montpellier Université Paul-Valéry Montpellier EPHE, Montpellier, France.,Université de Fribourg, Ecology and Evolution, Fribourg, Switzerland.,IFREMER Centre du Pacifique, Taravao, Tahiti, Polynésie Française
| | - Dominique Fasel
- Université de Fribourg, Ecology and Evolution, Fribourg, Switzerland
| | - Evelin Hürlimann
- Université de Fribourg, Ecology and Evolution, Fribourg, Switzerland
| | - Marinela Dukic
- Universität Basel, Zoology Institute, Evolutionary Biology, Basel, Switzerland
| | | | | | - Yan Galimov
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive CEFE UMR 5175, CNRS Université de Montpellier Université Paul-Valéry Montpellier EPHE, Montpellier, France.,Université de Fribourg, Ecology and Evolution, Fribourg, Switzerland
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28
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Sousa A, Fuchs J, Renner SS. Cytogenetic comparison of heteromorphic and homomorphic sex chromosomes in Coccinia (Cucurbitaceae) points to sex chromosome turnover. Chromosome Res 2017; 25:191-200. [PMID: 28343268 DOI: 10.1007/s10577-017-9555-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/17/2017] [Accepted: 02/27/2017] [Indexed: 11/26/2022]
Abstract
Our understanding of the evolution of plant sex chromosomes is increasing rapidly due to high-throughput sequencing data and phylogenetic and molecular-cytogenetic approaches that make it possible to infer the evolutionary direction and steps leading from homomorphic to heteromorphic sex chromosomes. Here, we focus on four species of Coccinia, a genus of 25 dioecious species, including Coccinia grandis, the species with the largest known plant Y chromosome. Based on a phylogeny for the genus, we selected three species close to C. grandis to test the distribution of eight repetitive elements including two satellites, and several plastid and mitochondrial probes, that we had previously found to have distinct accumulation patterns in the C. grandis genome. Additionally, we determined C-values and performed immunostaining experiments with (peri-)centromere-specific antibodies on two species (for comparison with C. grandis). In spite of no microscopic chromosomal heteromorphism, single pairs of chromosomes in male cells of all three species accumulate some of the very same repeats that are enriched on the C. grandis Y chromosome, pointing to either old (previous) sex chromosomes or incipient (newly arising) ones, that is, to sex chromosome turnover. A 144-bp centromeric satellite repeat (CgCent) that characterizes all C. grandis chromosomes except the Y is highly abundant in all centromeric regions of the other species, indicating that the centromeric sequence of the Y chromosome diverged very recently.
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Affiliation(s)
- Aretuza Sousa
- Department of Biology, University of Munich (LMU), 80638, Munich, Germany.
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Susanne S Renner
- Department of Biology, University of Munich (LMU), 80638, Munich, Germany.
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29
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Harkess A, Leebens-Mack J. A Century of Sex Determination in Flowering Plants. J Hered 2016; 108:69-77. [PMID: 27974487 DOI: 10.1093/jhered/esw060] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 09/07/2016] [Indexed: 11/14/2022] Open
Abstract
Plants have evolved a diverse array of strategies for sexual reproduction, particularly through the modification of male and female organs at distinct points in development. The immense variation in sexual systems across the land plants provides a unique opportunity to study the genetic, epigenetic, phylogenetic, and ecological underpinnings of sex determination. Here, we reflect on more than a century of research into flowering plant sex determination, placing a particular focus on the foundational genetic and cytogenetic observations, experiments, and hypotheses. Building on the seminal work on the genetics of plant sex, modern comparative genomic analyses now allow us to address longstanding questions about sex determination and the origins of sex chromosomes.
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Affiliation(s)
- Alex Harkess
- From the Department of Plant Biology, University of Georgia, Athens, GA 30602 (Harkess and Leebens-Mack), Alex Harkess is now at the Donald Danforth Plant Science Center, St. Louis MO 63132.
| | - Jim Leebens-Mack
- From the Department of Plant Biology, University of Georgia, Athens, GA 30602 (Harkess and Leebens-Mack), Alex Harkess is now at the Donald Danforth Plant Science Center, St. Louis MO 63132
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Takahata S, Yago T, Iwabuchi K, Hirakawa H, Suzuki Y, Onodera Y. Comparison of Spinach Sex Chromosomes with Sugar Beet Autosomes Reveals Extensive Synteny and Low Recombination at the Male-Determining Locus. J Hered 2016; 107:679-685. [PMID: 27563071 DOI: 10.1093/jhered/esw055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 08/22/2016] [Indexed: 01/06/2023] Open
Abstract
Spinach (Spinacia oleracea, 2n = 12) and sugar beet (Beta vulgaris, 2n = 18) are important crop members of the family Chenopodiaceae ss Sugar beet has a basic chromosome number of 9 and a cosexual breeding system, as do most members of the Chenopodiaceae ss. family. By contrast, spinach has a basic chromosome number of 6 and, although certain cultivars and genotypes produce monoecious plants, is considered to be a dioecious species. The loci determining male and monoecious sexual expression were mapped to different loci on the spinach sex chromosomes. In this study, a linkage map with 46 mapped protein-coding sequences was constructed for the spinach sex chromosomes. Comparison of the linkage map with a reference genome sequence of sugar beet revealed that the spinach sex chromosomes exhibited extensive synteny with sugar beet chromosomes 4 and 9. Tightly linked protein-coding genes linked to the male-determining locus in spinach corresponded to genes located in or around the putative pericentromeric and centromeric regions of sugar beet chromosomes 4 and 9, supporting the observation that recombination rates were low in the vicinity of the male-determining locus. The locus for monoecism was confined to a chromosomal segment corresponding to a region of approximately 1.7Mb on sugar beet chromosome 9, which may facilitate future positional cloning of the locus.
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Affiliation(s)
- Satoshi Takahata
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Takumi Yago
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Keisuke Iwabuchi
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Hideki Hirakawa
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Yutaka Suzuki
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Yasuyuki Onodera
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki).
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Moore RC, Harkess AE, Weingartner LA. How to be a seXY plant model: A holistic view of sex-chromosome research. AMERICAN JOURNAL OF BOTANY 2016; 103:1379-1382. [PMID: 27370315 DOI: 10.3732/ajb.1600054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/11/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Richard C Moore
- Miami University, Department of Botany, 316 Pearson Hall, Oxford, Ohio 45056 USA
| | - Alex E Harkess
- University of Georgia, Department of Plant Biology, 120 Carlton St, Athens, Georgia 30602 USA
| | - Laura A Weingartner
- Indiana University, Department of Biology, 1001 E Third St., Bloomington, Indiana 47405 USA
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Breeding Systems, Mating Systems, and Genomics of Gender Determination in Angiosperm Trees. COMPARATIVE AND EVOLUTIONARY GENOMICS OF ANGIOSPERM TREES 2016. [DOI: 10.1007/7397_2016_21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB. Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Mol Ecol 2015; 24:3243-56. [PMID: 25728270 DOI: 10.1111/mec.13126] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/15/2015] [Accepted: 02/19/2015] [Indexed: 12/16/2022]
Abstract
All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.
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Affiliation(s)
- A Geraldes
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - C A Hefer
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - A Capron
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - N Kolosova
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - F Martinez-Nuñez
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - R Y Soolanayakanahally
- Agroforestry Development Centre, Agriculture and Agri-Food Canada, Indian Head, SK, S0G 2K0, Canada
| | - B Stanton
- Greenwood Resources, Portland, OR, 97201, USA
| | - R D Guy
- Department of Forest and Conservation Sciences, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - S D Mansfield
- Department of Wood Science, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - C J Douglas
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Q C B Cronk
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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Pucholt P, Rönnberg-Wästljung AC, Berlin S. Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.). Heredity (Edinb) 2015; 114:575-83. [PMID: 25649501 PMCID: PMC4434249 DOI: 10.1038/hdy.2014.125] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/17/2014] [Accepted: 11/27/2014] [Indexed: 01/20/2023] Open
Abstract
Most eukaryotes reproduce sexually and a wealth of different sex determination mechanisms have evolved in this lineage. Dioecy or separate sexes are rare among flowering plants but have repeatedly evolved from hermaphroditic ancestors possibly involving male or female sterility mutations. Willows (Salix spp.) and poplars (Populus spp.) are predominantly dioecious and are members of the Salicaceae family. All studied poplars have sex determination loci on chromosome XIX, however, the position differs among species and both male and female heterogametic system exists. In contrast to the situation in poplars, knowledge of sex determination mechanisms in willows is sparse. In the present study, we have for the first time positioned the sex determination locus on chromosome XV in S. viminalis using quantitative trait locus mapping. All female offspring carried a maternally inherited haplotype, suggesting a system of female heterogamety or ZW. We used a comparative mapping approach and compared the positions of the markers between the S. viminalis linkage map and the physical maps of S. purpurea, S. suchowensis and P. trichocarpa. As we found no evidence for chromosomal rearrangements between chromosome XV and XIX between S. viminalis and P. trichocarpa, it shows that the sex determination loci in the willow and the poplar most likely do not share a common origin and has thus evolved separately. This demonstrates that sex determination mechanisms in the Salicaceae family have a high turnover rate and as such it is excellent for studies of evolutionary processes involved in sex chromosome turnover.
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Affiliation(s)
- P Pucholt
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - A-C Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - S Berlin
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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Pakull B, Kersten B, Lüneburg J, Fladung M. A simple PCR-based marker to determine sex in aspen. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:256-61. [PMID: 24943351 DOI: 10.1111/plb.12217] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/25/2014] [Indexed: 05/24/2023]
Abstract
The genus Populus features a genetically controlled sex determination system, located on chromosome 19. However, different Populus species vary in the position of the sex-linked region on the respective chromosome and the apparent heterogametic sex, and the precise mechanism of sex determination in Populus is still unknown. Using next generation sequencing of pooled samples of male and female aspens, we identified the aspen homologue of the P. trichocarpa gene Potri.019G047300 ('TOZ19') to be male-specific. While in P. tremuloides, the complete gene is missing in the genome of female plants, a short fragment of the 3'-part of the gene is still present in P. tremula females. The male-specific presence and transcription of TOZ19 was further verified using PCR in various different aspen individuals and RT-PCR expression analysis. TOZ19 is potentially involved in early steps of flower development, and represents an interesting candidate gene for involvement in sex determination in aspen. Regardless of its role as candidate gene, TOZ19 represents an ideal marker for determination of the sex of non-flowering aspen individuals or seedlings.
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Affiliation(s)
- B Pakull
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
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Robinson KM, Delhomme N, Mähler N, Schiffthaler B, Önskog J, Albrectsen BR, Ingvarsson PK, Hvidsten TR, Jansson S, Street NR. Populus tremula (European aspen) shows no evidence of sexual dimorphism. BMC PLANT BIOLOGY 2014; 14:276. [PMID: 25318822 PMCID: PMC4203875 DOI: 10.1186/s12870-014-0276-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 10/06/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Evolutionary theory suggests that males and females may evolve sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. Such sexual dimorphism would result in sex biased gene expression patterns in non-floral organs for autosomal genes associated with the control and development of such phenotypic traits. RESULTS We examined morphological, biochemical and herbivory traits to test for sexually dimorphic resource allocation strategies within collections of sexually mature and immature Populus tremula (European aspen) trees. In addition we profiled gene expression in mature leaves of sexually mature wild trees using whole-genome oligonucleotide microarrays and RNA-Sequencing. CONCLUSIONS We found no evidence of sexual dimorphism or differential resource investment strategies between males and females in either sexually immature or mature trees. Similarly, single-gene differential expression and machine learning approaches revealed no evidence of large-scale sex biased gene expression. However, two significantly differentially expressed genes were identified from the RNA-Seq data, one of which is a robust diagnostic marker of sex in P. tremula.
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Affiliation(s)
- Kathryn M Robinson
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
| | - Nicolas Delhomme
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
| | - Niklas Mähler
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Bastian Schiffthaler
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
| | - Jenny Önskog
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
| | - Benedicte R Albrectsen
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
- />Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871 Frederiksberg C, Denmark
| | - Pär K Ingvarsson
- />Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
| | - Torgeir R Hvidsten
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Stefan Jansson
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
| | - Nathaniel R Street
- />Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 901 87 Umeå, Sweden
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