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Tan L, Wu DD, Zhang CB, Cheng YR, Sha LN, Fan X, Kang HY, Wang Y, Zhang HQ, Escudero M, Zhou YH. Genome constitution and evolution of Elymus atratus (Poaceae: Triticeae) inferred from cytogenetic and phylogenetic analysis. Genes Genomics 2024; 46:589-599. [PMID: 38536618 DOI: 10.1007/s13258-024-01496-9] [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: 06/27/2023] [Accepted: 01/21/2024] [Indexed: 04/18/2024]
Abstract
BACKGROUND Elymus atratus (Nevski) Hand.-Mazz. is perennial hexaploid wheatgrass. It was assigned to the genus Elymus L. sensu stricto based on morphological characters. Its genome constitution has not been disentangled yet. OBJECTIVE To identify the genome constitution and origin of E. atratus. METHODS In this study, genomic in situ hybridization and fluorescence in situ hybridization, and phylogenetic analysis based on the Acc1, DMC1 and matK sequences were performed. RESULTS Genomic in situ hybridization and fluorescence in situ hybridization results reveal that E. atratus 2n = 6x = 42 is composed of 14 St genome chromosomes, 14 H genome chromosomes, and 14 Y genome chromosomes including two H-Y type translocation chromosomes, suggesting that the genome formula of E. atratus is StStYYHH. The phylogenetic analysis based on Acc1 and DMC1 sequences not only shows that the Y genome originated in a separate diploid, but also suggests that Pseudoroegneria (St), Hordeum (H), and a diploid species with Y genome were the potential donors of E. atratus. Data from chloroplast DNA showed that the maternal donor of E. atratus contains the St genome. CONCLUSION Elymus atratus is an allohexaploid species with StYH genome, which may have originated through the hybridization between an allotetraploid Roegneria (StY) species as the maternal donor and a diploid Hordeum (H) species as the paternal donor.
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Affiliation(s)
- Lu Tan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, 615000, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
| | - Dan-Dan Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Chang-Bing Zhang
- Sichuan Academy of Grassland Science, Chengdu, 610000, Sichuan, China
| | - Yi-Ran Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Li-Na Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Hai-Qin Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
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Chen S, Yan H, Sha L, Chen N, Zhang H, Zhou Y, Fan X. Chloroplast Phylogenomic Analyses Resolve Multiple Origins of the Kengyilia Species (Poaceae: Triticeae) via Independent Polyploidization Events. FRONTIERS IN PLANT SCIENCE 2021; 12:682040. [PMID: 34421940 PMCID: PMC8377392 DOI: 10.3389/fpls.2021.682040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Kengyilia is a group of allohexaploid species that arose from two hybridization events followed by genome doubling of three ancestral diploid species with different genomes St, Y, and P in the Triticeae. Estimating the phylogenetic relationship in resolution of the maternal lineages has been difficult, owing to the extremely low rate of sequence divergence. Here, phylogenetic reconstructions based on the plastome sequences were used to explore the role of maternal progenitors in the establishment of Kengyilia polyploid species. The plastome sequences of 11 Kengyilia species were analyzed together with 12 tetraploid species (PP, StP, and StY) and 33 diploid taxa representing 20 basic genomes in the Triticeae. Phylogenomic analysis and genetic divergence patterns suggested that (1) Kengyilia is closely related to Roegneria, Pseudoroegneria, Agropyron, Lophopyrum, Thinopyrum, and Dasypyrum; (2) both the StY genome Roegneria tetraploids and the PP genome Agropyron tetraploids served as the maternal donors during the speciation of Kengyilia species; (3) the different Kengyilia species derived their StY genome from different Roegneria species. Multiple origins of species via independent polyploidization events have occurred in the genus Kengyilia, resulting in a maternal haplotype polymorphism. This helps explain the rich diversity and wide adaptation of polyploid species in the genus Kengyilia.
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Affiliation(s)
- Shiyong Chen
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hao Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
| | - Ning Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya’an, China
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Chen N, Chen WJ, Yan H, Wang Y, Kang HY, Zhang HQ, Zhou YH, Sun GL, Sha LN, Fan X. Evolutionary patterns of plastome uncover diploid-polyploid maternal relationships in Triticeae. Mol Phylogenet Evol 2020; 149:106838. [PMID: 32304825 DOI: 10.1016/j.ympev.2020.106838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 03/25/2020] [Accepted: 04/09/2020] [Indexed: 10/24/2022]
Abstract
To investigate the diploid-polyploid relationships and the role of maternal progenitors in establishment of polyploid richness in Triticeae, 35 polyploids representing almost all genomic constitutions together with 48 diploid taxa representing 20 basic genomes in the tribe were analyzed. Phylogenomic reconstruction, genetic distance matrix, and nucleotide diversity patterns of plastome sequences indicated that (1) The maternal donor of the annual polyploid species with the U- and D-genome are related to extant Ae. umbellulata and Ae. tauschii, respectively. The maternal donor to the annual polyploid species with the S-, G-, and B-genome originated from the species of Sitopsis section of the genus Aegilops. The annual species with the Xe-containing polyploids were donated by Eremopyrum as the female parent; (2) Pseudoroegneria and Psathyrostachys were the maternal donor of perennial species with the St- and Ns-containing polyploids, respectively; (3) The Lophopyrum, Thinopyrum and Dasypyrum genomes contributed cytoplasm genome to Pseudoroegneria species as a result of incomplete lineage sorting and/or chloroplast captures, and these lineages were genetically transmitted to the St-containing polyploid species via polyploidization; (4) There is a reticulate relationship among the St-containing polyploid species. It can be suggested that genetic heterogeneity might associate with the richness of the polyploids in Triticeae.
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Affiliation(s)
- Ning Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Wen-Jie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China; Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China
| | - Hao Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Gen-Lou Sun
- Biology Department, Saint Mary's University, Halifax NS B3H 3C3, Canada
| | - Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China.
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Wang L, Jiang Y, Shi Q, Wang Y, Sha L, Fan X, Kang H, Zhang H, Sun G, Zhang L, Zhou Y. Genome constitution and evolution of Elytrigia lolioides inferred from Acc1, EF-G, ITS, TrnL-F sequences and GISH. BMC PLANT BIOLOGY 2019; 19:158. [PMID: 31023230 PMCID: PMC6485066 DOI: 10.1186/s12870-019-1779-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/15/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Elytrigia lolioides (Kar. et Kir.) Nevski, which is a perennial, cross-pollinating wheatgrass that is distributed in Russia and Kazakhstan, is classified into Elytrigia, Elymus, and Lophopyrum genera by taxonomists on the basis of different taxonomic classification systems. However, the genomic constitution of E. lolioides is still unknown. To identify the genome constitution and evolution of E. lolioides, we used single-copy nuclear genes acetyl-CoA carboxylase (Acc1) and elongation factor G (EF-G), multi-copy nuclear gene internal transcribed space (ITS), chloroplast gene trnL-F together with fluorescence and genomic in situ hybridization. RESULTS Despite the widespread homogenization of ITS sequences, two distinct lineages (genera Pseudoroegneria and Hordeum) were identified. Acc1 and EF-G sequences suggested that in addition to Pseudoroegneria and Hordeum, unknown genome was the third potential donor of E. lolioides. Data from chloroplast DNA showed that Pseudoroegneria is the maternal donor of E. lolioides. Data from specific FISH marker for St genome indicated that E. lolioides has two sets of St genomes. Both genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) results confirmed the presence of Hordeum genome in this species. When E genome was used as the probe, no signal was found in 42 chromosomes. The E-like copy of Acc1 sequences was detected in E. lolioides possibly due to the introgression from E genome species. One of the H chromosomes in the accession W6-26586 from Kazakhstan did not hybridize H genome signals but had St genome signals on the pericentromeric regions in the two-color GISH. CONCLUSIONS Phylogenetic and in situ hybridization indicated the presence of two sets of Pseudoroegneria and one set of Hordeum genome in E. lolioides. The genome formula of E. lolioides was designed as StStStStHH. E. lolioides may have originated through the hybridization between tetraploid Elymus (StH) and diploid Pseudoroegneria species. E and unknown genomes may participate in the speciation of E. lolioides through introgression. According to the genome classification system, E. lolioides should be transferred into Elymus L. and renamed as Elymus lolioidus (Kar. er Kir.) Meld.
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Affiliation(s)
- Long Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
| | - Yuanyuan Jiang
- College of Science, Sichuan Agricultural University, Ya’an, 625014 Sichuan China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, 100101 China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
| | - Lina Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
| | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, Nova Scotia Canada
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Ya’an, 625014 Sichuan China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan China
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Peng Y, Zhou P, Zhao J, Li J, Lai S, Tinker NA, Liao S, Yan H. Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene. PLoS One 2018; 13:e0200047. [PMID: 30408035 PMCID: PMC6224039 DOI: 10.1371/journal.pone.0200047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species.
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Affiliation(s)
- Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
| | - Jun Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Junzhuo Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Shikui Lai
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Nicholas A. Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Shu Liao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
- * E-mail:
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