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Yang X, Li X, Wang X, Chen C, Wu D, Cheng Y, Wang Y, Sha L, Kang H, Liu S, Fan X, Chen Y, Zhou Y, Zhang H. Identification and Characterization of LBD Gene Family in Pseudoroegneria libanotica Reveals Functions of PseLBD1 and PseLBD12 in Response to Abiotic Stress. Biochem Genet 2024:10.1007/s10528-024-10859-6. [PMID: 38850375 DOI: 10.1007/s10528-024-10859-6] [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: 02/18/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
The lateral organ boundaries domain (LBD) plays a vital role as a transcriptional coactivator within plants, serving as an indispensable function in growth, development, and stress response. In a previous study, we found that the LBD genes of Pseudoroegneria libanotica (a maternal donor for three-quarter of perennial Triticeae species with good stress resistance, holds great significance in exploring its response mechanisms to abiotic stress for the Triticeae tribe) might be involved in responding to drought stress. Therefore, we further identified the LBD gene family in this study. A total of 29 PseLBDs were identified. Among them, 24 were categorized into subclass I, while 5 fell into subclass II. The identification of cis-acting elements reveals the extensive involvement of PseLBDs in various biological processes in P. libanotica. Collinearity analysis indicates that 86% of PseLBDs were single-copy genes and have undergone a single whole-genome duplication event. Transcriptomic differential expression analysis of PseLBDs under drought stress reveals that the most likely candidates for responding to abiotic stress were PseLBD1 and PseLBD12. They have been demonstrated to respond to drought, salt, heavy metal, and heat stress in yeast. Furthermore, it is plausible that functional divergence might have occurred among their orthologous genes in wheat. This study not only establishes a foundation for a deeper understanding of the biological roles of PseLBDs in P. libanotica but also unveils novel potential genes for enhancing the genetic background of crops within Triticeae crops, such as wheat.
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Affiliation(s)
- Xunzhe Yang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- UWA School of Agriculture and Environment, and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Xiang Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xia Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Chen Chen
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yiran Cheng
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Lina Sha
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Houyang Kang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Songqing Liu
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yinglong Chen
- UWA School of Agriculture and Environment, and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yonghong Zhou
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Haiqin Zhang
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
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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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Kroupin PY, Yurkina AI, Ulyanov DS, Karlov GI, Divashuk MG. Comparative Characterization of Pseudoroegneria libanotica and Pseudoroegneria tauri Based on Their Repeatome Peculiarities. PLANTS (BASEL, SWITZERLAND) 2023; 12:4169. [PMID: 38140496 PMCID: PMC10747672 DOI: 10.3390/plants12244169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Pseudoroegneria species play an important role among Triticeae grasses, as they are the putative donors of the St genome in many polyploid species. Satellite repeats are widely used as a reliable tool for tracking evolutionary changes because they are distributed throughout the genomes of plants. The aim of our work is to perform a comparative characterization of the repeatomes of the closely related species Ps. libanotica and Ps. tauri, and Ps. spicata was also included in the analysis. The overall repeatome structures of Ps. libanotica, Ps. tauri, and Ps. spicata were similar, with some individual peculiarities observed in the abundance of the SIRE (Ty1/Copia) retrotransposons, Mutator and Harbinger transposons, and satellites. Nine new satellite repeats that have been identified from the whole-genome sequences of Ps. spicata and Ps. tauri, as well as the CL244 repeat that was previously found in Aegilops crassa, were localized to the chromosomes of Ps. libanotica and Ps. tauri. Four satellite repeats (CL69, CL101, CL119, CL244) demonstrated terminal and/or distal localization, while six repeats (CL82, CL89, CL168, CL185, CL192, CL207) were pericentromeric. Based on the obtained results, it can be assumed that Ps. libanotica and Ps. tauri are closely related species, although they have individual peculiarities in their repeatome structures and patterns of satellite repeat localization on chromosomes. The evolutionary fate of the identified satellite repeats and their related sequences, as well as their distribution on the chromosomes of Triticeae species, are discussed. The newly developed St genome chromosome markers developed in the present research can be useful in population studies of Ps. libanotica and Ps. tauri; auto- and allopolyploids that contain the St genome, such as Thinopyrum, Elymus, Kengyilia, and Roegneria; and wide hybrids between wheat and related wild species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
- Federal Research Center “Nemchinovka”, Bolshoi Blvd., 30 Bld. 1, Skolkovo Innovation Center, 121205 Moscow, Russia
- National Research Center “Kurchatov Institute”, Kurchatov Sq., 1, 123182 Moscow, Russia
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Sarina B, Jin F, Li J. Characterization of the complete chloroplast genome of Elymus alashanicus (Keng) S. L. Chen, and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1087-1091. [PMID: 37849653 PMCID: PMC10578103 DOI: 10.1080/23802359.2023.2267786] [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: 06/15/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
Elymus alashanicus (Keng) S. L. Chen, a herbaceous plant endemic to China, plays a crucial role in the local ecosystems. In this study, we sequenced and characterized the complete chloroplast (cp) genome of E. alashanicus, which is 135,072 bp in length and arranged in a circular form. The cp genome includes a pair of inverted repeats (IRa and IRb) of 20,813 bp each, separated by a large single-copy (LSC) region of 80,678 bp and a small single-copy (SSC) region of 12,768 bp. The cp genome contains 130 genes, including 83 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that E. alashanicus is closely related to Elymus breviaristatus and Campeiostachys dahurica var. tangutorum in current sampling. Our findings provide valuable insights into the cp genome of E. alashanicus, which could contribute to further studies on the evolution and conservation of this species.
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Affiliation(s)
- Bao Sarina
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Feng Jin
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Jinghuan Li
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
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Kroupin PY, Ulyanov DS, Karlov GI, Divashuk MG. The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae. Chromosoma 2023:10.1007/s00412-023-00789-4. [PMID: 36905415 DOI: 10.1007/s00412-023-00789-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/16/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023]
Abstract
Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for "classical" wheat probes (pSc119.2 and Afa family) and "universal" repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.
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Affiliation(s)
- Pavel Yu Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia.
| | - Daniil S Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Mikhail G Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
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Tan L, Huang QX, Song Y, Wu DD, Cheng YR, Zhang CB, Sha LN, Fan X, Kang HY, Wang Y, Zhang HQ, Zhou YH. Biosystematics studies on Elymus breviaristatus and Elymus sinosubmuticus (Poaceae: Triticeae). BMC PLANT BIOLOGY 2022; 22:57. [PMID: 35105308 PMCID: PMC8805286 DOI: 10.1186/s12870-022-03441-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/18/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Elymus breviaristatus and Elymus sinosubmuticus are perennial herbs, not only morphologically similar but also sympatric distribution. The genome composition of E. sinosubmuticus has not been reported, and the relationship between E. sinosubmuticus and E. breviaristatus is still controversial. We performed artificial hybridization, genomic in situ hybridization, and phylogenetic analyses to clarify whether the two taxa were the same species. RESULTS The high frequency bivalent (with an average of 20.62 bivalents per cell) at metaphase I of pollen mother cells of the artificial hybrids of E. breviaristatus (StYH) × E. sinosubmuticus was observed. It illustrated that E. sinosubmuticus was closely related to E. breviaristatus. Based on genomic in situ hybridization results, we confirmed that E. sinosubmuticus was an allohexaploid, and the genomic constitution was StYH. Phylogenetic analysis results also supported that this species contained St, Y, and H genomes. In their F1 hybrids, pollen activity was 53.90%, and the seed setting rate was 22.46%. Those indicated that the relationship between E. sinosubmuticus and E. breviaristatus is intersubspecific rather than interspecific, and it is reasonable to treated E. sinosubmuticus as the subspecies of E. breviaristatus. CONCLUSIONS In all, the genomic constitutions of E. sinosubmuticus and E. breviaristatus were StYH, and they are species in the genus Campeiostachys. Because E. breviaristatus was treated as Campeistachys breviaristata, Elymus sinosubmuticus should be renamed Campeiostachys breviaristata (Keng) Y. H. Zhou, H. Q. Zhang et C. R. Yang subsp. sinosubmuticus (S. L. Chen) Y. H. Zhou, H. Q. Zhang et L. Tan.
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Affiliation(s)
- Lu Tan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Qing-Xiang Huang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Yang Song
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Dan-Dan Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Yi-Ran Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Chang-Bin Zhang
- Sichuan Academy of Grassland Science, Chengdu, 610000, Sichuan, China
| | - Li-Na Sha
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China
| | - Hai-Qin Zhang
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
- State Key Laboratory of Crop Genetic Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, 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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Zhang Z, Xie W, Zhao Y, Zhang J, Wang N, Ntakirutimana F, Yan J, Wang Y. EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species. BMC PLANT BIOLOGY 2019; 19:235. [PMID: 31159732 PMCID: PMC6547490 DOI: 10.1186/s12870-019-1825-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/09/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Elymus L. is the largest genus in the tribe Triticeae Dumort., encompassing approximately 150 polyploid perennial species widely distributed in the temperate regions of the world. It is considered to be an important gene pool for improving cereal crops. However, a shortage of molecular marker limits the efficiency and accuracy of genetic breeding for Elymus species. High-throughput transcriptome sequencing data is essential for gene discovery and molecular marker development. RESULTS We obtained the transcriptome dataset of E. sibiricus, the type species of the genus Elymus, and identified a total of 8871 putative EST-SSRs from 6685 unigenes. Trinucleotides were the dominant repeat motif (4760, 53.66%), followed by dinucleotides (1993, 22.47%) and mononucleotides (1876, 21.15%). The most dominant trinucleotide repeat motif was CCG/CGG (1119, 23.5%). Sequencing of PCR products showed that the sequenced alleles from different Elymus species were homologous to the original SSR locus from which the primer was designed. Different types of tri-repeats as abundant SSR motifs were observed in repeat regions. Two hundred EST-SSR primer pairs were designed and selected to amplify ten DNA samples of Elymus species. Eighty-seven pairs of primer (43.5%) generated clear and reproducible bands with expected size, and showed good transferability across different Elymus species. Finally, thirty primer pairs successfully amplified ninety-five accessions of seventeen Elymus species, and detected significant amounts of polymorphism. In general, hexaploid Elymus species with genomes StStHHYY had a relatively higher level of genetic diversity (H = 0.219, I = 0.330, %P = 63.7), while tetraploid Elymus species with genomes StStYY had low level of genetic diversity (H = 0.182, I = 0.272, %P = 50.4) in the study. The cluster analysis showed that all ninety-five accessions were clustered into three major clusters. The accessions were grouped mainly according to their genomic components and origins. CONCLUSIONS This study demonstrated that transcriptome sequencing is a fast and cost-effective approach to molecular marker development. These EST-SSR markers developed in this study are valuable tools for genetic diversity, evolutionary, and molecular breeding in E. sibiricus, and other Elymus species.
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Affiliation(s)
- Zongyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People’s Republic of China
| | - Wengang Xie
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People’s Republic of China
| | - Yongqiang Zhao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People’s Republic of China
| | - Junchao Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People’s Republic of China
| | - Na Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People’s Republic of China
| | - Fabrice Ntakirutimana
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People’s Republic of China
| | - Jiajun Yan
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731 People’s Republic of China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People’s Republic of China
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Rodionov AV, Dobryakova KS, Nosov NN, Gnutikov AA, Punina EO, Kriukov AA, Shneyer VS. Polymorphism of ITS sequences in 35S rRNA genes in Elymus dahuricus aggregate species: two cryptic species? Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear ribosomal internal transcribed spacer (ITS) sequences were sequenced for 23 species and subspecies of Elymus sensu lato collected in Russia. The Neighbor-Net analysis of ITS sequences suggested that there are four ribotypes called Core Northern St-rDNA, Core Southern St-rDNA, Northern dahuricus St-rDNA and Southern dahuricus St-rDNA. The Core Southern variant of St-rDNA is closely related to rDNA of diploid Pseudoroegneria stipifolia (PI 313960) and P. spicata (PI 547161). The Core Northern St-rDNA is closely related to rDNA of P. cognata (PI 531720), a diploid species of Kyrgyzstan carrying StY variant of the St genome. The Core Northern St-rDNA is widespread among the Elymus species of Siberia and the Far East, including Yakutia and Chukotka. The Core Southern St-ribotype is typical of southern Elymus and Pseudoroegneria of the South Caucasus, Primorye, Pakistan, and South Korea. The Northern dahuricus St-ribotype and Southern dahuricus St-ribotype are derivatives of the Core Northern and Core Southern St-ribotypes, correspondingly. Both of them were found in all four studied species of the E. dahuricus aggregate: E. dahuricus Turcz. ex Griseb., E. franchetii Kitag., E. excelsus Turcz. ex Griseb. and Himalayan E. tangutorum (Nevski) Hand.-Mazz. In other words, there are at least two population groups (two races) of the Elymus dahuricus aggregate species that consistently differ in their ITS-sequences in Siberia, the Far East and Northern China. Each contains all morphological forms, which taxonomists now attribute either to different species of E. dahuricus aggr. (E. dahuricus sensu stricto, E. franchetii, E. tangutorum, E. excelsus) or subspecies of Campeiostachys dahurica (Turcz. ex Griseb.) B.R. Baum, J.L. Yang et C.C. Yen. At the moment it is unknown if there are any morphological differences between plants carrying either Northern or Southern dahuricus rDNA. Probably, they are cryptic species, but it is certain that if differences in morphology between the two races exist, they are not associated with signs that are now considered taxonomically significant and are used to separate E. dahuricus s. s., E. franchetii, E. tangutorum, and E. excelsus.
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Affiliation(s)
- A. V. Rodionov
- Komarov Botanical Institute, RAS; Saint-Petersburg State University
| | | | | | - A. A. Gnutikov
- Komarov Botanical Institute, RAS; Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | | | - A. A. Kriukov
- All-Russia Research Institute for Agricultural Microbiology
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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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Rodionov AV, Dobryakova KS, Punina EO. Polymorphic Sites in ITS1-5.8S rDNA-ITS2 Region in Hybridogenic Genus × Elyhordeum and Putative Interspecific Hybrids Elymus (Poaceae: Triticeae). RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Yang Y, Fan X, Wang L, Zhang HQ, Sha LN, Wang Y, Kang HY, Zeng J, Yu XF, Zhou YH. Phylogeny and maternal donors of Elytrigia Desv. sensu lato (Triticeae; Poaceae) inferred from nuclear internal-transcribed spacer and trnL-F sequences. BMC PLANT BIOLOGY 2017; 17:207. [PMID: 29157213 PMCID: PMC5697114 DOI: 10.1186/s12870-017-1163-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Elytrigia Desv. is a genus with a varied array of morphology, cytology, ecology, and distribution in Triticeae. Classification and systematic position of Elytrigia remain controversial. We used nuclear internal-transcribed spacer (nrITS) sequences and chloroplast trnL-F region to study the relationships of phylogenetic and maternal genome donor of Elytrigia Desv. sensu lato. RESULTS (1) E, F, P, St, and W genomes bear close relationship with one another and are distant from H and Ns genomes. Ee and Eb are homoeologous. (2) In ESt genome species, E genome is the origin of diploid Elytrigia species with E genome, St genome is the origin of Pseudoroegneria. (3) Diploid species Et. elongata were differentiated. (4) Et. stipifolia and Et. varnensis sequences are diverse based on nrITS data. (5) Et. lolioides contains St and H genomes and belongs to Elymus s. l. (6) E genome diploid species in Elytrigia serve as maternal donors of E genome for Et. nodosa (PI547344), Et. farcta, Et. pontica, Et. pycnantha, Et. scirpea, and Et. scythica. At least two species act as maternal donor of allopolyploids (ESt and EStP genomes). CONCLUSIONS Our results suggested that Elytrigia s. l. species contain different genomes, which should be divided into different genera. However, the genomes of Elytrigia species had close relationships with one another. Diploid species were differentiated, because of introgression and different geographical sources. The results also suggested that the same species and the same genomes of different species have different maternal donor. Further study of molecular biology and cytology could facilitate the evaluation of our results of phylogenetic in a more specific and accurate way.
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Affiliation(s)
- Yan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009 Sichuan People’s Republic of China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Long Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Xiao-Fang Yu
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
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Gao G, Deng J, Zhang Y, Li Y, Tong S, Zhang C, Zhou Y, Yang R. Phylogeny and maternal donor of Elymus (Triticeae: Poaceae) in China based on chloroplast matK sequences. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Gao G, Deng J, Zhang Y, Li Y, Li W, Zhou Y, Yang R. Phylogeny and maternal donor of Chinese Elymus (Triticeae: Poaceae) inferred from chloroplast trnH-psbA sequences. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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