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Nasiri A, Kazempour-Osaloo S, Hamzehee B, Bull RD, Saarela JM. A phylogenetic analysis of Bromus (Poaceae: Pooideae: Bromeae) based on nuclear ribosomal and plastid data, with a focus on Bromus sect. Bromus. PeerJ 2022; 10:e13884. [PMID: 36193423 PMCID: PMC9526414 DOI: 10.7717/peerj.13884] [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: 01/07/2022] [Accepted: 07/21/2022] [Indexed: 01/18/2023] Open
Abstract
To investigate phylogenetic relationships among and within major lineages of Bromus, with focus on Bromus sect. Bromus, we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid (rpl32-trnLUAG , matK) regions. We sampled 103 ingroup accessions representing 26 taxa of B. section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B. sect. Boissiera and B. sect. Nevskiella, respectively. These species are sister groups and are closely related to B. densus (B. sect. Mexibromus) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis, Ceratochloa, Neobromus, and Genea plus B. rechingeri of B. sect. Bromus form a clade, in which B. tomentellus is sister to a B. sect. Genea-B. rechingeri clade. In the plastid trees, by contrast, B. sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B. sect. Bromus and B. sect. Genea species. Affinities of B. gedrosianus, B. pulchellus, and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii, are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B. sect. Bromus and B. sect. Genea. Within B. sect. Bromus, B. alopecuros subsp. caroli-henrici, a clade comprising B. hordeaceus and B. interruptus, and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B. sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B. sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus.
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Affiliation(s)
- Akram Nasiri
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran,Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Hamzehee
- Botany Research Division, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Roger D. Bull
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Jeffery M. Saarela
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
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Xuan Y, Wu Y, Li P, Liu R, Luo Y, Yuan J, Xiang Z, He N. Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences. PeerJ 2019; 7:e8158. [PMID: 31844573 PMCID: PMC6911693 DOI: 10.7717/peerj.8158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/04/2019] [Indexed: 11/20/2022] Open
Abstract
Background Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information. Methods We sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry. Results We found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades. Conclusions Two species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution.
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Affiliation(s)
- Yahui Xuan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yue Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Peng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ruiling Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yiwei Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Jianglian Yuan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 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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Edet OU, Gorafi YSA, Cho SW, Kishii M, Tsujimoto H. Novel molecular marker-assisted strategy for production of wheat-Leymus mollis chromosome addition lines. Sci Rep 2018; 8:16117. [PMID: 30382155 PMCID: PMC6208378 DOI: 10.1038/s41598-018-34545-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Developing wheat–alien chromosome introgression lines to improve bread wheat’s resistance to stresses, such as drought, salinity stress and diseases, requires reliable markers to identify and characterize the alien chromatins. Leymus mollis is a wild relative of bread wheat resistant to salinity and economically important diseases of wheat, but its genome sequence and cytological markers are not available. We devised a molecular marker-assisted strategy for L. mollis chromosome identification and applied it to produce 10 wheat–L. mollis chromosome addition lines. Using 47 L. racemosus genome polymorphic PCR markers and DArTseq genotyping, we distinguished the L. mollis chromosomes and differentiated disomic and monosomic lines by progeny test. DArTseq genotyping generated 14,530 L. mollis SNP markers and the chromosome-specific SNP markers were used to determine the homoeologous groups of L. mollis chromosomes in the addition lines. To validate the marker-based results, genomic in situ hybridization was applied to confirm the presence and cytological status of L. mollis chromosomes in the lines. This study demonstrates that adequate molecular markers allow the production and characterization of wheat–alien addition lines without in situ hybridization, which saves considerable time and effort.
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Affiliation(s)
- Offiong U Edet
- Arid Land Research Center, Tottori University, Tottori, Japan.,United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Yasir S A Gorafi
- Arid Land Research Center, Tottori University, Tottori, Japan.,Agricultural Research Corporation (ARC), Wad Madani, Sudan
| | - Seong-Woo Cho
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju, Republic of Korea
| | - Masahiro Kishii
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
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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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Sha LN, Fan X, Li J, Liao JQ, Zeng J, Wang Y, Kang HY, Zhang HQ, Zheng YL, Zhou YH. Contrasting evolutionary patterns of multiple loci uncover new aspects in the genome origin and evolutionary history of Leymus (Triticeae; Poaceae). Mol Phylogenet Evol 2017; 114:175-188. [PMID: 28533082 DOI: 10.1016/j.ympev.2017.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 05/14/2017] [Accepted: 05/16/2017] [Indexed: 12/28/2022]
Abstract
Leymus Hochst. (Triticeae: Poaceae), a group of allopolyploid species with the NsXm genomes, is a perennial genus with diversity in morphology, cytology, ecology, and distribution in the Triticeae. To investigate the genome origin and evolutionary history of Leymus, three unlinked low-copy nuclear genes (Acc1, Pgk1, and GBSSI) and three chloroplast regions (trnL-F, matK, and rbcL) of 32 Leymus species were analyzed with those of 36 diploid species representing 18 basic genomes in the Triticeae. The phylogenetic relationships were reconstructed using Bayesian inference, Maximum parsimony, and NeighborNet methods. A time-calibrated phylogeny was generated to estimate the evolutionary history of Leymus. The results suggest that reticulate evolution has occurred in Leymus species, with several distinct progenitors contributing to the Leymus. The molecular data in resolution of the Xm-genome lineage resulted in two apparently contradictory results, with one placing the Xm-genome lineage as closely related to the P/F genome and the other splitting the Xm-genome lineage as sister to the Ns-genome donor. Our results suggested that (1) the Ns genome of Leymus was donated by Psathyrostachys, and additional Ns-containing alleles may be introgressed into some Leymus polyploids by recurrent hybridization; (2) The phylogenetic incongruence regarding the resolution of the Xm-genome lineage suggested that the Xm genome of Leymus was closely related to the P genome of Agropyron; (3) Both Ns- and Xm-genome lineages served as the maternal donor during the speciation of Leymus species; (4) The Pseudoroegneria, Lophopyrum and Australopyrum genomes contributed to some Leymus species.
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Affiliation(s)
- Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 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, Wenjiang 611130, Sichuan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, Sichuan, China
| | - Jin-Qiu Liao
- College of Life Science, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 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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Giudicelli GC, Mäder G, Silva-Arias GA, Zamberlan PM, Bonatto SL, Freitas LB. Secondary structure of nrDNA Internal Transcribed Spacers as a useful tool to align highly divergent species in phylogenetic studies. Genet Mol Biol 2017; 40:191-199. [PMID: 28199443 PMCID: PMC5452138 DOI: 10.1590/1678-4685-gmb-2016-0042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
Recently, it has been suggested that internal transcribed spacer (ITS) sequences are under selective constraints to preserve their secondary structure. Here, we investigate the patterns of the ITS nucleotide and secondary structure conservation across the Passiflora L. genus to evaluate the potential use of secondary structure data as a helpful tool for the alignment in taxonomically complex genera. Considering the frequent use of ITS, this study also presents a perspective on future analyses in other plant groups. The ITS1 and ITS2 sequences presented significant differences for mean values of the lowest energy state (LES) and for number of hairpins in different Passiflora subgenera. Statistical analyses for the subgenera separately support significant differences between the LES values and the total number of secondary structures for ITS. In order to evaluate whether the LES values of ITS secondary structures were related to selective constraints, we compared these results among 120 ITS sequences from Passiflora species and 120 randomly generated sequences. These analyses indicated that Passiflora ITS sequences present characteristics of a region under selective constraint to maintain the secondary structure showing to be a promising tool to improve the alignments and identify sites with non-neutral substitutions or those correlated evolutionary steps.
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Affiliation(s)
- Giovanna C Giudicelli
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Geraldo Mäder
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gustavo A Silva-Arias
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Priscilla M Zamberlan
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Sandro L Bonatto
- Laboratory of Genomic and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Pinar MS, Dizkirici A, Yigit O. Understanding taxonomic position of local endemic Agropyron deweyi (Poaceae) using morphological characters and sequences of nuclear and chloroplast DNA regions. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Dong ZZ, Fan X, Sha LN, Wang Y, Zeng J, Kang HY, Zhang HQ, Wang XL, Zhang L, Ding CB, Yang RW, Zhou YH. Phylogeny and differentiation of the St genome in Elymus L. sensu lato (Triticeae; Poaceae) based on one nuclear DNA and two chloroplast genes. BMC PLANT BIOLOGY 2015; 15:179. [PMID: 26164196 PMCID: PMC4499217 DOI: 10.1186/s12870-015-0517-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 04/29/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND Hybridization and polyploidization can be major mechanisms for plant evolution and speciation. Thus, the process of polyploidization and evolutionary history of polyploids is of widespread interest. The species in Elymus L. sensu lato are allopolyploids that share a common St genome from Pseudoroegneria in different combinations with H, Y, P, and W genomes. But how the St genome evolved in the Elymus s. l. during the hybridization and polyploidization events remains unclear. We used nuclear and chloroplast DNA-based phylogenetic analyses to shed some light on this process. RESULTS The Maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) data showed that the Pseudoroegneria, Hordeum and Agropyron species served as the St, H and P genome diploid ancestors, respectively, for the Elymus s. l. polyploids. The ML tree for the chloroplast genes (matK and the intergenic region of trnH-psbA) suggests that the Pseudoroegneria served as the maternal donor of the St genome for Elymus s. l. Furthermore, it suggested that Pseudoroegneria species from Central Asia and Europe were more ancient than those from North America. The molecular evolution in the St genome appeared to be non-random following the polyploidy event with a departure from the equilibrium neutral model due to a genetic bottleneck caused by recent polyploidization. CONCLUSION Our results suggest the ancient common maternal ancestral genome in Elymus s. l. is the St genome from Pseudoroegneria. The evolutionary differentiation of the St genome in Elymus s. l. after rise of this group may have multiple causes, including hybridization and polyploidization. They also suggest that E. tangutorum should be treated as C. dahurica var. tangutorum, and E. breviaristatus should be transferred into Campeiostachys. We hypothesized that the Elymus s. l. species origined in Central Asia and Europe, then spread to North America. Further study of intraspecific variation may help us evaluate our phylogenetic results in greater detail and with more certainty.
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Affiliation(s)
- Zhen-Zhen Dong
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
| | - Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
| | - Jian Zeng
- College of Resources and Environment, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
| | - Xiao-Li Wang
- College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China.
| | - Li Zhang
- College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China.
| | - Chun-Bang Ding
- College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China.
| | - Rui-Wu Yang
- College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China.
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
- Key Laboratory of Genetic Resources and Crop Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang 611130, Chengdu, Sichuan, China.
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