Relationships among Avena species as revealed by consensus chloroplast simple sequence repeat (ccSSR) markers

Li, Weitao; Peng, Yuanying; Wei, Yuming; Baum, Bernard R.; Zheng, Youliang

doi:10.1007/s10722-008-9379-x

Cited by 19 publications

(12 citation statements)

References 83 publications

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“…Furthermore, this might provide one explanation for the lack of differentiation between the AC and ACD sequences into separate clades. of the clones of A. damascena and A. fatua , indicating the close relationship between these two species, which is in agreement with the results of in situ hybridization ( JELLEN et al 1994a;LEGGETT and MARKHAND 1995) and with the study using ccSSR ( LI et al 2009). Recently using chloroplast sequences to investigate the maternal donor of the polyploid, we found that A. damascena is closely related to A. fatua (Wei et al unpubl.).…”

Section: Phylogenetic Inferences In Avena Based On Its Sequencessupporting

confidence: 90%

“…They also provided evidence that in the polyploids the nuclear genome of maternal origin undergoes fewer changes with time than the nuclear genome of paternal origin. In Avena the ITS sequences of the A and C genomes might have diverged in a similar fashion and since the A genome was determined as the maternal donor of AACC tetraploids (Nishiyama and Yabuno 1975; Leggett 1984; Nishiyama 1984; Murai and Tsunewaki 1987; Rines et al 1988; Nikoloudakis and Katsiotis 2008; Li et al 2009; Peng et al unpubl. ), it has undergone fewer mutational changes than the paternal donor, the C‐genome.…”

Section: Discussionmentioning

confidence: 99%

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The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae)

et al. 2010

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Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and these repeats often undergo rapid concerted evolution within and between arrays. Therefore, the rDNA ITS copies appear to be virtually identical and can sometimes be treated as a single gene. In this paper we examined ITS polymorphism within and among 13 diploid (A and C genomes), seven tetraploid (AB, AC and CC genomes) and four hexaploid (ACD genome) to infer the extent and direction of concerted evolution, and to reveal the phylogenetic and genome relationship among species of Avena. A total of 170 clones of the ITS1-5.8S-ITS2 fragment were sequenced to carry out haplotype and phylogenetic analysis. In addition, 111 Avena ITS sequences retrieved from GenBank were combined with 170 clones to construct a phylogeny and a network. We demonstrate the major divergence between the A and C genomes whereas the distinction among the A and B/D genomes was generally not possible. High affinity among the A(d) genome species A. damascena and the ACD genome species A. fatua was found, whereas the rest of the ACD genome hexaploids and the AACC tetraploids were highly affiliated with the A(l) genome diploid A. longiglumis. One of the AACC species A. murphyi showed the closest relationship with most of the hexaploid species. Both C(v) and C(p) genome species have been proposed as paternal donors of the C-genome carrying polyploids. Incomplete concerted evolution is responsible for the observed differences among different clones of a single Avena individual. The elimination of C-genome rRNA sequences and the resulting evolutionary inference of hexaploid species are discussed.

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Section: Phylogenetic Inferences In Avena Based On Its Sequencessupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae)

et al. 2010

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“…This is in agreement with the results of ccSSR markers (Li et al 2009) and matK gene sequences (Peng et al 2010b). In situ hybridization (Jellen et al 1994;Yang et al 1999;Shelukhina et al 2008) also provides evidence for the close relationship between these two species.…”

Section: Relationships Among Avena Speciessupporting

confidence: 92%

Genetic diversity of seed storage proteins in diploid, tetraploid and hexaploid Avena species

et al. 2014

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Genetic diversities of 106 Avena accessions, including diploid, tetraploid and hexaploid species, derived from different countries were characterized based on seed storage proteins polymorphism using SDS-PAGE. A total of 24 protein bands and 72 protein patterns were detected in all 106 accessions. The genetic similarity value varied from 0.50 to 1.00. The seed storage protein patterns were largely independent of environmental fluctuation. Accessions of the same species or with identical genome constitutions had the same or similar protein patterns. Relatively lower within-species variations were observed compared with among-species variations. The AACCDD genome hexaploid species and the AA genome diploid species were more divergent than other species, with percentages of polymorphic bands of 85.7% and 61.1% respectively. In the AA genome diploid species, the A s A s genome diploids displayed higher variations than the modified AA genome diploid species. Clustering results showed a close relationship between the hexaploid species and the AACC genome tetraploid species. The AABB genome tetraploid species were similar to the A s A s genome diploid species, with the exception of the species A. agadiriana with AABB genome constitution, which showed a close relationship with the A c A c genome diploid species A. canariensis and the polyploid species carrying the A and C genomes.

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“…Fourn., Pseudarrhenatherum Rouy, Rostraria Trin., Sphenopholis Scribn., Trisetaria Forssk., Tricholemma (Röser) Röser, Trisetopsis Röser & Wölk, Trisetum Pers., Tzveleviochloa Röser & A. Wölk and × Trisetopsotrichon Röser & A. Wölk. Of these, the best studied genus is Avena (oats) (Drossou et al 2004, Peng et al 2008, 2010a, 2010b, Li et al 2009, Yan et al 2014). Several studies have identified Helictotrichon s.l.…”

Section: Introductionmentioning

confidence: 99%

Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

Saarela¹,

Bull²,

Paradis³

et al. 2017

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Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3’-end of the external transcribed spacer (ETS)) and five plastid regions (matK, trnL–trnF, atpF–atpH, psbK–psbI, psbA–rps19–trnH), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of Trisetum are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises Avellinia, Gaudinia, Koeleria, Rostraria, Trisetaria and Trisetum subg. Trisetum, and the other Calamagrostis/Deyeuxia p.p. (multiple species from Mexico to South America), Peyritschia, Leptophyllochloa, Sphenopholis, Trisetopsis and Trisetum subg. Deschampsioidea. Graphephorum, Trisetum cernuum, T. irazuense and T. macbridei fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and matK trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of Lagurus ovatus with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of Lagurus in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises Calamagrostis coarctata, Dichelachne, Echinopogon (Agrostidinae p.p.) and Relchela (Calothecinae p.p.), and another comprises Chascolytrum (Calothecinae p.p.) and Deyeuxia effusa (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of Deyeuxia and Calamagrostis s.str. are closely related, supporting classification of Dey...

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Relationships among Avena species as revealed by consensus chloroplast simple sequence repeat (ccSSR) markers

Cited by 19 publications

References 83 publications

The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae)

The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae)

Genetic diversity of seed storage proteins in diploid, tetraploid and hexaploid Avena species

Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

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