Phylogenetic reconstruction and diversification of the Triticeae (Poaceae) based on single-copy nuclear Acc1 and Pgk1 gene data

Fan, Xing; Li, Sha; Yu, Shuang-Bin; Wu, Dandan; Chen, Xiaohong; Zhuo, Xiao-Feng; Zhang, Haiqin; Kang, Houyang; Wang, Yi; Zheng, Yu; Zhou, Yong‐Hong

doi:10.1016/j.bse.2013.05.010

Cited by 17 publications

(19 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, the minimum-evolution dendrogram obtained on the basis of the matK sequences (Fig. 2a) revealed a close relationship between the Pseudoroegneria and the Taeniatherum clades, as well as a clear distinction of the Psathyrostachys and the Hordeum clades, which is consistent with the previous molecular studies (Fan et al 2013;Escobar et al 2011;Petersen and Seberg 1997). Thus, out of the three analyzed loci, the matK reflects intergeneric phylogenetic relationships of the Triticeae in the most complete manner.…”

Section: Phylogenetic Relationshipssupporting

confidence: 87%

Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species

2014

View full text Add to dashboard Cite

This study presents a phylogenetic analysis of the selected representatives of the Triticeae tribe and the assessment of possibilities of species identification on the basis of sequence variation in the three regions from the chloroplast DNA (matK, rbcL and trnH-psbA). The analysis included diploid and polyploid species of the following genomic compositions: E b , E e , H, I, Ns, St, Ta, Xu, NsXm, XoXr, XuXu, E b E e , E b E b E e , E b E e St, StH, StStH. The obtained matK and rbcL sequences revealed three well-supported clades: (1) Elymus, Lopophyrum, Pseudoroegneria, Thinopyrum (genomes E b , E e , St, StH, E b E e , E b E b E e , E b E e St, StStH); (2) Leymus, Hordelymus, Psathyrostachys (genomes Ns, NsXm, XoXr); (3) Hordeum (genomes H, I, Xu). This results support the view that the analyzed Elymus species (E. caninus, E. repens) acquired the Pseudoroegneria St genome maternally. They also indicate that Hordelymus europaeus carries the Ns genome from Psathyrostachys and point at the maternal origin of this component. Moreover, the presented results confirm the contribution of Psathyrostachys in the origin of Leymus as well as indicate the maternal character of this input. Differentiation observed within the Hordeum clade aligns with the alleged genome composition of the analyzed species. The DNA barcoding potential of the analyzed sequences was low. Nevertheless, several informative polymorphisms were found like e.g. the matK substitution specific for Thinopyrum bessarabicum, the trnH-psbA substitution differentiating Leymus arenarius from Psathyrostachys juncea and the group of speciesspecific deletions within trnH-psbA. In the DNA barcoding context we have also demonstrated negative importance of the high frequency cpDNA inversion leading to intraspecific variation.

show abstract

Section: Phylogenetic Relationshipssupporting

confidence: 87%

Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species

2014

View full text Add to dashboard Cite

show abstract

“…The hybridization hypothesis is likely because sympatric distribution of Leymus and Pseudoroegneria species in Eurasia have provided an opportunity in physical proximity for hybridization events. The hypothesis of incomplete lineage sorting may also explain the contribution of the Pseudoroegneria genome to Leymus because a history of incomplete lineage sorting has been reported not only for diploid lineages (Kellogg et al, ; Mason‐Gamer & Kellogg, ; Escobar et al, ; Fan et al, ) but also for polyploid species (Mason‐Gamer, ; Fan et al, , , ; Mahelka & Kopecký, ; Sha et al, ) within the tribe Triticeae. This hypothesis is further strengthened by the estimate of the number of shared and fixed differences at the DMC1 locus.…”

Section: Discussionmentioning

confidence: 99%

“…The lack of fossils for the Triticeae precluded a direct calibration of tree topologies. Instead, molecular dating was based on the divergence age of 12 Ma between Hordeum and Aegilops/ Triticum lineage because the assumption of a split between Hordeum and Aegilops/Triticum lineage ranged from 11 to 13 Ma (Gaut, 2002;Huang et al, 2002;Blattner, 2006;Fan et al, 2013b). Calibration points were carried out using a relaxed uncorrelated lognormal molecular clock.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

Fan

Zhang

et al. 2016

J of Sytematics Evolution

Self Cite

View full text Add to dashboard Cite

The level and pattern of nucleotide variation in duplicate genes provide important information on the evolutionary history of polyploids and divergent processes between homoeologous loci within lineages. Leymus, a group of allopolyploid species with the NsXm genomes, is a perennial genus with a diverse array of morphology, ecology, and distribution in Triticeae. To estimate the phylogeny and molecular evolution of a single-copy DMC1 gene in Leymus and its diploid relatives, DMC1 homoeologous sequences were isolated from the sampled Leymus species and were analyzed with those from 30 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that: (i) different Leymus species might derive their Ns genome from different Psathyrostachys species; (ii) Pseudoroegneria has contributed to the nuclear genome of some Leymus species, which might result from recurrent hybridization or incomplete lineage sorting; (iii) the Xm genome origin of Leymus could differ among species; (iv) rapid radiation and multiple origin might account for the rich diversity, numbers of species, and wide ecological adaptation of Leymus species; and (v) the DMC1 sequence diversity of the Ns genome in Leymus species was lower than that in the Psathyrostachys diploids, while the level of DMC1 sequence diversity in Leymus was higher than that in diploid Pseudoroegneria. Our results provide new insight on the evolutionary dynamics of duplicate DMC1 genes, polyploid speciation, and the phylogeny of Leymus species.

show abstract

“…They were analyzed together with 36 diploid taxa representing 19 basic genomes in the tribe Triticeae (). Bromus L. species was used as the outgroup based on previously phylogenetic analyses of Triticeae (Liu et al, ; Fan et al, ). Chloroplast trnH‐psbA and mitochondrial coxII intron sequences for 36 diploid taxa representing 19 basic genomes in Triticeae were obtained from published data (Seberg & Petersen, ; Zeng et al, ; Petersen et al, , ; Luo et al, ), except for the trnH‐psbA sequences of Australopyrum retrofractum (Vickery) Á. Löve, Crithopsis delileana (Schult) Roshev., Dasypyrum villosum (L.) Candargy, Eremopyrum distans (C. Koch) Nevski, Eremopyrum triticeum (Gaertn.)…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic relationships in Leymus (Triticeae; Poaceae): Evidence from chloroplast trnH‐psbA and mitochondrial coxII intron sequences

Fan

Zhang

et al. 2014

J of Sytematics Evolution

Self Cite

View full text Add to dashboard Cite

Leymus Hochst. is a polyploid genus with a diverse array of morphology, cytology, ecology, and distribution in Triticeae. To investigate the phylogenetic relationships and maternal genome donor of polyploid Leymus, the chloroplast trnH-psbA region and mitochondrial coxII intron sequences of 33 Leymus taxa were analyzed with those of 36 diploid perennial species representing 19 basic genomes in Triticeae. The results showed that reticulate evolution occurred in Leymus species, with the cytoplasmic lineage of Leymus contributed by different progenitors. Interspecific relationships of Leymus were also elucidated on the basis of orthologous comparison. Our data suggested that: (i) due to incomplete lineage sorting and/or difference in the pattern of chloroplast and mitochondrial inheritance, the genealogical conflict between the two genealogical patterns suggest the contribution of Psathyrostachys Nevski, Agropyron J. Gaertn, Eremopyrum

show abstract

Phylogenetic reconstruction and diversification of the Triticeae (Poaceae) based on single-copy nuclear Acc1 and Pgk1 gene data

Cited by 17 publications

References 54 publications

Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species

Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species

Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

Phylogenetic relationships in Leymus (Triticeae; Poaceae): Evidence from chloroplast trnH‐psbA and mitochondrial coxII intron sequences

Contact Info

Product

Resources

About