Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

Huang, Chi‐Cheng; Hung, Kuo Hsiang; Wang, Wei Kuang; Ho, Chuan-Wen; Huang, Chao; Hsu, Tsai Wen; Osada, Naoki; Hwang, Chyi; Chiang, Tzen‐Yuh

doi:10.1016/j.gene.2012.02.037

Cited by 23 publications

(22 citation statements)

References 61 publications

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“…The synonymous substitution rate between Col-0 and C24 is 4.20 × 10 − 3 per site. The synonymous substitution rate between A. lyrata and A. thaliana (Col-0) is 1.04 × 10 − 1 per site, similar to previous results (Koch et al 2000; Huang et al 2012). Using a divergence time of 5 Ma for A. thaliana and A. lyrata (Koch et al 2000) results in a rate of 2.08 × 10 − 8 substitutions per site per year, similar to that previously obtained for nuclear genes in the Brassicales (Franzke et al 2011).…”

Section: Introductionsupporting

confidence: 90%

Plant Mitochondrial Genome Evolution Can Be Explained by DNA Repair Mechanisms

Christensen

2013

Genome Biology and Evolution

169

148

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Plant mitochondrial genomes are notorious for their large and variable size, nonconserved open reading frames of unknown function, and high rates of rearrangement. Paradoxically, the mutation rates are very low. However, mutation rates can only be measured in sequences that can be aligned—a very small part of plant mitochondrial genomes. Comparison of the complete mitochondrial genome sequences of two ecotypes of Arabidopsis thaliana allows the alignment of noncoding as well as coding DNA and estimation of the mutation rates in both. A recent chimeric duplication is also analyzed. A hypothesis is proposed that the mechanisms of plant mitochondrial DNA repair account for these features and includes different mechanisms in transcribed and nontranscribed regions. Within genes, a bias toward gene conversion would keep measured mutation rates low, whereas in noncoding regions, break-induced replication (BIR) explains the expansion and rearrangements. Both processes are types of double-strand break repair, but enhanced second-strand capture in transcribed regions versus BIR in nontranscribed regions can explain the two seemingly contradictory features of plant mitochondrial genome evolution—the low mutation rates in genes and the striking expansions of noncoding sequences.

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Section: Introductionsupporting

confidence: 90%

Plant Mitochondrial Genome Evolution Can Be Explained by DNA Repair Mechanisms

Christensen

2013

Genome Biology and Evolution

169

148

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“…Recently, Huang et al . () published ITS evolutionary rates between Arabidopsis thaliana (L.) Heynh. (Brassicaceae) and its outcrossing congeneric species.…”

Section: Discussionmentioning

confidence: 99%

“…Those of Huang et al . () ranged from 1.56 × 10 −9 to 3.44 × 10 −9 with a mean of 2.5 × 10 −9 sub/site/yr, and thus are c . 1.5 times lower than evolutionary rates given by Kay et al .…”

Section: Discussionmentioning

confidence: 99%

“…() mean value mainly for the following reason: To calibrate the substitution rates, Huang et al . () adopted a split time between Arabidopsis thaliana and its relatives of 13 Ma as given by Beilstein et al . ().…”

Section: Discussionmentioning

confidence: 99%

“…Huang et al . () published a mean ITS substitution rate of 2.5 × 10 −9 sub/site/yr. Therefore, we also calculated a tree with an ucld.mean of 2.5 × 10 −9 with a SD of 6.0 × 10 −10 .…”

Section: Methodsmentioning

confidence: 99%

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Dated phylogenies and historical biogeography of Dontostemon and Clausia (Brassicaceae) mirror the palaeogeographical history of the Eurasian steppe

Friesen

German

Hurka

et al. 2015

Journal of Biogeography

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Aim We hypothesize that molecular signals in Eurasian steppe plants reflect their biogeographical history as well as the climate/landscape history of the Eurasian steppe. To test this hypothesis we focus here on the characteristic Eurasian steppe genera Dontostemon and Clausia (Brassicaceae), and have included all presently accepted species in our study. Location Eurasian steppe from eastern Asia to south‐eastern Europe. Methods To elucidate their phylogeny, we sequenced the nuclear ribosomal ITS and chloroplast trnL‐F regions. Sequence data were analysed with parsimony and Bayesian phylogenetic approaches. Divergence times were estimated using BEAST, relying on published ITS substitution rates. Distribution maps of all species of the two genera were compiled, and ancestral areas reconstructed using LAGRANGE. Results Both genera originated in central and eastern Asia, with Clausia later extending its range to eastern Europe. Dated phylogenies revealed: onset of diversification in the lower and middle Miocene; evolution of the majority of groups in the upper Miocene/lower Pliocene, and further speciation events during the Quaternary. Origin and diversification within these genera coincide with the evolution and history of the modern Eurasian steppe. Main conclusions Dated phylogenies and historical biogeography of Clausia and Dontostemon mirror the climate/landscape dynamics of the steppe from its origin in the early Miocene up to the Pleistocene and Holocene.

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A roadmap of phylogenomic methods for studying polyploid plant genera

Ning,

Meudt,

Tate

2024

Appl Plant Sci

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Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole‐genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid‐rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long‐read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.

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Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

Cited by 23 publications

References 61 publications

Plant Mitochondrial Genome Evolution Can Be Explained by DNA Repair Mechanisms

Plant Mitochondrial Genome Evolution Can Be Explained by DNA Repair Mechanisms

Dated phylogenies and historical biogeography of Dontostemon and Clausia (Brassicaceae) mirror the palaeogeographical history of the Eurasian steppe

A roadmap of phylogenomic methods for studying polyploid plant genera

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