CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes)

Li, Zhaofeng; Yuan, Huipin; Yue, Bisong

doi:10.1016/j.gene.2012.04.068

Cited by 16 publications

(33 citation statements)

References 53 publications

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“…In addition, several new subfamilies different from other previously described avian CR1 subfamilies were also identified in waterfowl, and despite the possible lack of an active CR1 in chicken, at least one of these subfamilies in this order was suggested to be likely active (St. John et al 2005; John and Quinn 2008). On the other hand, these insertion polymorphisms of these CR1 retrotransposons also used as phylogenetic markers to elucidate the evolution of bird and reflecting the rapid diversification of these birds (Kaiser et al 2007; Treplin and Tiedemann 2007; Liu et al 2012; Suh et al 2012). While DNA TEs just occupy about 1% or less of the avian genomes, and SINEs comprise 0.06–0.08%, the activity, diversity, and density of DNA and SINE TEs are also substantially lower than that in most vertebrates (Chalopin et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Low diversity, activity, and density of transposable elements in five avian genomes

Gao

Wang

et al. 2017

Funct Integr Genomics

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In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.Electronic supplementary materialThe online version of this article (doi:10.1007/s10142-017-0545-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Low diversity, activity, and density of transposable elements in five avian genomes

Gao

Wang

et al. 2017

Funct Integr Genomics

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“…China boasts 56 species of Phasianidae belonging to 21 genera, with many of the species being distributed in the southwestern mountains and southeastern Himalayas of China (Lei and Lu, 2006). There have been numerous attempts to reconstruct the phylogenetic relationships of the Phasianidae (Kimball et al, 1999Armstrong et al, 2001;Dimcheff et al, 2002;Bush and Strobeck, 2003;Dyke et al, 2003;Pereira and Baker, 2006;Kaiser et al, 2007;Kriegs et al, 2007;Kimball and Braun, 2008;Huang et al, 2009;Liu et al, 2012). However, the taxonomic status of some species and genera within the Phasianidae family remain controversial.…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding and evolutionary relationships of the Phasianidae family in China

Huang

2014

Genet. Mol. Res.

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ABSTRACT.A DNA barcode is a short sequence of standardized genomic region that is specific to a species. According to studies of bird species, the 694-bp sequence of the mitochondrial gene encoding cytochrome c oxidase 1 (COI) is extremely useful for species identification and phylogeny. In the present study, we analyzed the COI barcodes of 31 species from 18 genera belonging to the Phasianidae family in China. Kimura two-parameter (K2P) distances were calculated between barcodes. We found that the average genetic distance between congeneric species was 24 times higher compared to the average genetic distance within species. Each bird species had a barcode that was distinct to all other bird species. The neighbor-joining method was used to construct a phylogenetic tree, which grouped all of the genera into 2 divergent clades. In conclusion, DNA barcoding is an effective molecular tool for Phasianidae species identification and phylogenetic inference.

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“…However, recent studies have shown that monal-partridge formed a sister relationship with monal [28][29][30]. Phylogenetic analysis of Sichuan partridge position based on CR1 retroposons is incongruent with the mtDNA results [24,25,29,31,32]. The phylogenetic position of the koklass pheasant varied [1,2,4,28,33].…”

Section: Genetic Characteristicsmentioning

confidence: 99%