Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

Yin, Wei; Wang, Zongji; Li, Qiye; Lian, Jin-ming; Zhou, Yang; Lu, Bingzheng; Jin, Lijun; Qiu, Pengxin; Zhang, Pei; Zhu, Wenbo; Wen, Bo; Huang, Yijun; Lin, Zhilong; Qiu, Bitao; Su, Xingwen; Yang, Huanming; Zhang, Guojie; Yan, Guiyun; Zhou, Qi

doi:10.1038/ncomms13107

Cited by 93 publications

(110 citation statements)

References 79 publications

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“…Analysis of GC3 in the green anole reveals that microchromosomes have significantly higher values than macrochromosomes, and this is similar to the chicken pattern [Figuet et al, 2014]. It is reported that the local GC content of snakes shows the presence of isochore structures as observed in turtles and crocodiles [Yin et al, 2016]. The GC content can be increased by the process of GC-biased gene conversion [Duret and Galtier, 2009].…”

Section: Discussionmentioning

confidence: 58%

Squamate Chromosome Size and GC Content Assessed by Flow Karyotyping

Kasai¹,

O’Brien²,

Ferguson‐Smith³

2019

Cytogenet Genome Res

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Chromosome homologies in reptiles have been investigated extensively by gene mapping and chromosome painting. Relative chromosome size can be estimated roughly from conventional karyotypes, but chromosome GC content cannot be evaluated by any of these approaches. However, GC content can be obtained by whole-genome sequencing, although complete data are available only for a limited number of reptilian species. Chromosomes can be characterized by size and GC content in bivariate flow karyotypes, in which the distribution of peaks represents the differences. We have analysed flow karyotypes from 9 representative squamate species and show chromosome profiles for each species based on the relationship between size and GC content. Our results reveal that the GC content of macrochromosomes is invariable in the 9 species. A higher GC content was found in microchromosomes, similar to profiles previously determined in crocodile, turtle, and chicken. The findings suggest that karyotype evolution in reptiles is characterized by unique features of chromosome GC content.

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Section: Discussionmentioning

confidence: 58%

Squamate Chromosome Size and GC Content Assessed by Flow Karyotyping

Kasai¹,

O’Brien²,

Ferguson‐Smith³

2019

Cytogenet Genome Res

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“…First, there is extensive variation in their TE content, ranging from 31.82% readily identifiable TEs (in the Burmese Python) to 49.6% (in the legless anguid lizard). While there have been extensive gene family expansions and contractions in squamate lineages, no clear correlations have been found linking these to TE content fluctuations [Yin et al, 2016]. The diversity in genomic TE landscapes is best exemplified in snakes.…”

Section: The Diversity Of Reptilian Mobilomementioning

confidence: 99%

“…Older (divergent) copies of L1 and L2 occur in both basal and advanced groups of snakes, suggesting these elements were more active in ancestral snakes [Yin et al, 2016]. While recent expansions include the snake1 CR1 LINEs that have primarily expanded in colubroid snakes [Castoe et al, 2013], expansion of DNA transposons ( hAT-Charlie, Tc1/Mariner ) and LTR ( Gypsy ) sequences have occurred in the viper genomes and L2 and CR1 in boas and pythons [Yin et al, 2016]. Such recent TE expansions of elements suggest that the repetitive fraction of squamate genomes remains highly dynamic.…”

Section: The Diversity Of Reptilian Mobilomementioning

confidence: 99%

“…Despite these fascinating aspects of squamate biology and their obvious utility as a research tool, only a limited number of highquality squamate genome assemblies are available and have been analyzed for their repeat content. High-quality genome assemblies exist for the green anole A. carolinensis [Alföldi et al, 2011]; the Burmese python, Python molurus bivittatus [Castoe et al, 2013]; the king cobra, Ophiophagus hannah [Vonk et al, 2013], and the five-pace viper, Deinagkistrodon acutus [Yin et al, 2016] in addition to high-coverage assemblies of the Australian dragon lizard, Pogona vitticeps [Georges et al, 2015] and the Chinese crocodile lizard, Shinisaurus crocodilurus [Gao J et al, 2017] as well as draft assemblies of the Burmese glass lizard, Ophisaurus gracilis , a legless anguid lizard [Song et al, 2015]; the leopard gecko, Eublepharis macularius [Xiong et al, 2016], and the corn snake, Pantherophis guttatus [Ullate-Agote et al, 2014]. This collection of genomes, when considered together, reveals that squamates are as diverse in TE content as they are diverse morphologically, physiologically, or ecologically.…”

Section: The Diversity Of Reptilian Mobilomementioning

confidence: 99%

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The Mobilome of Reptiles: Evolution, Structure, and Function

Boissinot¹,

Bourgeois²,

Manthey

et al. 2019

Cytogenet Genome Res

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Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

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“…Cytogenetic and individual gene studies suggest an astounding diversity of both ZW and XY sex chromosome systems in other vertebrate lineages ). However, while various studies have shed light on sex chromosome evolution in reptiles and fishes (e.g., Chen et al 2014;White et al 2015;Rovatsos et al 2016;Yin et al 2016;Rupp et al 2017), integrated genome-scale investigations of the origins and functional adaptations of vertebrate sex chromosomes outside of mammals and birds remain scarce.…”

mentioning

confidence: 99%

Convergent origination of aDrosophila-like dosage compensation mechanism in a reptile lineage

Cortez²,

et al. 2017

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Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.

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Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

Cited by 93 publications

References 79 publications

Squamate Chromosome Size and GC Content Assessed by Flow Karyotyping

Squamate Chromosome Size and GC Content Assessed by Flow Karyotyping

The Mobilome of Reptiles: Evolution, Structure, and Function

Convergent origination of aDrosophila-like dosage compensation mechanism in a reptile lineage

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