Complete mitochondrial genome of Siamese cobra (<i>Naja kaouthia</i>) determined using next-generation sequencing

Singchat, Worapong; Areesirisuk, Prapatsorn; Sillapaprayoon, Siwapech; Muangmai, Narongrit; Baicharoen, Sudarath; Suntrarachun, Sunutcha; Chanhome, Lawan; Peyachoknagul, Surin; Srikulnath, Kornsorn

doi:10.1080/23802359.2018.1558123

Cited by 6 publications

(7 citation statements)

References 8 publications

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“…This result was consistent with the patchy distribution of Bov-B LINE among vertebrates [17]. Inconsistencies between Bov-B LINE, COI, and BDNF tree topologies with snake phylogenies derived from other sequence datasets were also noted (Figures S2 and S3), which points to the incidence of HT events [17,19,[80][81][82]. Furthermore, the…”

Section: Discussionsupporting

confidence: 83%

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Puinongpo

Singchat

Petpradub

et al. 2020

Genes

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Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.

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Section: Discussionsupporting

confidence: 83%

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Puinongpo

Singchat

Petpradub

et al. 2020

Genes

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“…A well-known example is the genome of the Indian cobra, which is closely related to the Siamese cobra [179]. This genome encompasses a total size of 1.79 Gb with W and Z chromosomes spanning 52.1 Mb and 154.6 Mb, respectively [60].…”

Section: Repeats: a Driver For Sex Chromosome Conformation After The Split Of An Ancestral Amniote Super-sex Chromosomementioning

confidence: 99%

Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome

Singchat

Ahmad

Laopichienpong

et al. 2020

Cells

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: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.

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“…The nucleotide CR sequence is the most rapidly evolving region of the mitogenome, and it lacks coding sequences; thus, it is widely used as a molecular marker in population genetics, phylogenetic studies, and phylogeographic studies [ 3 , 4 , 5 ]. Vertebrates such as birds, snakes, turtles, and fish exhibit segmental duplications within the CR or an entire duplication of the CR, leading to the formation of repeats or possible homogenization between the duplicated copies of CR [ 6 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

“…GenBank contains 17,489 complete mitogenomes for squamate reptiles (as of April 2021, ), with several duplicate CRs observed in varanids and snakes [ 6 , 7 ]. A comparison between two CRs (CR1 and CR2) revealed identical or highly similar nucleotide sequences, similar to the concerted evolution as found in Bothidae and Samaridae [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Thapana

Ariyaraphong

Wongtienchai

et al. 2022

Animals

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Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

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Complete mitochondrial genome of Siamese cobra (Naja kaouthia) determined using next-generation sequencing

Cited by 6 publications

References 8 publications

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome

Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

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