Cargando…

Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae

Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore se...

Descripción completa

Detalles Bibliográficos
Autores principales: Xiaokaiti, Xiakena, Hashiguchi, Yasuyuki, Ota, Hidetoshi, Kumazawa, Yoshinori
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9407768/
https://www.ncbi.nlm.nih.gov/pubmed/36011381
http://dx.doi.org/10.3390/genes13081470
_version_ 1784774443625611264
author Xiaokaiti, Xiakena
Hashiguchi, Yasuyuki
Ota, Hidetoshi
Kumazawa, Yoshinori
author_facet Xiaokaiti, Xiakena
Hashiguchi, Yasuyuki
Ota, Hidetoshi
Kumazawa, Yoshinori
author_sort Xiaokaiti, Xiakena
collection PubMed
description Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.
format Online
Article
Text
id pubmed-9407768
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-94077682022-08-26 Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae Xiaokaiti, Xiakena Hashiguchi, Yasuyuki Ota, Hidetoshi Kumazawa, Yoshinori Genes (Basel) Article Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny. MDPI 2022-08-17 /pmc/articles/PMC9407768/ /pubmed/36011381 http://dx.doi.org/10.3390/genes13081470 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Xiaokaiti, Xiakena
Hashiguchi, Yasuyuki
Ota, Hidetoshi
Kumazawa, Yoshinori
Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
title Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
title_full Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
title_fullStr Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
title_full_unstemmed Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
title_short Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
title_sort evolution of the noncoding features of sea snake mitochondrial genomes within elapidae
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9407768/
https://www.ncbi.nlm.nih.gov/pubmed/36011381
http://dx.doi.org/10.3390/genes13081470
work_keys_str_mv AT xiaokaitixiakena evolutionofthenoncodingfeaturesofseasnakemitochondrialgenomeswithinelapidae
AT hashiguchiyasuyuki evolutionofthenoncodingfeaturesofseasnakemitochondrialgenomeswithinelapidae
AT otahidetoshi evolutionofthenoncodingfeaturesofseasnakemitochondrialgenomeswithinelapidae
AT kumazawayoshinori evolutionofthenoncodingfeaturesofseasnakemitochondrialgenomeswithinelapidae