Dataset Information

Sequence comparison of the mitochondrial genomes of five brackish water species of the family Neritidae: Phylogenetic implications and divergence time estimation.

ABSTRACT: Neritids are ancient gastropod species which can live in marine, brackish water, and freshwater environments. In this study, we sequenced and annotated the mitochondrial genomes of five brackish water neritids (i.e., Clithon corona, Clithon lentiginosum, Clithon squarrosum, Neritina iris, and Septaria lineata). The mitogenomes ranged from 15,618 to 15,975 bp, and all contain 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a closed ring structure. We calculated the Ka/Ks values of all 13 PCGs of Neritidae species, all ratios are less than 1, under purification selection. Phylogenetic analysis of the 13 PCGs showed that Neritimorpha is a sister group with Vetigastropoda and Caenogastopoda, genus Clithon is a sister group with Neritina and Septaria. Estimation of divergence time for all species of Neritidae showed that the main differentiation of Neritidae occurred in Cenozoic period (65 Mya), C. corona and C. lentiginosum were differentiated in the Cenozoic Neogene, the other three species diverged in the Cenozoic Paleogene. These results will help to better understand the evolutionary position of Neritidae and provide reference for further phylogenetic research on Neritidae species.

SUBMITTER: Miao J

PROVIDER: S-EPMC9170520 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Sequence comparison of the mitochondrial genomes of five brackish water species of the family Neritidae: Phylogenetic implications and divergence time estimation.

Miao Jing J Feng Jiantong J Liu Xiaojuan X Yan Chengrui C Ye Yingying Y Li Jiji J Xu Kaida K Guo Baoying B Lü Zhenming Z

Ecology and evolution 20220606 6

Neritids are ancient gastropod species which can live in marine, brackish water, and freshwater environments. In this study, we sequenced and annotated the mitochondrial genomes of five brackish water neritids (i.e., Clithon corona, Clithon lentiginosum, Clithon squarrosum, Neritina iris, and Septaria lineata). The mitogenomes ranged from 15,618 to 15,975 bp, and all contain 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a closed ring s ...[more]

PMID: 35784089

Similar Datasets

Project description:Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7,rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

Dataset Information

Sequence comparison of the mitochondrial genomes of five brackish water species of the family Neritidae: Phylogenetic implications and divergence time estimation.

Publications

Sequence comparison of the mitochondrial genomes of five brackish water species of the family Neritidae: Phylogenetic implications and divergence time estimation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets