Genome-wide survey and genetic characteristics of Ophichthus evermanni based on Illumina sequencing platform

Abstract

Ophichthidae fishes limit to continental shelf of all tropical and subtropical oceans, and contain more than 350 species, representing the greatest specialization diversity in the order Anguiliformes. In this study, we conducted a genome survey sequencing (GSS) analysis of Ophichthus evermanni by Illumina sequencing platform to briefly reveal its genomic characteristics and phylogenetic relationship. The first de novo assembled 1.97 Gb draft genome of O. evermanni was predicted based on K-mer analysis without obvious nucleotide bias. The heterozygosity ratio was 0.70%, and the sequence repeat ratio was calculated to be 43.30%. A total of 9,016 putative coding genes were successfully predicted, in which 3,587 unigenes were identified by gene ontology (GO) analysis and 4,375 unigenes were classified into cluster of orthologous groups for enkaryotic complete genomes (KOG) functional categories. About 2,812,813 microsatellite motifs including mono-, di-, tri-, tetra-, penta-, and hexanucleotide motifs were identified, with an occurrence frequency of 23.32%. The most abundant type was dinucleotide repeat motifs, accounting for 49.19% of the total repeat types. The mitochondrial genome, as a byproduct of GSS, was assembled to investigate the evolutionary relationships between O. evermanni and its relatives. Bayesian inference (BI) phylogenetic tree inferring from concatenated 12 protein-coding genes (PCGs) showed complicated relationships among Ophichthidae species, indicating a polyphyletic origin of the family. The results would achieve more thorough genetic information of snake eels and provide a theoretical basis and reference for further genome-wide analysis of O. evermanni.

The whole-genome survey of Acer griseum, its polymorphic simple sequence repeats development and application

“…When plant genome size is determined by flow cytometry, differences in the results of the same species can occur due to different operations and testing conditions (e.g., lysis methods and internal standard selection) during the test (Doležel et al, 2007;Lin et al, 2019). Genome survey based on next-generation highthroughput sequencing technology has the advantage of obtaining a large number of gene sequences while determining genomic features and is increasingly valued and applied by researchers (Kirkness et al, 2003;Yang et al, 2022).…”

Genome-wide survey reveals the phylogenomic relationships of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes)

“…Microsatellite DNA markers shows many advantages, such as codominant, extensive distribution, abundant polymorphisms, and a convenient analysis, and was considered to be an effective tool in genetic analysis and evolutionary research ( Yang et al 2022 ). In this study, the highest number and type of repeats is dinucleotide repeats, which was consistent with data for Ophichthus evermanni ( Yang et al 2022 ), Padon nehereus ( Yang et al 2021 ), Cociella crocodilus ( Zhao et al 2021 ), Acanthogobius ommaturus ( Chen et al 2020 ), Sillago sihama ( Qiu et al 2020 ), and other species. SSR polymorphic loci are mainly distributed among mononucleotide and dinucleotide repeats.…”