Genome survey and microsatellite motif identification of Pogonophryne albipinna.

Euna Jo,Eunkyung Choi,Seung Jae Lee,Young Min Chi,Yll Hwan Cho,Jeong-Hoon Kim,Jinmu Kim,Hyun Park

doi:10.1042/bsr20210824

Euna Jo, Eunkyung Choi + Show 6 more

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https://doi.org/10.1042/bsr20210824

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Abstract

The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.

Highlights

The genus Pogonophryne Regan, 1914 is the most species-rich group among the perciform suborder Notothenioidei, with 28 species reported to date [1,2]
The genome survey sequencing of P. albipinna yielded a total of ∼57.1 Gb of raw reads through the Illumina paired-end library (Table 1)
The Illumina paired-end data were used to predict the genomic characteristics of P. albipinna by K-mer analysis

Summary

Introduction

The genus Pogonophryne Regan, 1914 is the most species-rich group among the perciform suborder Notothenioidei, with 28 species reported to date [1,2]. They inhabit coastal or deep waters of the Southern Ocean off Antarctica [2]. It is difficult to compare the morphology of the species from this genus because many of them were described based on only a few specimens from a single sampling site [9,10]. Taxonomists have divided the genus Pogonophryne into five species groups: P. mentella, P. scotti, P. barsukovi, P. marmorata, and P. albipinna groups [5,11]

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