Genome‐wide characterization of microsatellites in cobia Rachycentron canadum (Linnaeus, 1766): survey and analysis of their abundance and diversity

Abstract

The cobia Rachycentron canadum, mainly distributed in the warm waters of tropical and subtropical regions around the world, remains a fish of considerable economic importance. Detailed diversity and the number of microsatellite sequences in the cobia genome are still unintelligible. The primary objective of this work is to identify and quantify the miscellaneous SSR sequences in the cobia genome. More than 280,000 sequences were sequenced and screened by Next‐generation sequencing technology and microsatellite identification. Perfect mononucleotide repeats, dinucleotide, and trinucleotide microsatellites (DNMs & TNMs) contain (A)₁₀/(T)₁₀, (AC)₆/(TG)₆, and (AAT)_5~32 as the largest number of motifs in each type of microsatellite, respectively. The tetranucleotide and pentanucleotide microsatellites (TTMs & PTMs) consist of the largest number of motifs of both (ATCT)_5~32 and (TCAT)_5~31 in TTMs, and (CTCTC)_5~9 in PTMs, whereas the hexanucleotide microsatellites are rarely observed in the cobia genome. All approximately 3.8 thousand sequences of composite microsatellites are extremely diverse, including compound (11.71%), interrupted compound (71.77%), complex (0.45%), and interrupted complex (16.07%). In this study, we developed a convenient and useful recording system for writing down and categorizing diverse composite microsatellite types. This system will provide great support for exploring repeat origins, evolutionary mechanisms, and the application of polymorphic microsatellites.

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