Investigating the patterns of simple sequence repeats (SSRs) inferred from the whole genome of a critically endangered species Cassine koordersii kosterm

Abstract

Cassine koordersii Kosterm. (Celastraceae) is a critically endangered species indigenous to Jember, East Java. Programs for genetic conservation and plant breeding have recently implemented next-generation sequencing (NGS) techniques based on genomic data. This research aims to explore and distinguish between perfect and imperfect SSR patterns in the assembled genome. The Abyss assembler produced 3,060,362 scaffolds with 35.63 % GC content for the assembled genome. The investigation and identification of SSRs using the Krait tool found 139,236 and 582,360 sequences for including perfect and imperfect SSRs, respectively. There were six motif repeats of perfect and imperfect SSRs consisting of 73,175 and 202,438 sequences of mononucleotide (the most motif was A); 17,179 and 65,705 sequences of dinucleotide (the most motif was AT); 5,175 and 51,948 sequences of trinucleotide (the most motif was AAT); 3,824 and 14,010 sequences of tetranucleotide (the most motif was AAAT); 659 and 3,082 sequences of pentanucleotide (the most motif is AAAAT); 118 and 757 sequences of hexanucleotide (the most motif is AAAAAT). The depicted perfect and imperfect SSRs markers can be employed in future genetic studies of Cassine and related genera for either recommendation effort or improvement in conservation genetic concerns.