Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826)

Abstract

Earthworms belong to the main groups of soil-dwelling invertebrates and are an important element for soil biota. The ecological importance of earthworms on terrestrial ecosystem is mainly attributed to their close synergistic interaction with soil biota. Among earthworms, Eisenia fetida has been considered as preferred for vermiculture and vermicomposting practices due to their reproductive potentials, short life cycle and wide temperature and density pressure tolerances. Although the genome and transcriptome data for E. fetida are available, the EST-SSRs composition and frequency of this species, which used for phylogenetic studies, genus-level taxonomy and population genetics, remain poorly defined. In current study, we mined publicly available transcriptome data and characterised genome-wide EST-SSR markers for this epigeic species. A total of 13,060 EST-SSRs were identified from 162,609 contigs. The most abundant EST-SSR types were found to be trimeric repeats (5,998, 46%) followed by dimeric (4,762, 36%), tetrameric (1,716, 13%), pentameric (478, 4%) and hexameric repeats (106, 1%). For SSR motifs, the most prevalent motifs were AC/GT (14.72%), followed by AT/AT (13.20%), ATC/ATG (13.03%), AAT/ATT (12.30%) and AG/CT (8.46%). Following validation of the species using COI sequences and to test the designed primer pairs, the eight primer pairs were designed, but only six of them were successfully amplified. Although EST-SSR information is scarce for annelids, the EST-SSR patterns of E. fetida seem to be similar to annelids. Overall, the EST-SSR markers help in taxonomic resolution of Eisenia genus from other earthworm genera and in studying the population structure and geographic distributions of E. fetida.