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

Year 2018, Volume: 14 Issue: 1, 135 - 140, 30.03.2018

Vahap Eldem

https://doi.org/10.18466/cbayarfbe.390277

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.

Keywords

EST-SSRs, Eisenia fetida, Annelids, Sequence repeats

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