Yıl 2018, Cilt 14, Sayı 1, Sayfalar 135 - 140 2018-03-30

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

Vahap Eldem [1]

56 70

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.

EST-SSRs, Eisenia fetida, Annelids, Sequence repeats
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Orcid: 0000-0003-3767-5661
Yazar: Vahap Eldem (Sorumlu Yazar)
E-posta: vahap.eldem@istanbul.edu.tr
Ülke: Turkey

Bibtex @araştırma makalesi { cbayarfbe390277, journal = {Celal Bayar Üniversitesi Fen Bilimleri Dergisi}, issn = {1305-130X}, address = {Celal Bayar Üniversitesi}, year = {2018}, volume = {14}, pages = {135 - 140}, doi = {10.18466/cbayarfbe.390277}, title = {Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826)}, key = {cite}, author = {Eldem, Vahap} }
APA Eldem, V . (2018). Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826). Celal Bayar Üniversitesi Fen Bilimleri Dergisi, 14 (1), 135-140. DOI: 10.18466/cbayarfbe.390277
MLA Eldem, V . "Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826)". Celal Bayar Üniversitesi Fen Bilimleri Dergisi 14 (2018): 135-140 <http://dergipark.gov.tr/cbayarfbe/issue/36240/390277>
Chicago Eldem, V . "Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826)". Celal Bayar Üniversitesi Fen Bilimleri Dergisi 14 (2018): 135-140
RIS TY - JOUR T1 - Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826) AU - Vahap Eldem Y1 - 2018 PY - 2018 N1 - doi: 10.18466/cbayarfbe.390277 DO - 10.18466/cbayarfbe.390277 T2 - Celal Bayar Üniversitesi Fen Bilimleri Dergisi JF - Journal JO - JOR SP - 135 EP - 140 VL - 14 IS - 1 SN - 1305-130X-1305-1385 M3 - doi: 10.18466/cbayarfbe.390277 UR - http://dx.doi.org/10.18466/cbayarfbe.390277 Y2 - 2018 ER -
EndNote %0 Celal Bayar Üniversitesi Fen Bilimleri Dergisi Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826) %A Vahap Eldem %T Genome-wide EST-SSR Marker Identification in Red Wiggler Worm Eisenia fetida (Savigny, 1826) %D 2018 %J Celal Bayar Üniversitesi Fen Bilimleri Dergisi %P 1305-130X-1305-1385 %V 14 %N 1 %R doi: 10.18466/cbayarfbe.390277 %U 10.18466/cbayarfbe.390277