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

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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1. Edwards, C. A, The importance of earthworms as key representatives of the soil fauna. In: Edwards C.A.(ed) Earthworm Ecology, 2nd edn. CRC press, NY, Washington, 2004, pp 3-11.
2. Dominguez, J, Edwards, C.A, Subler, S, A comparison of vermicomposting and composting, Biocycle, 1997, 38(4), 57-59.
3. Blouin, M, Hodson, M.E, Delgado, E.A, Baker, G, Brussaard, L, Butt, K.R, Dai, J, Dendooven, L, Peres, G, Tondoh, J.E, Cluzeau, D, Brun, J.J, A review of earthworm impact on soil function and ecosystem services, European Journal of Soil Science, 2013, 64(2), 161-82.
4. Gómez-Brandón, M, Domínguez, J, Recycling of solid organic wastes through vermicomposting: microbial community changes throughout the process and use of vermicompost as a soil amendment, Critical Reviews in Environmental Science and Technology, 2014, 44(12), 1289-1312.
5. Bouché, M.B, Strategies lombriciennes. In: U, Lohm, T, Persson(ed) Soil Organism as Components of Ecosystems, 1nd edn, Stockholm, 1977, pp 122-132.
6. Deka, H, Deka, S, Baruah, C. K, Das, J, Hoque, S, Sarma, H, Sarma, N. S, Vermicomposting potentiality of Perionyx excavatus for recycling of waste biomass of Java citronella--an aromatic oil yielding plant, Bioresource Technology, 2011, 102(24), 11212-11217.
7. Ponmani, S, Udayasoorian, C, Jayabalakrishnan, R. M, Kumar, K. V, Vermicomposting of paper mill solid waste using epigeic earthworm Eudrilus eugeniae, Journal of Environmental Biology, 2014, 35(4), 617-622.
8. Suthar, S, Vermicomposting potential of Perionyx sansibaricus (Perrier) in different waste materials, Bioresource Technology, 2007, 98(6), 1231-1237.
9. Cheng, J, Zhao, Z, Li, B, Qin, C, Wu, Z, Trejo-Saavedra, D. L, Luo, X, Cui, J, Rivera-Bustamante, R. F, Li, S, Hu, K, A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum, Scientific Reports, 2016, 6, 18919.
10. Eujayl, I, Sledge, M. K, Wang, L, May, G. D, Chekhovskiy, K, Zwonitzer, J. C, Mian, M. A, Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp, Theoretical and Applied Genetics, 2004, 108(3), 414-422.
11. Bolger, A. M, Lohse, M, Usadel, B, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 2014, 30(15), 2114-2120.
12. Haas, B. J, A, Papanicolaou, M, Yassour, M, Grabherr, P. D, Blood, J, Bowden, M. B, Couger, D, Eccles, B, Li, M, Lieber, M. D, MacManes, M. Ott, J, Orvis, N, Pochet, F, Strozzi, N, Weeks, R, Westerman, T, William, C. N, Dewey, R, Henschel, R. D, LeDuc, N, Friedman, A, Regev, De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, 2013, 8(8), 1494-512.
13. Huang, Y, Niu, B, Gao, Y, Fu, L, Li, W, CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, 2010, 26(5), 680-682.
14. Nishimura, O, Hara, Y, Kuraku, S, gVolante for standardizing completeness assessment of genome and transcriptome assemblies, Bioinformatics, 2017, 33(22), 3635-3637.
15. Simão, F. A, Waterhouse, R. M, Ioannidis, P, Kriventseva, E. V, Zdobnov, E. M, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 2015, 31(19), 3210-3212.
16. Jiang, Q, Li, Q, Yu, H, Kong, L, Genome-wide analysis of simple sequence repeats in marine animals-a comparative approach, Marine Biotechnology, 2014, 16(5), 604-619.
17. Zwarycz, A. S, Nossa, C. W, Putnam, N. H, Ryan, J. F, Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida, Genome Biology and Evolution, 2015, 8(1), 271-281.
18. Csuzdi, C, Zicsi, A, Misirlioğlu, M, An annotated checklist of the earthworm fauna of Turkey (Oligochaeta: Lumbricidae), Zootaxa, 2006, 1175, 1-29.
19. Mısırlıoğlu, M, Valchovski, H, Contributions to Earthworm (Clitellata; Annelida) Fauna of Turkish Thrace, Sakarya Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2017, 21(3), 385-388.
20. Bhambri, A, Dhaunta, N, Patel, S. S, Hardikar, M, Srikakulam, N, Shridhar, S, Vellarikkal, S, Suryawanshi, H, Pandey, R, Jayarajan, R, Verma, A, Kumar, V, Bhatt, A, Gautam, P, Rai, M, Khan, J. A, Fromm, B, Peterson, K. J, Scaria, V, Sivasubbu, S, Pillai, B, Insights into regeneration from the genome, transcriptome and metagenome analysis of Eisenia fetida, bioRxiv,2017.