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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #349071

Research Project: Genetics, Breeding and Reproductive Physiology to Enhance Production of Catfish

Location: Warmwater Aquaculture Research Unit

Title: The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus)

item YUAN, ZIHAO - Auburn University
item ZHOU, TAO - Auburn University
item BAO, LISUI - Auburn University
item LIU, SHIKAI - Auburn University
item SHI, HUITONG - Auburn University
item YANG, YUJIA - Auburn University
item GAO, DONGYA - Auburn University
item DUNHAM, REX - Auburn University
item Waldbieser, Geoffrey - Geoff
item LIU, ZHANJIANG - Auburn University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/7/2018
Publication Date: 5/15/2018
Citation: Yuan, Z., Zhou, T., Bao, L., Liu, S., Shi, H., Yang, Y., Gao, D., Dunham, R., Waldbieser, G.C., Liu, Z. 2018. The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus). PLoS One. 13:e0197371.

Interpretive Summary: Genomes of vertebrate species contain repetitive sequences that occur in multiple locations throughout the genome. As part of our efforts to characterize the channel catfish genome, scientists at Auburn University and an ARS scientist in Stoneville, MS, used bioinformatics methods to categorize repetitive sequences. The scientists found that approximately 44% of the catfish genome consists of repetitive elements, with Tc1/mariner transposons the most abundant type. These transposons were distributed across the entire genome. Furthermore, 16% of the catfish repetitive sequences were not found in other species. These results provide a more comprehensive map of the catfish genome for use in genomic selection of catfish broodstock, and can aid genome annotation in other bony fishes.

Technical Abstract: Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome. Among them, the DNA/TcMar-Tc1 transposons are the most abundant type, making up ~20% of the total repetitive elements, followed by the microsatellites (14%). The prevalent of repetitive elements, especially the mobile elements, may have provided a driving force for the evolution of the catfish genome. A number of catfish-specific repetitive elements were identified including the previously reported Xba elements whose divergence rate was relatively low, slower than that in untranslated regions of genes but faster than the protein coding sequences, suggesting its evolutionary restrictions.