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

Zihao Yuan, Tao Zhou, Lisui Bao, Shikai Liu, Huitong Shi, Yujia Yang, Dongya Gao, Rex Dunham, Geoff Waldbieser, Zhanjian "John" Liu

Research output: Contribution to journalArticle

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 ectother-mic 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 Mega-base (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 prevalence 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.

Original languageEnglish (US)
Article numbere0197371
JournalPLoS One
Volume13
Issue number5
DOIs
StatePublished - May 1 2018

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Ictaluridae
Ictalurus punctatus
Catfishes
Genes
catfish
Genome
genome
Comparative Physiology
Untranslated Regions
Aquaculture
toxicology
Allergy and Immunology
immunology
transposons
Microsatellite Repeats
Immunology
Toxicology
Vertebrates
aquaculture
Proteins

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus). / Yuan, Zihao; Zhou, Tao; Bao, Lisui; Liu, Shikai; Shi, Huitong; Yang, Yujia; Gao, Dongya; Dunham, Rex; Waldbieser, Geoff; Liu, Zhanjian "John".

In: PLoS One, Vol. 13, No. 5, e0197371, 01.05.2018.

Research output: Contribution to journalArticle

Yuan, Z, Zhou, T, Bao, L, Liu, S, Shi, H, Yang, Y, Gao, D, Dunham, R, Waldbieser, G & Liu, ZJ 2018, 'The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus)', PLoS One, vol. 13, no. 5, e0197371. https://doi.org/10.1371/journal.pone.0197371
Yuan, Zihao ; Zhou, Tao ; Bao, Lisui ; Liu, Shikai ; Shi, Huitong ; Yang, Yujia ; Gao, Dongya ; Dunham, Rex ; Waldbieser, Geoff ; Liu, Zhanjian "John". / The annotation of repetitive elements in the genome of channel catfish (Ictalurus punctatus). In: PLoS One. 2018 ; Vol. 13, No. 5.
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