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Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra)

  • Wencong Liu
  • Yongtao Xu
  • Zekun Li
  • Jun Fan
  • Yi YangEmail author
Original Article
  • 49 Downloads

Abstract

The complete genome sequence provides the opportunity for genome-wide and coding region analysis of SSRs in the king cobra and for cross-species identification of microsatellite markers in the Chinese cobra. In the Ophiophagus hannah genome, tetranucleotide repeats (38.03%) were the most abundant category, followed by dinucleotides (23.03%), pentanucleotides (13.07%), mononucleotides (11.78%), trinucleotides (11.49%) and hexanucleotides (2.6%). Twenty predominant motifs in the O. hannah genome were (A)n (C)n, (AC)n, (AG)n, (AT)n, (AGG)n, (AAT)n, (AAG)n, (AAC)n, (ATG)n, (ATAG)n, (AAGG)n, (ATCT)n, (CCTT)n, (ATTT)n, (AAAT)n, (AATAG)n, (ATTCT)n, (ATATGT)n, (AGATAT)n. In total, 4344 SSRs were found in coding sequences (CDSs). Tetranucleotides (52.79%) were the most abundant microsatellite type in CDS, followed by trinucleotides (28.50%), dinucleotides (11.02%), pentanucleotides (4.42%), mononucleotides (1.77%), and hexanucleotides (1.50%). A total of 984 CDSs containing microsatellites were assigned 11152 Gene Ontology (GO) functional terms. Gene Ontology (GO) analysis demonstrated that cellular process, cell and binding were the most frequent GO terms in biological process, cellular component and molecular function, respectively. Thirty-two novel highly polymorphic (PIC > 0.5) SSR markers for Naja atra were developed from cross-species amplification based on the tetranucleotide microsatellite sequences in the king cobra genome. The number of alleles (NA) per locus had between 3 and 11 alleles with an average of 6.5, the polymorphism information content (PIC) value ranged from 0.521 to 0.858 (average = 0.707), the observed heterozygosity (Ho) of 32 microsatellite loci ranged from 0.292 to 0.875 (mean = 0.678), the expected heterozygosity (HE) ranged from 0.561 to 0.889 (average = 0.761), and 3 microsatellite loci exhibited statistically significant departure from Hardy–Weinberg equilibrium (HWE) after Bonferroni correction (p < 0.003).

Keywords

King cobra Chinese cobra Genome SSR markers Tetranucleotide repeats Polymorphic 

Notes

Acknowledgements

This research was funded by 973 Projects NSFC31671455 and 2015CB755702.

Compliance with ethical standards

Conflicts of interest

There are no conflicts of interest among authors.

Supplementary material

11033_2019_5044_MOESM1_ESM.docx (17 kb)
Supplementary material 1 (DOCX 17 kb)
11033_2019_5044_MOESM2_ESM.csv (2 mb)
Supplementary material 2 (CSV 2048 kb)
11033_2019_5044_MOESM3_ESM.xlsx (26 kb)
Supplementary material 3 (XLSX 26 kb)

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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life SciencesSichuan UniversityChengduChina
  2. 2.College of Materials and Chemistry & Chemical EngineeringChengdu University of TechnologyChengduChina
  3. 3.College of ForestryJiangxi Agricultural UniversityNanchangChina

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