Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra)
| Autor: | Wencong Liu, Zekun Li, Jun Fan, Yi Yang, Yongtao Xu |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Genetic Markers King cobra Naja Locus (genetics) Genome Loss of heterozygosity 03 medical and health sciences 0302 clinical medicine Genetics Chinese cobra Animals Molecular Biology Alleles Whole genome sequencing Polymorphism Genetic biology Ophiophagus hannah Naja naja General Medicine Sequence Analysis DNA biology.organism_classification 030104 developmental biology Genetic Loci 030220 oncology & carcinogenesis Microsatellite Genome-Wide Association Study Microsatellite Repeats |
| Zdroj: | Molecular biology reports. 46(6) |
| ISSN: | 1573-4978 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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