ABSTRACT
The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.
Subject(s)
Microsatellite Repeats , Transcriptome , Animals , Gene Library , High-Throughput Nucleotide Sequencing , Microsatellite Repeats/genetics , Molecular Sequence Annotation , Polymorphism, Genetic , Transcriptome/geneticsABSTRACT
In the present study, the complete mitochondrial genome of Microphysogobio tungtingensis has been amplified with 16 pairs of primers. There are 16 627 base pairs has been identified and deposited in the GenBank with accession numbers MN970213. The arrangement was similar to typical vertebrate mitochondrial, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region. The overall base composition of M. tungtingensis was G + C: 42.9%, A + T: 57.1%, apparently with a slight AT bias. Phylogenetic analysis showed that M. tungtingensis was close to M. fukiensis.
ABSTRACT
The first complete mitochondrial genome of Acrossocheilus Labiatus from the Qingshui River were reported in this study with accession number MG878098. The overall nucleotide composition was 31.13% A, 25.10% T, 27.52% C, 16.24% G, respectively. Phylogenetic analysis shows that the A. parallens and A. Hemispinus showed a closest phylogenetic relationship, then clustal with A. Labiatus.
