Abstract
Labeo catla is a widely cultured species in monoculture and polyculture systems of the Indian subcontinent. In this study, the complete mitochondrial genome sequence of catla was reconstructed from Oxford Nanopore sequence data. The mitochondrial genome is 16,600 bp in length (accession no. is MN830943) which is larger than the previously reported catla mitogenomes. Like other vertebrate mitochondrial genomes, it has 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a putative control region. Most of the mitogenes are encoded on H-strand. Phylogenetic analysis showed that Labeo catla is more closely related to Labeo rohita than other labeo species. The catla mtgenome reported here will facilitate population genetics, phylogenetics and molecular taxonomy of Indian major carps.
Labeo catla (Hamilton, 1822) commonly known as ‘catla’ is one of the Indian major carp and the second most popular freshwater aquaculture species in the Indian subcontinent due to its fast growing nature and appealing taste. Mitochondrial DNA has been widely used to trace the geographic distribution of genetic variation due to its maternal inheritance and a high mutation rate (Avise et al. Citation1987). In comparison with partial mtDNA sequences, complete mtDNA sequence has numerous advantages, and it can provide novel frame of reference on teleost phylogenies (Miya et al. Citation2003). The complete mitochondrial genome of catla has been sequenced and reported using Sanger’s and Illumina sequencing (Accession no.– NC016892, JQ087872 and KY419138). Although the advantages of the NGS technology were explored by the previous study through Illumina sequencing technology (Sahoo et al. Citation2017), here we have reconstructed the complete mitochondrial genome of catla (Accession no. – MN830943) from Oxford Nanopore reads for the first time and compared with complete mitogenomes of other cyprinids.
Total genomic DNA was extracted from testis tissue of catla stored at ICAR-CIFA (Voucher no. CIFA-CC01), India (20.1861° N, 85.8564° E) using standard phenol chloroform method (Sambrook and Russel Citation2001). Nanopore libraries were prepared from genomic DNA from one individual and sequenced on Oxford Nanopore (MinION) platform. A total of 20 GB sequence data was obtained. De novo assembly was performed with default parameters using MaSuRCA-3.2.8. Contigs ranging from 10 to 16 kb in length were subjected to blast in NCBI database. The longest contigs of 16,600 bp in size was found to be the mitogenome of catla and was annotated using MitoAnnotator (Iwasaki et al. Citation2013). The complete mitogenome sequences for other cyprinids were downloaded from the NCBI database. A maximum likelihood phylogenetic tree was constructed by taking 13 complete cypriniformes mitogenome, one siluriformes mitogenome as outgroup along with the reconstructed catla mitogenome using MEGA X (Kumar et al. Citation2018).
In this study, the complete mitogenome of catla is 16,600 bp in length with GeneBank accession no. MN830943 and composed of 13 protein coding genes, 22 tRNAs, 2 rRNAs and a putative control region. The mitogenome of catla reconstructed from Nanopore data is largest in size in comparison to the mtDNAs reported earlier, which shows 2 and 1 bp variation in D-loop and intergenic spacer region in between tRNAAsn and tRNACys, respectively. Organization of genes in the catla mitogenome is similar to other vertebrates. Except for few genes, the most of the mitogenes are encoded in the H-strand. The overall base composition of catla mitogenome is as follows: A: 30.48% G: 14.63% C: 28.09% T: 26.78% and A + T content is 57.26%. Mostly, in all the protein coding genes, ATG is used as start codon except CO1 gene, which encodes GTG. Likewise, TAA and an incomplete stop codon T– are encoded by protein-coding genes except for ND6, which uses TAG in catla. Out of 22 tRNA genes, 21 tRNA genes of catla can fold into a typical cloverleaf structure, except for tRNASer(AGY) lacking dihydrouridine arm identified by the online software tRNAscan SE 2.0 (Chan and Lowe Citation2019). The size of tRNA genes varied from 67 to 76 bp. The D-loop is 931 bp in size and contains a microsatellite (TA)7, a putative termination-associated sequence and three conserved sequence blocks. There are 6 overlaps and 14 intergenic spacer regions with a 37 bp long intergenic spacer region in between tRNAAsn and tRNACys. Fascinatingly, the mitochondrial genome yielded from the present study showing 99% resemblance to the mitochondrial genome sequenced earlier in our laboratory (Bej et al. Citation2012; Sahoo et al. Citation2017) having 16,594 and 16,597 bp length, respectively. The phylogenetic analysis inferred that Labeo catla () is closely related to Labeo rohita. The complete mitogenome sequence of L. catla will facilitate population genetics and evolutionary studies of cyprinidae family.
Figure 1. ML tree of complete mitogenome sequences of 15 teleosts (*present study).
Acknowledgments
The authors are thankful to the Director, ICAR-CIFA, Bhubaneswar, for providing the laboratory facility to carry out the present work.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability statement
The data that support the findings of this study are openly available in “NCBI” at https://www.ncbi.nlm.nih.gov/, reference number MN830943.
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Funding
References
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