Molecular characterization and sequencing of the whole mitochondrial genome of native duck breed Maithili (Anas platyrhynchos)

Abstract

The Maithili duck breeds are indigenous to southern Asia and hold significant socioeconomic value for duck farmers in India. Though, they face endangerment primarily due to unregulated crossbreeding practices. Present study aimed to characterize the whole mitochondrial genome of the Maithili duck (Anas platyrhynchos, Anseriformes), which is still unexplored. This is first report about sequencing and annotation of full length mitochondrial DNA (mtDNA) of the Maithili duck, revealing a size of 16,607 bp. Thirteen protein-coding genes (PCGs), several ribosomal RNA (rRNA) genes, twenty three transfer RNA (tRNA) genes and a prominent non-coding control region (D-loop) were present in the mtDNA. The initiation codon for each PCG was ATG, except for ND1 (ACA), ND5 (GTG), and COX2 (GTG). Among the 13 PCGs, six terminated with the typical single T-- codon, while the rest ended with TAA, CAA, AGG, and TAG. Moreover, these 13 PCGs' relative synonymous codon usage matched quite well with previous published Anseriformes genomes. Every tRNA gene showed normal secondary structures of a clover-leaf, except for tRNA-Ser (GCT), which did not have the dihydrouridine 'DHU' arm. Phylogenetic analysis positioned the Maithili duck breed in close relation to the mallard breed of Anas platyrhynchos. With the entire mitochondrial genome sequence now available, researchers will find it easier to investigate the evolutionary links between ducks and other bird species and trace the history of domestication.