关键词: 线粒体基因组, 鸟类, 基因富集

Abstract:

The mitochondrial genes of animals are frequently utilized as molecular markers in phylogenetic studies， environmental DNA （eDNA） analysis， and species identification， including COX1 and 12S rRNA. However， the variability in locus selection among researchers has contributed to a lack of consistency in reference databases. Adopting complete mitochondrial genome sequences as references can efficiently solve this problem. For environmental DNA research， establishing a localized mitochondrial genome database for various species is particularly imperative. In our study， we designed bird-specific mitochondrial genome gene capture probes based on 10 conserved loci within the avian mitochondrial genome. Employing these probes， we captured， assembled， and annotated the mitochondrial genomes of 17 species， encompassing 19 bird samples collected in Shanghai， China. Despite the absence of a reference mitochondrial genome for the Pale Thrush， we successfully assembled its complete mitochondrial genome. A comparative analysis of sequencing outcomes utilizing both methods， namely direct library construction without enrichment and enrichment preceding library construction， for Pale Thrush samples revealed that gene capture significantly enhanced the proportion of mitochondrial DNA in the overall genome library. A subsequent random sampling of the sequencing outcomes from both methodologies revealed that， under stringent conditions involving roughly 40 000 reads （equivalent to approximately 0.012 gigabytes of sequencing data）， the captured results achieved a coverage of approximately 75%， whereas the non-captured samples exhibited only a 25% coverage. Notably， with an increased sequencing data of approximately 0.24 gigabytes， the gene-captured samples attained 100% coverage for the first time. In comparison to the conventional approach of segmentally amplifying mitochondrial genomes using primers， the probes introduced in this study offer a more efficient and expedited method for acquiring bird mitochondrial genomes.

Key words: mitochondrial genome, aves, gene capture