Effect of sequencing data quantity on mitochondrial genome assembling efficiency of Platycephalus yoshinoi and Chiloscyllium plagiosum mitochondria

ZHAO Ruirui; LU Dingfang; LI Pengfei; HAN Zhiqiang; XU Shengyong

doi:10.13984/j.cnki.cn37-1141.2025.02.012

Abstract：The rapid development of high-throughput sequencing technologies and bioinformatic meth-ods has made it possible to conduct large-scale genomic sequencing of non-model organisms.However,how to obtain genomic information cost-effectively has become an important limitation for the promo-tion of high-throughput sequencing technologies.Given the diversity and genome size heterogeneity of marine fishes,herein the Osteichthyes Platycephalus yoshinoi and Chondrichthyes Chiloscyllium pla-giosum were chosen to conduct mitochondrial genome assembling,and investigate the effect of sequen-cing data quantity and depth on mitochondrial genome assembling efficiency of marine fish species.High depth Illumina sequencing data of P.yoshinoi and C.plagiosum were generated and 10 sequen-cing data gradients each species were constructed using in silico bioinformatic approaches.Mitochon-drial genome assembly was performed using NOVOPlasty software and the effectiveness and times of assembly were statistically analyzed.The results showed that the assembly time reduced significantly with the decrease of sequencing data and depth(Wilcoxon signed rank test,P＜0.01).The mitochon-drial genome of P.yoshinoi was failed to assemble when sequencing data were less than 0.3 Gb(se-quencing depth～0.4x)while the assembly time of C.plagiosum increased gradually when sequencing data were less than 0.15 Gb(～0.03x).Integrating the assembly effectiveness and times,the optimal sequencing data for mitochondrial genome assembly of P.yoshinoi and C.plagiosum were determined to be 0.3 Gb and 0.5 Gb,respectively,suggesting that 0.5 Gb sequencing data is optimal for mito-chondrial genome assembly of marine fish.Our results not only provided references for subsequent re-lated studies,but also facilitated mitochondrial assembly of marine fishes in a cost-effective manner,which will widen population genetic and phylogeny studies at the genomics level.Considering the limit-ed numbers of investigated species,further studies with increased species are warranted to verify the re-liability of the optimal sequencing data in this study.