Comparison of genetic characteristics between captive and wild giant pandas based on 13 mitochondrial coding genes

Abstract

Background: Research on genetic diversity based on mitochondrial DNA of giant pandas mainly focused on a single marker or a few genes.

Objective: To provide a more comprehensive assessment of the genetic diversity on giant pandas based on 13 mitochondrial protein coding genes.

Methods: We assembled 13 protein coding genes in the mitochondrial genome of the giant panda based on the whole genome sequencing data, including ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, ND6 and Cyt b.

Results: We successfully obtained long sequence of 11,416 base pairs with all 13 genes for 110 giant panda individual, accounting for 67.93% in length of the mitochondrial reference genome. Haplotype diversity was 0.9518 ± 0.009 and nucleotide diversity (π) was 0.00157 ± 0.00014. We detected three new haplotypes, including GPC10 and GPC21 for the CR sequence and GPB12 for the Cyt b gene.

Conclusion: These multi-gene sequences provided more genetic variable information to compare captive and wild giant panda population.

Keywords: Genetic diversity; Giant panda; Haplotype diversity; Mitochondrial genome.