Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives

Abstract

High-altitude inhospitable environments impose a formidable life challenge for the local animals. Training and exposure to high-altitude environments produce both distinct physiological and phenotypic characteristics. The mitochondrion, an organelle crucial for the energy production, plays an important role in hypoxia adaptation. In this study, we investigated the mitochondrial DNA (mtDNA) polymorphism and copy number variation between the population pairs from distinct altitudes across the multi-species. Higher mitochondrial DNA control region's genetic diversity is conspicuous in highaltitude animals versus low-altitude relatives. We also found an accordant decrease of mtDNA copy number in most of the tissues from high-altitude animals. Compared to mammals, chickens have significantly distinct mitogenomic characteristics, and more significant changes in the skeletal muscle mtDNA copy number between high-and low-altitude individuals. Our study catches a snapshot of the biological similarities and differences in the mitochondrial high-altitude acclimation across the species.

Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers

“…The mtDNA sequences have been deposited in GenBank with accession numbers MT684350-MT684456. All sequences were compared with the reference sequence (Liu et al 2018) and classified in haplotypes and haplogroups, following the nomenclature previously published by Miao et al (2013).…”

Bushmeat Species Identification: Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow (LF) Strip for Identification of Formosan Reeves’ Muntjac (Muntiacus reevesi micrurus)

“…The length of incubation time might be associated with the initial number of DNA copies [20]. Considering that there are thousands of copies of mitochondrial DNA per cell [41], the number of DNA copies might also contribute to the highly efficient amplification of frmRPA-LF. Ten minutes of amplification time was decided in order for the frmRPA-LF assay to compensate for the low reaction rate caused by the low temperature.…”

Relative species abundance estimation in artificial mixtures of insects using mito‐metagenomics and a correction factor for the mitochondrial DNA copy number

“…Such methods do exist In medicine, the mitochondrial DNA copy number is usually estimated using quantitative PCR (qPCR; Thyagarajan et al, 2012); this method requires two primer pairs, one for a mitochondrial marker and one for a single-copy nuclear marker. These primers are known for humans, but it would be costly to generate them for every species in an environmental sample, especially for those species whose genome has not yet been sequenced (but see Liu et al, 2018). The qPCR itself is cheap, but the preparative work for each species would be long.…”

“…Thus, a species i with twice the number of mitogenomes per nuclear genome than another species j will produce twice many mitochondrial reads as well; without a proper correcting factor, species i would, apparently, be twice more abundant in the mixture than species j . This fact is known (Bista et al, 2018; Piñol et al, 2015; Tang et al, 2014), but there are not reliable solutions to the problem because little is known about the causes of the variation of the mitochondrial copy number across ‐species (but see Liu et al, 2018, that reported a higher mitochondrial copy number in organs with a high metabolic rate and in species living at low altitude than in their counterparts at high altitude in the Tibetan Plateau).…”