Hypoxic and Cold Adaptation Insights from the Himalayan Marmot Genome

Abstract

SummaryThe Himalayan marmot (Marmota himalayana) is a hibernating mammal that inhabits the high-elevation regions of the Himalayan mountains. Here we present a draft genome of the Himalayan marmot, with a total assembly length of 2.47 Gb. Phylogenetic analyses showed that the Himalayan marmot diverged from the Mongolian marmot approximately 1.98 million years ago. Transcriptional changes during hibernation included genes responsible for fatty acid metabolism in liver and genes involved in complement and coagulation cascades and stem cell pluripotency pathways in brain. Two selective sweep genes, Slc25a14 and ψAamp, showed apparent genotyping differences between low- and high-altitude populations. As a processed pseudogene, ψAamp may be biologically active to influence the stability of Aamp through competitive microRNA binding. These findings shed light on the molecular and genetic basis underlying adaptation to extreme environments in the Himalayan marmot.

Calcium-Binding Proteins in the Nervous System during Hibernation: Neuroprotective Strategies in Hypometabolic Conditions?

“…These adaptations are paralleled by significant changes in gene expression, which are thought to occur through differential control by transcription factors and chromatin remodeling [84,117,118,119]. These changes involve among other functions metabolism, response to hypoxia, DNA repair, cytoskeletal remodeling, and Ca 2+ signaling [120,121,122].…”

Genomic Analyses Reveal Evidence of Independent Evolution, Demographic History, and Extreme Environment Adaptation of Tibetan Plateau Agaricus bisporus

“…The diploid consensus sequence was converted to the desired input format file using fq2psmcfa tool (Kozma et al, 2016). The mutation rate was estimated using the formula: μ = D × g /2 T , where D is the sequence difference of homolog pair genes between two species, g is the estimated generation time, and T is the estimated divergence time (Bai et al, 2018). Firstly, genes from two genomes were blast by all-vs.-all manner to identify the best hit homolog gene pairs.…”

iMarmot: an integrative platform for comparative and functional genomics of marmots

“…At present the iMarmot possesses three de novo genome assemblies, including Himalayan marmot, Alpine marmot and Yellow-bellied marmot. The assembly sequence of Alpine marmot and Yellow-bellied marmot were downloaded from the GenBank assembly database of NCBI, while the assembly of Himalayan marmot was derived from our previous work [10]. Totally, 21,609 protein-coding genes have been predicted for Himalayan marmot, 23,923 for Alpine marmot and 24,575 for Yellow-bellied marmot.…”

“…In 2018, the Yellow-bellied marmot (Marmota flaviventris) draft genome was also released (accession number: GCA_003676075.2). Meanwhile, our group has assembled and published the genome sequence of the Himalayan marmot (Marmota himalayana) and resequenced the whole genomes of another four marmots, including Mongolia marmot (Marmota sibirica), Gray marmot (Marmota baibacina), Long-tailed marmot (Marmota caudata) and Yellow-bellied marmot in 2019 [10]. Particularly, RNA-seq or microarray data from a broad range of mammal hibernators and plague hosts provide novel insight into understanding the special biological features of marmots, especially the molecular mechanism of hibernation [10][11][12][13][14][15][16].…”