Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude

Abstract

Background: The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial.

Results: Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions.

Conclusions: Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.

Figure 1

Sequencing depth of the ground tit genome assembly. The sequencing depth was measured by initially mapping all the raw reads to the assembly, and then calculating the number of reads for each base. More than 99% of the assembly sequences were covered 20× at least, indicating high accuracy at the nucleotide level.

Figure 2

Micro-synteny between the zebra finch and ground tit genomes. The X-axis represents the zebra finch (T. gut) chromosomes and the Y-axis represents the ground tit (P. hum) scaffolds. The 'dots' represent ortholog gene pairs between the two genomes. The scaled-up regions of the dot plot show two obvious chromosome inversions. In the right most up-scaled figure, one part of the scaffold54 sequence of P. hum is aligned in the forward orientation (colored in orange) to that of Chr4 of T. gut, while the other part of the scaffold54 sequence were aligned in the reverse orientation (colored in blue sky) to that of Chr4 of T. gut, indicating that there was a chromosome inversions in P. hum compared with T. gut. A similar inversion is shown on the left.

Figure 3

Phylogenetic tree reconstructed using all single-copy orthologs from nine species. The scale at the bottom of the figure represents the divergence time. The red dots represent the divergence time and its range (in brackets) between two branches.