Gene family expansions in Antarctic winged midge as a strategy for adaptation to cold environments

Abstract

Parochlus steinenii is the only flying insect native to Antarctica. To elucidate the molecular mechanisms underlying its adaptation to cold environments, we conducted comparative genomic analyses of P. steinenii and closely related lineages. In an analysis of gene family evolution, 68 rapidly evolving gene families, involved in the innate immune system, unfolded protein response, DNA packaging, protein folding, and unsaturated fatty acid biosynthesis were detected. Some gene families were P. steinenii-specific and showed phylogenetic instability. Acyl-CoA delta desaturase and heat shock cognate protein 70 (Hsc70) were representative gene families, showing signatures of positive selection with multiple gene duplication events. Acyl-CoA delta desaturases may play pivotal roles in membrane fluidity, and expanded Hsc70 genes may function as chaperones or thermal sensors in cold environments. These findings suggest that multiple gene family expansions contributed to the adaptation of P. steinenii to cold environments.

Figure 1

BUSCO assessment of gene set and Comparison of P. steinenii protein-coding genes. (a) Completeness assessment of gene sets using BUSCO. The BUSCO dataset of the Insecta odb9 were used to assess the gene sets predicted from the initial assembled genome using SNAP and the gene sets from the final assembled genome using SNAP or AUGUSTUS. (b) Venn diagram of orthologous gene families among six dipteran genomes. (c) Lineage-specific gene gains and losses in six dipteran genomes. The number of gene gains, losses, and the rapidly evolving gene families were marked in red, blue, and green, respectively. E, M, O, and P denote Eocene, Miocene, Oligocene, and Paleocene, respectively. The aligned sequences of orthologous gene families were used to construct a phylogenetic tree using FastTree (v.2.1.10) and divergence time between species was inferred using TimeTree.

Figure 2

Enriched GO term of rapidly evolving gene families in P. steinenii. (a) TreeMap summarized from the redundant GO terms using REVIGO for all GO terms linked to rapidly evolving gene families. (b) GO terms linked to 25 P. steinenii-specific gene families. Enriched biological process terms were visualized using REVIGO. The terms “detection of mechanical stimulus involved in sensory perception of pain,” “larval turning behavior,” “sensory perception of pain,” and “sodium ion transport” were related to expansions of pickpocket protein 28 gene family (group51) and group6074. “Positive regulation of cholesterol esterification,” “fatty-acyl-CoA biosynthetic process”, and “unsaturated fatty acid biosynthetic process” were related to the expanded acyl-CoA delta desaturase gene family (group1599), and “protein folding” was related to the expanded Hsc70 gene family (group513).

Figure 3

The expanded acyl-CoA delta desaturase gene family of P. steinenii. (a) Phylogenetic analysis of acyl-CoA desaturase genes in the P. steinenii-specific gene family (group1599) and orthologous gene family (group2588). Orthologous gene families in C. elegans were designated as outgroups. Numbers at nodes are bootstrap values from 1000 replicates and GenBank accession numbers are indicated at the ends of branches. (b) Amino acid sequence similarity matrix of acyl-CoA delta desaturase genes. P. steinenii-specific acyl-CoA delta desaturase (group1599), orthologous groups of acyl-CoA delta desaturase among in six insect species (group2588), stearoyl-CoA desaturase NP_005054.3 (Homo sapiens), and NP_033153.2 (Mus musculus) were used for the similarity matrix. Percent identities were calculated using the result of BlastP. (c) Expanded acyl-CoA delta desaturase gene families identified in the P. steinenii genome. P. steinenii-specific gene families are indicated by green arrows and orthologous genes are indicated by red arrows. Other genes are indicated in blue arrows. Each arrow indicates a gene orientation (5′ → 3′).

Figure 4

The expanded Hsc70 gene family of P. steinenii. (a) Phylogenetic analysis of Hsc70 genes in the P. steinenii-specific gene family (group513) and orthologous gene family (group441). Orthologous gene families in C. elegans were designated as outgroups. Numbers at nodes are bootstrap values from 1000 replicates and GenBank Accession numbers are indicated at the ends of branches. (b) Amino acid sequence similarity matrix of Hsc70 genes. P. steinenii-specific Hsc70 (group513), orthologous groups of Hsc70 genes among in six insect species (group441), NP_006588.1 (H. sapiens), NP_034609.2 (M. musculus), and NP_503068.1 (C. elegans) were used for the similarity matrix. Percent identities were calculated using the result of BlastP. (c) Expanded Hsc70 gene families identified in the P. steinenii genome. P. steinenii-specific gene families are indicated by pink arrows and orthologous genes are indicated by yellow arrows. Other genes are indicated in blue arrows. Each arrow indicates a gene orientation (5′ → 3′).