The genome-wide landscape of small insertion and deletion mutations in Monopterus albus

Abstract

Insertion and deletion (indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1–21 bp deletions and 1–15 bp insertions, were detected. Each indel gene had ∼1.1 deletions/insertions, and 2–4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to non-indel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.

Introduction

The swamp eel (Monopterus albus), a fresh-water teleost fish, taxonomically belongs to the family Synbranchidae of the order Synbranchiformes. The fish is distributed mainly in tropical and subtropical freshwater areas of Asia, Indo-Malayan archipelago and northern Australia. It is also present in western Africa, Mexico, Central and South America (Collins et al., 2002; Joseph, 2006). Swamp eel is not only an economically important species for fish production as its high nutritional and potential medical values, but also an emerging model species in development, genetics and evolution (Cheng et al., 2003). It has a characteristic feature of sex reversal from female to male via intersex during its life (Liu, 1944; Bullough, 1947), and also a small genome size (806 Mb) (Zhao et al., 2018). As a wide geographic distribution and attractive biological features of the species, its speciation process may provide insights into vertebrate evolution. However, population genetic structure of the species remains unknown.

Genetic variation often occurs to adapt to biogeographically various and changeable ecosystems, which are mainly divided into structural variations (SVs) (>100 bp) and simple nucleotide variations (SNVs) (<100 bp) (Gonzaga-Jauregui et al., 2012). SVs include small copy number variants (CNVs) (100 bp‒1 kb), large CNVs (>1 kb), and inversions, while SNVs consist of SNPs and small insertions and deletions (indels). SNPs have a highly polymorphic information content, which were mainly used as a genome-wide tool in GWAS (Lee et al., 2017), QTL mapping of quantitative traits (El-Soda et al., 2014) and selective sweep analysis (Li et al., 2013). Small indels are involved in duplicated gene evolution (Guo et al., 2012), tRNA origination (Zuo et al., 2013), genome structure variations (Tian et al., 2008), cellular lineage and gene expression (Imielinski et al., 2017). All these variations are usually detected from alignments of different genomes or transcriptomes with reference genome. However, microsatellite, which is a tract of tandem nucleotide repeated motifs (one to six or up to ten nucleotides, and typically repeated 5–50 times) (Toth et al., 2000), can be easily identified through just the information of one genome. Although expansions occur mainly in noncoding regions, microsatellites are associated with important biological roles, such as expression regulation (Bilgin Sonay et al., 2015). The genes that contain microsatellites in their promoters have higher expression divergence compared to genes with fixed or no microsatellite in their promoters (Bilgin Sonay et al., 2015). Thus, identification of genetic variations is a fundamental task for understanding of genome structure, functions and evolution.

Mutations are mostly arisen from replication error, transposition and DNA damage. In addition, transcription error is another factor for mutation occurrence (Datta and Jinksrobertson, 1995; Aguilera, 2002; Svejstrup, 2002; Hanawalt and Spivak, 2008; Kim and Jinks-Robertson, 2012; Park et al., 2012). In the process of transcription, the non-template strand is exposed as a single-stranded DNA (ssDNA) which is convenient for mutation (Kim and Jinks-Robertson, 2012). Transcription-associated supercoiling and collision between replication forks and transcription machinery may also lead to mutations (Kim and Jinks-Robertson, 2012). Because these mutations were detected mainly based on SNPs, it remains unclear whether transcription has a genome-wide role on indel formation. In addition, indels could be probably generated by unequal crossover during DNA duplication. Nevertheless, genetic and evolutionary mechanisms of indels remain elusive.

In this study, we applied a comparative genome-transcriptome-alignment approach, and obtained thousands of short indels in coding genes in the genome of swamp eel. We observed more deletions than insertions on the genome and population levels. Most of the indels occurred in non-domain regions. Sizes of indels mainly were multiples of three, which led to in frame mutations. Compared to non-indel genes, indel genes had higher expression levels and lower evolution rates. We further indicated that divergent evolution has occurred in the swamp eel populations. These data reveal not only genome-wide landscape of indels in the genome of swamp eel, but also provide new genetic markers for further analysis of population genetic structure and evolution of the species.