High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

Abstract

Background Ants with complex societies have fascinated scientists for centuries. Comparative genomic and transcriptomic analyses across ant species and castes have revealed important insights into the molecular mechanisms underlying ant caste differentiation. However, most current ant genomes and transcriptomes are highly fragmented and incomplete, which hinders our understanding of the molecular basis for complex ant societies. Findings By hybridizing Illumina, Pacific Biosciences, and Hi-C sequencing technologies, we de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb. Our new assembly provides better resolution for the discovery of genome rearrangement events at the chromosome level. Analysis of full-length isoform sequencing (ISO-seq) suggested that ∼15 Gb of ISO-seq data were sufficient to cover most expressed genes, but the number of transcript isoforms steadily increased with sequencing data coverage. Our high-depth ISO-seq data greatly improved the quality of gene annotation and enabled the accurate detection of alternative splicing isoforms in different castes of M. pharaonis. Comparative transcriptome analysis across castes based on the ISO-seq data revealed an unprecedented number of transcript isoforms, including many caste-specific isoforms. We also identified a number of conserved long non-coding RNAs that evolved specifically in ant lineages and several that were conserved across insect lineages. Conclusions We produced a high-quality chromosome-level genome for M. pharaonis, which significantly improved previous short-read assemblies. Together with full-length transcriptomes for all castes, we generated a highly accurate annotation for this ant species. These long-read sequencing results provide a useful resource for future functional studies on the genetic mechanisms underlying the evolution of social behaviors and organization in ants.

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

“…This is higher than the values recently reported for humans (3.62) and two species of bats (1.92 and 1.49), but lower than pharaoh ants (9) (Q. Gao et al, 2020; Wen et al, 2018). Less than 5% of genes had more than 20 different transcripts.…”

“…Iso-seq is now also used to annotate de novo genome assemblies of non-model organisms, like the cave nectar bat ( Eonycteris spelaea ) (Wen et al, 2018), the pharaoh ant ( Monomorium pharaonis ) (Q. Gao et al, 2020), the red-eared slider turtle ( Trachemys scripta elegans ) (Simison et al, 2020), or the sponge gourd ( Luffa spp.) (Pootakham et al, 2020), allowing for the characterization of both gene functions and alternative splicing patterns.…”

A genomic investigation of the marine teleost tarakihi (Nemadactylus macropterus) provides insights into its genome evolution and population structure

“…Intron retention was thought, until recently, to be the least prevalent alternative splicing form in animals, but our results are part of growing evidence showing that this may not be the case (Q. Gao et al, 2020;. Interestingly, intron retention events were more abundant in the tarakihi and the goldfish, while they were much less abundant than alternative 5'/3' splice sites events in the bat (see Chapter 3).…”

“…Q. Gao et al, 2020;Gong et al, 2018;Simison et al, 2020;Sun et al, 2021;Yang et al, 2019;Zhang et al, 2020). While useful for the applications used in this study, the tarakihi genome assembly produced for this thesis could be improved with further Hi-C scaffolding.…”

“…Iso-seq is now also used to annotate de novo genome assemblies of non-model organisms, like the cave nectar bat (Eonycteris spelaea) (Wen et al, 2018), the pharaoh ant (Monomorium pharaonis) (Q. Gao et al, 2020), the red-eared slider turtle (Trachemys scripta elegans) (Simison et al, 2020), or the sponge gourd (Luffa spp.) (Pootakham et al, 2020).…”