Enhanced genome assembly and a new official gene set for Tribolium castaneum

Abstract

Background: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.

The Easter Egg Weevil (Pachyrhynchus) genome reveals synteny in Coleoptera across 200 million years of evolution

“…To examine the gene synteny between other Coleoptera genomes, we downloaded chromosome-level genomes from NCBI or supplied form the journal or authors website (Supplemental Information file “NCBI_all_taxa_genomes_list”) (Fallon et al 2018; Zhang et al 2020; Herndon et al 2020; Van Belleghem 2018). We also used the unpublished genome assemblies ( Tribolium castaneum [GCF_000002335.3], Bombyx mori [GCA_000151625.1], Clogmia albipunctata [clogmia.6], Culex quinquefasciatus [CpipJ3], and Rhodnius prolixus [Rhodnius_prolixus-3.0.3]), generated by the DNA Zoo Consortium ( dnazoo.org ).…”

“…Given their vast diversity and economic importance as pollinators and crop pests, knowing more about the genomic architecture of beetles should be of broad applicability. However, to date, there are only four available genomes resolved to chromosome level for Coleoptera and none for weevils or the hyperdiverse beetle lineage Phytophaga (Van Belleghem et al 2018, Fallon et al 2018, Zhang et al 2020, Herndon et al 2020). Here we present the first genome resolved to chromosome level for the Phytophaga beetle lineage Pachyrhynchus sulphureomaculatus Schultze, 1922.…”

“…In addition, in situ Hi-C technology has shown that the 3D conformation of genomes is not random and that this conformation can influence gene expression and linkage (Sanborn et al 2015). The result of these new sequencing techniques has increased the number of high quality genomes for non-model insect species, including beetles (Matthews et al 2018, Hill et al 2019, Lu et al 2019, Liu et al 2019, Biello et al 2020, Herndon et al 2020, Zhang et al 2020). Because in situ Hi-C orders scaffolds and corrects misjoins, we can study synteny between organisms with more confidence (Dudchenko et al 2017, Ghurye et al 2019).…”

Arthropod IGF, Relaxin and Gonadulin, putative orthologs ofDrosophilainsulin-like peptides 6, 7 and 8, likely originated from an ancient gene triplication

“…Aedes aegypti (Matthews et al, 2018), Blattella germanica (Harrison et al, 2018), Bombyx mori (Kawamoto et al, 2019), Galleria melonella (Lange et al, 2018), Glossina morsitans (Attardo et al, 2019), Hermetia illucens (Zhan et al, 2020), Latrodectus hesperus (unpublished), Mesobuthus martensii (Cao et al, 2013), Oncopeltus fasciatus (Panfilio et al, 2019), Parasteatoda tepidariorum (Schwager et al, 2017), Pardosa pseudoannulata (Yu et al, 2019), Periplaneta americana (Li et al, 2018), Stegodyphus dumicola , Tetranychus urticae (Grbić et al, 2011), Timema cristinae (Riesch et al, 2017), Tribolium castaneum (Herndon et al, 2020) and Zootermopsis nevadensis (Terrapon et al, 2014). All genomes were downloaded from https://www.ncbi.nlm.nih.gov/genome/.…”

Peer Review #1 of "Arthropod IGF, relaxin and gonadulin, putative orthologs of Drosophila insulin-like peptides 6, 7 and 8, likely originated from an ancient gene triplication (v0.1)"

“…Aedes aegypti (Matthews et al, 2018), Blattella germanica (Harrison et al, 2018), Bombyx mori (Kawamoto et al, 2019), Galleria melonella (Lange et al, 2018), Glossina morsitans (Attardo et al, 2019), Hermetia illucens (Zhan et al, 2020), Latrodectus hesperus (https://www.ncbi.nlm.nih.gov/genome/?term=Latrodectus+hesperus), Mesobuthus martensii (Cao et al, 2013), Oncopeltus fasciatus (Panfilio et al, 2019), Parasteatoda tepidariorum (Schwager et al, 2017), Pardosa pseudoannulata (Yu et al, 2019), Periplaneta americana (Li et al, 2018), Stegodyphus dumicola (Liu et al, 2019), Tetranychus urticae (Grbić et al, 2011), Timema cristinae (Riesch et al, 2017), Tribolium castaneum (Herndon et al, 2020) and Zootermopsis nevadensis (Terrapon et al, 2014). All genomes were downloaded from https://www.ncbi.nlm.nih.gov/genome/.…”