Enhanced genome assembly and a new official gene set for Tribolium castaneum - from a draft to a reference genome

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 before the advent of next generation sequencing and with a small set of RNA sequence data limiting annotation quality. Results: Here, we present a new 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 and using an improved assembly pipeline, the gaps in the genome assembly were reduced and the N50 increased to 4,753kbp. 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 1,452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and miRNA 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.

Unexpected mutual regulation underlies paralogue functional diversification and promotes epithelial tissue maturation in Tribolium

“…Draft genome assemblies for T. freemani, T. madens, and T. confusum were obtained as assembled scaffolds in FASTA format (version 26 March 2013 for each species), accessed from the BeetleBase.org FTP site at Kansas State University (ftp://ftp.bioinformatics.ksu.edu/pub/BeetleBase/). Transcripts for Tc-zen1 (TC000921-RA) and Tc-zen2 (TC000922-RA) were obtained from the T. castaneum official gene set 3 (OGS3) 67 . These sequences were used as queries for BLASTn searches in the other species' genomes (BLAST + 2.2.30) 68,69 .…”

“…For serosal immune genes, a given gene was considered to be expressed in the late serosa if we detected ≥100 RNA-seq reads in each of the four biological replicates for our wild-type samples. Throughout, our reporting of "DE genes" refers to analyses across all isoforms (18,536 isoform models) in the T. castaneum official gene set OGS3 67 .…”

“…The overrepresented sequences of mitochondrial and ribosomal RNA were filtered out by mapping to a database of 1266 T. castaneum mitochondrial and ribosomal sequences extracted from the NCBI nucleotide database (accessed 21 October 2016, search query “tribolium [organism] AND (ribosomal OR mitochondrial OR mitochondrion) NOT (whole genome shotgun) NOT (Karroochloa purpurea)”) with Bowtie2 v2.2.9 84 . Trimmed and filtered reads were mapped to the T. castaneum OGS3 67 (file name: Tcas5.2_GenBank.corrected_v5.renamed.mrna.fa) with RSEM 85 . The raw read count output from RSEM was compiled into count tables.…”

Unexpected mutual regulation underlies paralogue functional diversification and promotes maturation of a protective epithelial tissue

“…For serosal immune genes, a given gene was considered to be expressed in the late serosa if we detected ≥100 RNA-seq reads in each of the four biological replicates for our wild type samples. Note that, throughout, our reporting of "DE genes" refers to analyses across all isoforms (18,536 isoform models) in the T. castaneum official gene set OGS3 67 .…”