Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani

Abstract

The flour beetle Tribolium freemani is a sibling species of the model organism and important pest Tribolium castaneum. The two species are so closely related that they can produce hybrid progeny, but the genetic basis of their differences has not been revealed. In this work, we sequenced the T. freemani genome by applying PacBio HiFi technology. Using the well-assembled T. castaneum genome as a reference, we assembled 262 Mb of the T. freemani genomic sequence and anchored it in 10 linkage groups corresponding to nine autosomes and sex chromosome X. The assembly showed 99.8% completeness of conserved insect genes, indicating a high-quality reference genome. Comparison with the T. castaneum assembly revealed that the main differences in genomic sequence between the two sibling species come from repetitive DNA, including interspersed and tandem repeats. In this work, we also provided the complete assembled mitochondrial genome of T. freemani. Although the genome assembly needs to be ameliorated in tandemly repeated regions, the first version of the T. freemani reference genome and the complete mitogenome presented here represent useful resources for comparative evolutionary studies of related species and for further basic and applied research on different biological aspects of economically important pests.

Genome assembly and annotation of the red flour beetle (Tribolium castaneum)from India

“…Comparing inTcas1 with the closest relatives T. freemani (Volarić et al, 2022) and T. confusum (Bracewell et al, 2023), we observed that the former shows better synteny between linkage groups (Figures 1C-D), consistent with the recent finding that T. freemani is the sister species of T. castaneum , instead of T. confusum as was previously believed (Ramesh et al 2021). However, across the ∼13.7 My (million years) divergence between T. castaneum and T. freemani , we do see several structural differences within LGs.…”

“…generations. We used one female from the fifth generation to extract high molecular weight DNA (Volarić et al, 2022) using the Qiagen DNeasy blood and tissue kit, confirmed that the peak fragment size was >1Kb, and sequenced it on the Oxford Nanopore MinION platform.…”

“…Despite subsequent updates (Herndon et al, 2020 ), 6.6% of the genome (13.5 Mb) consists of unspanned gaps and 8.3% (17 Mb) is in unplaced contigs (Volarić et al, 2022). The Y chromosome is also poorly assembled into 27 putative scaffolds.…”

“…The published T. castaneum reference (Tcas5.2) was sequenced using Sanger and Illumina shotgun sequencing technology at 7X coverage (Richards et al, 2008). Despite subsequent updates (Herndon et al, 2020), 6.6% of the genome (13.5 Mb) consists of unspanned gaps and 8.3% (17 Mb) is in unplaced contigs (Volarić et al, 2022). The Y chromosome is also poorly assembled into 27 putative scaffolds.…”

The First Five Mitochondrial Genomes for the Family Nidulariaceae Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of Agaricales

“…The mitogenome of organisms is known to contain various types of repetitive sequences, including tandem and interspersed repeats [ 39 , 40 ]. We analyzed the mitogenomes of five Cyathus species to identify and characterize their repetitive sequences.…”