DOI: 10.5061/dryad.dr7sqv9zx
title: A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae)

description: The Orange wheat blossom midge Sitodiplosis mosellana Géhin (Diptera:
 Cecidomyiidae), an important insect pest, has caused serious yield losses
 in most wheat-growing areas worldwide in the past half-century. In this
 study, we assembled the first chromosomal level genome for S. mosellana
 using PacBio long-read, Illumina short-read sequences and high-throughput
 chromatin conformation capture (Hi-C) genome scaffolding techniques. The
 final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of
 998.71 kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored
 four pseudochromosomes, accounting for 99.67% of the assembled genome. The
 assembly showed high integrity and quality, with 91.7% of short reads
 mapped to the genome and a coverage rate of 99.8%. The assembly quality
 was evaluated using Core Eukaryotic Genes Mapping Approach and
 Benchmarking Universal Single-Copy Orthologs. In total, 12,269
 protein-coding genes were predicted, of which 91% were functionally
 annotated. Phylogenetic analysis indicated that S. mosellana and its close
 relative the swede midge Contarinia nasturtii diverged about 32.7 million
 years ago. S. mosellana genome showed high chromosomal synteny with the
 genome of Drosophila melanogaster and Anopheles gambiae. The key gene
 families involved in chemosensation and detoxification of plant secondary
 chemistry were analysed. The high-quality S. mosellana genome data will
 provide an invaluable resource for research in a broad range of areas,
 including the biology, ecology, genetics, and evolution of midges as well
 as insect-plant interactions and co-evolution, and their relatives more
 generally.
description: High-quality DNA extracted
 from the larvae was used for library preparation and high-throughput
 sequencing. Short-insert (350 bp) paired-end libraries were prepared
 according to the Illumina protocol and sequenced on the Illumina NovaSeq
 6000 (Illumina, Inc.) with paired-end 150 (PE150) read layout. Whole
 genome sequencing was performed using the PacBio Sequel sequencer (Pacific
 Biosciences). 20-Kb single-molecule real-time sequencing (SMRT) bell
 libraries were constructed using the standard protocol. In total, 46.49 Gb
 of raw data for <i>S. mosellana</i> was obtained.
 All raw reads from the
 PacBio platform were aligned to each other using ‘daligner’ (Myers, 2014)
 executed using the mail script of the FALCON assembler (Chin et al.,
 2016). Overlapping reads and raw subreads were processed to generate
 consensus sequences, and error correction of the assembly was polished
 using the consensus-calling algorithm Quiver (Chin et al., 2013). The
 paired-end clean reads from the Illumina platform were further corrected
 any remaining errors using Pilon (Walker et al., 2014), and the reads
 obtained after strict error correction were further used for the
 subsequent scaffolding. To assist the
 chromosome-level assembly, we used the high-throughput chromosome
 conformation capture (Hi-C) technique to capture genome-wide chromatin
 interactions (Belaghzal et al., 2017). For Hi-C sequencing, chromosomal
 structure was fixed by formaldehyde crosslinking, and then MboI enzyme was
 used to shear DNA. Hi-C library with 350 bp insert size was constructed,
 which was sequenced on Illumina NovaSeq 6000 according to the
 manufacturer’s instructions. We then used the pruning, partition, rescue,
 optimization, and building of the ALLHiC pipeline (Dudchenko et al., 2017;
 Zhang et al., 2019) to construct the chromosomal-level scaffolds of
 <i>S. mosellana</i> genome.
description: Genome.tar.gz The genome file of
 <em>Sitodiplosis mosellana </em>.
 repeat_annotation.tar.gz The repeat
 annotation files of <em>Sitodiplosis mosellana</em>.
 ncRNA_annotation.tar.gz The ncRNA annotation
 files of <em>Sitodiplosis mosellana</em>.
 Structure_annotation.tar.gz The structure
 annotation files of <em>Sitodiplosis mosellana</em>.
 Function_annotation.tar.gz The function
 annotation files of <em>Sitodiplosis mosellana</em>.