A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae)

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.