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. 2024 May 4;11(1):451.
doi: 10.1038/s41597-024-03289-x.

Chromosome-level genome assembly of Odontothrips loti Haliday (Thysanoptera: Thripidae)

Luo Yingning  1 , Wei Shuhua  2 , Dai Wenting  1 , Miao Miao  1 , Wang Ying  2 , Zhang Rong  2 , Ban Liping  3
Affiliations

Chromosome-level genome assembly of Odontothrips loti Haliday (Thysanoptera: Thripidae)

Luo Yingning et al. Sci Data. .

Abstract

As the predominant pest of alfalfa, Odontothrips loti Haliday causes great damages over the major alfalfa-growing regions of China. The characteristics of strong mobility and fecundity make them develop rapidly in the field and hard to be controlled. There is a shortage of bioinformation and limited genomic resources available of O. loti for us to develop novel pest management strategies. In this study, we constructed a chromosome-level reference genome assembly of O. loti with a genome size of 346.59 Mb and scaffold N50 length of 18.52 Mb, anchored onto 16 chromosomes and contained 20128 genes, of which 93.59% were functionally annotated. The results of 99.20% complete insecta_odb10 genes in BUSCO analysis, 91.11% short reads mapped to the ref-genome, and the consistent tendency among the thrips in the distribution of gene length reflects the quality of genome. Our study provided the first report of genome for the genus Odontothrips, which offers a genomic resource for further investigations on evolution and molecular biology of O. loti, contributing to pest management.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Odontothrips loti (a), alfalfa with O. loti damage (b) and without O. loti damage (c).
Fig. 2
Fig. 2
Characteristics of the Illumina short-read sequencing of the Odontothrips loti genome.
Fig. 3
Fig. 3
Heatmap of genome-wide Hi-C data and circular representation of the chromosomes of Odontothrips loti. (a) The heatmap of chromosome interactions in O. loti. The frequency of Hi-C interaction links is represented by colors, which ranges from yellow (low) to red (high). (b) Circos plot of distribution of the genomic elements in O. loti. The tracks indicate (i) length of the chromosome, (ii) gene density, (iii) distribution of transposable element (TE) density, and (iv) GC density. Center: intra-genomic syntenic blocks of O. loti. The densities of genes, TEs, and GC were calculated in 500 kb windows.
Fig. 4
Fig. 4
Benchmarking of genome completeness of Odontothrips loti genome assembly and annotation, evaluated by BUSCO based on insect_odb10 database which includes 1,367 genes. C: the number of complete genes, S: the number of complete and single-copy genes, D: the number of complete and duplicated genes, F: the number of incomplete genes, M: the number of missing genes.
Fig. 5
Fig. 5
Annotated genes comparison of the distribution of (a) gene length (b) CDS length (c) exon length (d) intron length in Odontothrips loti with Drosophila melanogaster and four closely related species. The x-axis represents the length, and the y-axis represents the density of genes.
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