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. 2024 Sep 16;11(1):1003.
doi: 10.1038/s41597-024-03737-8.

Chromosome-level genome assembly of cotton thrips Thrips tabaci (Thysanoptera: Thripidae)

Yue Gao #  1   2   3 , Jichao Ji #  4   5   6 , Chao Xu  1   3   7 , Li Wang  1   8 , Kaixin Zhang  1   8 , Dongyang Li  1   8 , Xiaoyun Wang  3 , Miaomiao Xin  9 , Hongxia Hua  3 , Lizhen Chen  3 , Xueke Gao  1   8 , Xiangzhen Zhu  10   11 , Jinjie Cui  12   13 , Junyu Luo  14   15
Affiliations

Chromosome-level genome assembly of cotton thrips Thrips tabaci (Thysanoptera: Thripidae)

Yue Gao et al. Sci Data. .

Abstract

Cotton thrip, Thrips tabaci is a major polyphagous pest widely distributed on a variety of crops around the world, causing huge economic losses to agricultural production. Due to its biological and genomic characteristics, this pest can reproduce quickly and develop resistance to various pesticides in a very short time. However, the lack of high-quality reference genomes has hindered deeper gene function exploration and slows down the development of new management strategies. Here, we assembled a high-quality genome of T. tabaci at the chromosome level for the first time by using Illumina, PacBio long reads, and Hi-C technologies. The 329.59 Mb genome was obtained from 320 contigs, with a contig N50 of 1.53 Mb, and 94.21% of the assembly was anchored to 18 chromosomes. In total, 17,816 protein-coding genes were annotated, and 96.78% of BUSCO genes were fully represented. In conclusion, this high-quality genome provides a valuable genetic basis for our understanding of the biology of T. tabaci and contributes to the development of management strategies for cotton thrip.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Morphological characteristics of Thrips tabaci across different development stages.
Fig. 2
Fig. 2
Genome assembly and temporal transcriptome of Thrips tabaci. (A) Genome scope profiles of 19-mer analysis. (B) Hi-C interactive heatmap of eighteen linkage pseudo-chromosomes in Thrips tabaci genome. Color indicates the intensity of the interaction signal. The darker the color, the higher the intensity. (C) Circle genome landscape of Thrips tabaci. Circle a represents chromosomes, while circles b-e indicate repeat density, SSR density, gene density, and GC content of each respective chromosome, respectively. (D) Protein-coding gene prediction of Thrips tabaci through three strategies.
Fig. 3
Fig. 3
Differential expressed genes in pairwise comparison of Thrips tabaci across different developmental stages. (A) Venn diagrams of DEGs among those pairwise comparisons. (B–G) Volcanic maps of different expressed genes in separate comparison among different developmental stages. The red and green balls represent the significantly up- and down-regulated expressed genes, respectively.
Fig. 4
Fig. 4
Significantly enriched KEGG pathways of DEGs in these pairwise comparison of Thrips tabaci at different developmental stages.
See this image and copyright information in PMC

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