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. 2017 Dec 1;6(12):1-12.
doi: 10.1093/gigascience/gix109.

Genome sequence of the small brown planthopper, Laodelphax striatellus

Affiliations

Genome sequence of the small brown planthopper, Laodelphax striatellus

Junjie Zhu et al. Gigascience. .

Abstract

Background: Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from 2 other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will further the understanding of the genetic basis of the biological differences among the 3 rice planthoppers.

Findings: A total of 190 Gb of Illumina data and 32.4 Gb of Pacbio data were generated and used to assemble a high-quality L. striatellus genome sequence, which is 541 Mb in length and has a contig N50 of 118 Kb and a scaffold N50 of 1.08 Mb. Annotated repetitive elements account for 25.7% of the genome. A total of 17 736 protein-coding genes were annotated, capturing 97.6% and 98% of the BUSCO eukaryote and arthropoda genes, respectively. Compared with N. lugens and S. furcifera, L. striatellus has the smallest genome and the lowest gene number. Gene family expansion and transcriptomic analyses provided hints to the genomic basis of the differences in important traits such as host range, migratory habit, and plant virus transmission between L. striatellus and the other 2 planthoppers.

Conclusions: We report a high-quality genome assembly of L. striatellus, which is an important genomic resource not only for the study of the biology of L. striatellus and its interactions with plant hosts and plant viruses, but also for comparison with other planthoppers.

Keywords: annotation; comparative genomics; genome sequencing; insects; virus transmission.

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Figures

Figure 1:
Figure 1:
Photograph of Laodelphax striatellus on a rice plant leaf. Scale bar, 1 mm.
Figure 2:
Figure 2:
Gene cluster analysis among 22 arthropod species. 1:1:1 and N: N: N represent universal orthologs with single-copy or multiple-copy numbers, respectively. Insect, Diptera, Hemiptera, Hymenoptera, Lepidoptera, and Coleoptera stand for taxon-specific orthologs, respectively. Other indicates orthlogs that do not belong to any abovementioned ortholog categories. SD indicates species-specifically duplicated genes. ND indicates genes that cannot be classified into any other categories. The location of Laodelphax striatellus is indicated by an arrow.
Figure 3:
Figure 3:
Venn diagram of functional annotation by 4 databases. NR: nonredundant protein databases.
Figure 4:
Figure 4:
Phylogenetic analysis of 22 arthropod species. The phylogenetic tree was constructed based on amino acid sequences of 277 single-copy orthologs among 22 arthropod species (Anopheles gambiae, Anoplophora glabripennis, Apis mellifera, Acyrthosiphon pisum, Bombyx mori, Bemisia tabaci, Cimex lectularius, Diaphorina citri, Drosophila melanogaster, Diuraphis noxia, Danaus plexippus, Daphnia pulex, Locusta migratoria, Laodelphax striatellus, Nilaparvata lugens, Nasonia vitripennis, Oncopeltus fasciatus, Pediculus humanus, Rhodnius prolixus, Sogatella furcifera, Tribolium castaneum, Zootermopsis nevadensis) using the maximum likelihood algorithm. The tree was rooted with D. pulex.

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