Background: Sweetpotato whitefly, Bemisia tabaci MED/Q and MEAM1/B, are two economically important invasive species that cause considerable damages to agriculture crops through direct feeding and indirect vectoring of plant pathogens. Recently, a draft genome of B. tabaci MED/Q has been assembled. In this study, we focus on the genomic comparison between MED/Q and MEAM1/B, with a special interest in MED/Q’s genomic signatures that may contribute to the highly invasive nature of this emerging insect pest.
Results: The genomes of both species share similarity in syntenic blocks, but have significant divergence in the gene coding sequence. Expansion of cytochrome P450 monooxygenases and UDP glycosyltransferases in MED/Q and MEAM1/B genome is functionally validated for mediating insecticide resistance in MED/Q using in vivo RNAi. The amino acid biosynthesis pathways in MED/Q genome are partitioned among the host and endosymbiont genomes in a manner distinct from other hemipterans. Evidence of horizontal gene transfer to the host genome may explain their obligate relationship. Putative loss-of-function in the immune deficiency-signaling pathway due to the gene loss is a shared ancestral trait among hemipteran insects.
Conclusions: The expansion of detoxification genes families, such as P450s, may contribute to the development of insecticide resistance traits and a broad host range in MED/Q and MEAM1/B, and facilitate species’ invasions into intensively managed cropping systems. Numerical and compositional changes in multiple gene families (gene loss and gene gain) in the MED/Q genome sets a foundation for future hypothesis testing that will advance our understanding of adaptation, viral transmission, symbiosis, and plant-insect-pathogen tritrophic interactions.
Digital Object Identifier (DOI)
This research was supported by the National Natural Science Foundation of China (31420103919 and 31672032), the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS), Beijing Nova Program (Z171100001117039) and the Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables.
MED/Q P450, UGT, ABC transporter, COE and GST dataset will be available from the corresponding authors on reasonable requests. The final, assembly Portiera (PRJNA299729/SAMN04214819/LNJY00000000) and Hamiltonella (PRJNA299727/SAMN04214805/LNJW00000000) genome of MED/Q, respectively, are accessible at NCBI.
Xie, Wen; Yang, Xin; Chen, Chunhai; Yang, Zezhong; Guo, Litao; Wang, Dan; Huang, Jinqun; Zhang, Hailin; Wen, Yanan; Zhao, Jinyang; Wu, Qingjun; Wang, Shaoli; Coates, Brad S.; Zhou, Xuguo; and Zhang, Youjun, "The Invasive MED/Q Bemisia tabaci Genome: A Tale of Gene Loss and Gene Gain" (2018). Entomology Faculty Publications. 153.
Additional file 1: Annotation of the unique genes from MED/Q genome relative to MEAM1/B.
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Additional file 2: Annotation of the unique genes from MEAM1/B genome relative to MED/Q.
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Additional file 3: Table S1. Reads mapped ratio of MED/Q and MEAM1/B with each other.
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Additional file 4: Table S2. Syntenic alignment between MED/Q and MEAM1/B genome.
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Additional file 5: Figure S1. Syntenic blocks between Bemisia tabaci MED/Q and MEAM1/B genome.
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Additional file 6: Table S3. Identification and analysis of the orthologous genes between MED/Q and MEAM1/B.
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Additional file 7: Orthologs with existed both Ka and Ks.
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Additional file 8: Orthologous with Ka/Ks value larger than 1.
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Additional file 9: GO enriched results of the sequences between MED/Q and MEAM1/B with Ka/Ks values > 1.
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Additional file 10: KEGG enriched results of the sequences between MED/Q and MEAM1/B with Ka/Ks values > 1.
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Additional file 11: Figure S2. Estimated divergence times among insect genomes using PAML mcmctree.
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Additional file 12: Orthologous gene families specific from MEAM1/B in the MED/Q.
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Additional file 13: Orthologous gene families specific from others in the MED/Q.
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Additional file 14: Table S4. Gene ontology of gene families specific in MED/Q from MEAM1/B (FDR < 0.05).
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Additional file 15: Table S5. Gene ontology of gene families specific in MED/Q from other 15 species (FDR < 0.05).
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Additional file 16: Candidate PSGs in MED/Q.
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Additional file 17: Candidate PSGs in MED/Q and MEAM1/B.
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Additional file 18: Table S6. Gene ontology of PSG in MED/Q and MEAM1/B (FDR < 0.05, P < 0.01).
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Additional file 19: Table S7. Gene ontologies for gene families that have expanded number of members on MED/Q branch (FDR < 0.05, p < =0.000515776699029126).
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Additional file 20: Figure S3. Gene family expansion and contraction in B. tabaci Q genome compared to other arthropods.
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Additional file 21: Table S8. Gene ontologies for gene families that have expanded number of members on Bemisia tabaci branch (FDR < 0.05, p < =0.000879854368932039).
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Additional file 22: Table S9. Gene ontology over-representation of gene families contracted on Bemisia tabaci branch (FDR < 0.05, p < =0.000572390572).
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Additional file 23: Table S10. Gene ontology over-representation of gene families contracted on Bemisia tabaci branch (FDR < 0.05, p < =0.000572390572).
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Additional file 24: Table S11. Immune system-related and virus transport genes in phloem- and blood-feeding insects.
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Additional file 25: Figure S4. Pathways encoded by Candidatus hamiltonella for amino acid biosynthesis.
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Additional file 26: Table S12. Genes involved in B vitamin biosynthesis in MED/Q.
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Additional file 27: Table S13. Genes involved in B vitamin biosynthesis in Candidatus Hamiltonella defense.
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Additional file 28: Figure S5. Phylogenetic trees for 11 horizontally transferred genes (HGTs).
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Additional file 29: Table S14. Horizontally transferred genes involved in amino acid biosynthesis in MED/Q.
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Additional file 30: Table S15. Comparison of transaminases in three symbiotic systems Bemisia tabaci/Portiera, Acyrthosiphum pisum/Buchnera and Nilaparvata lugens/Yeast-like.
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Additional file 31: Figure S6. The RNA interference efficiency of nine CYP450 and three GST gene.
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Additional file 32: Table S16. Primers used in this study.