Abstract
The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 437 kb, and a total length of 658 Mb. Annotation of repetitive elements and coding regions resulted in 265.0 Mb TEs (40.3%) and 20 786 protein-coding genes with putative gene family expansions, respectively. Phylogenetic analysis based on orthologs across 14 arthropod taxa suggested that MED/Q is clustered into a hemipteran clade containing A. pisum and is a sister lineage to a clade containing both R. prolixus and N. lugens. Genome completeness, as estimated using the CEGMA and Benchmarking Universal Single-Copy Orthologs pipelines, reached 96% and 79%. These MED/Q genomic resources lay a foundation for future 'pan-genomic' comparisons of invasive vs. noninvasive, invasive vs. invasive, and native vs. exotic Bemisia, which, in return, will open up new avenues of investigation into whitefly biology, evolution, and management.
Document Type
Article
Publication Date
3-10-2017
Digital Object Identifier (DOI)
https://doi.org/10.1093/gigascience/gix018
Funding Information
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) the China Agriculture Research System (CARS-26-10), Beijing Nova Program (Z171100001117039), Beijing Training Project for the Leading Talents in S & T (LJRC201412) and the Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables.
Related Content
This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession LIED00000000. The version described in this paper is version LIED01000000 accessible at NCBI. Further data, including annotation files and assembled transcripts, are available in the GigaScience GigaDB repository.
Figure S1. Schematic illustration of the assembly pipeline for MED/Q genome based on the combined assemblies from WGS and BACs.
Table S1. Statistics of the whole genome sequencing data.
Table S2. Repeat Masker analysis in four hemiptera species.
Table S3. Evidenced use within GLEAN MED/Q protein-coding genes.
Table S4. Summary of GLEAN gene models.
Table S5. Functional annotation of the MED/Q genome.
Table S6. Orthologous gene comparison among genomes of 14 arthropod species.
Table S7. Quality control of assembled genome.
Repository Citation
Xie, Wen; Chen, Chunhai; Yang, Zezhong; Guo, Litao; Yang, Xin; Wang, Dan; Chen, Ming; Huang, Jinqun; Wen, Yanan; Zeng, Yang; Liu, Yating; Xia, Jixing; Tian, Lixia; Cui, Hongying; Wu, Qingjun; Wang, Shaoli; Xu, Baoyun; Li, Xianchun; Tan, Xinqiu; Ghanim, Murad; Qiu, Baoli; Pan, Huipeng; Chu, Dong; Delatte, Helene; Maruthi, M. N.; Ge, Feng; Zhou, Xueping; Wang, Xiaowei; Wan, Fanghao; Du, Yuzhou; and Zhou, Xuguo Joe, "Genome Sequencing of the Sweetpotato Whitefly Bemisia tabaci MED/Q" (2017). Entomology Faculty Publications. 140.
https://uknowledge.uky.edu/entomology_facpub/140
gix018_GIGA-D-16-00061_Original_Submission
gix018_GIGA-D-16-00061_Revision_1.pdf (6765 kB)
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gix018_Response_to_reviewer_comments_Revision_1.pdf (62 kB)
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gix018_Reviewer_1_Report_(Original_Submission).pdf (78 kB)
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gix018_Reviewer_2_Report_(Original_Submission)
gix018_Reviewer_2_Report_(Revision_1).pdf (76 kB)
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gix018_Reviewer_2_Report_(revision_2).pdf (67 kB)
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gix018_S1_Fig.png (19 kB)
Figure S1. Schematic illustration of the assembly pipeline for MED/Q genome based on the combined assemblies from WGS and BACs.
gix018_S1_Table (1).pdf (46 kB)
Table S1. Statistics of the whole genome sequencing data.
gix018_S2_Table.pdf (62 kB)
Table S2. Repeat Masker analysis in four hemiptera species.
gix018_S3_Table.pdf (44 kB)
Table S3. Evidenced use within GLEAN MED/Q protein-coding genes.
gix018_S4_Table.pdf (62 kB)
Table S4. Summary of GLEAN gene models.
gix018_S5_Table.pdf (41 kB)
Table S5. Functional annotation of the MED/Q genome.
gix018_S6_Table.pdf (53 kB)
Table S6. Orthologous gene comparison among genomes of 14 arthropod species.
gix018_S7_Table.pdf (12 kB)
Table S7. Quality control of assembled genome.
Notes/Citation Information
Published in GigaScience, v. 6, issue 5, gix018, p. 1-7.
© The Author 2017.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Due to the large number of authors, only the first 30 and the authors affiliated with the University of Kentucky are listed in the author section above. For the complete list of authors, please download this article.