Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q

Wen Xie, Chunhai Chen, Zezhong Yang, Litao Guo, Xin Yang, Dan Wang, Ming Chen, Jinqun Huang, Yanan Wen, Yang Zeng, Yating Liu, Jixing Xia, Lixia Tian, Hongying Cui, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xianchun Li, Xinqiu Tan, Murad Ghanim & 23 others Baoli Qiu, Huipeng Pan, Dong Chu, Helene Delatte, M. N. Maruthi, Feng Ge, Xueping Zhou, Xiaowei Wang, Fanghao Wan, Yuzhou Du, Chen Luo, Fengming Yan, Evan L. Preisser, Xiaoguo Jiao, Brad S. Coates, Jinyang Zhao, Qiang Gao, Jinquan Xia, Ye Yin, Yong Liu, Judith K Brown, Xuguo Joe Zhou, Youjun Zhang

Research output: Contribution to journalComment/debate

18 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbergix018
Pages (from-to)1-7
Number of pages7
JournalGigaScience
Volume6
Issue number5
DOIs
StatePublished - May 1 2017

Fingerprint

Hemiptera
Genes
Genome
Libraries
Agricultural Crops
Insecticide Resistance
Quarantine
Phloem
Benchmarking
Arthropods
Host Specificity
Firearms
Insecticides
DNA sequences
Pathogens
Scaffolds
Crops
Pipelines
Proteins

Keywords

  • Annotation
  • Assembly
  • Genomics
  • Whitefly Bemisia tabaci

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

Xie, W., Chen, C., Yang, Z., Guo, L., Yang, X., Wang, D., ... Zhang, Y. (2017). Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q. GigaScience, 6(5), 1-7. [gix018]. https://doi.org/10.1093/gigascience/gix018

Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q. / 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; Luo, Chen; Yan, Fengming; Preisser, Evan L.; Jiao, Xiaoguo; Coates, Brad S.; Zhao, Jinyang; Gao, Qiang; Xia, Jinquan; Yin, Ye; Liu, Yong; Brown, Judith K; Zhou, Xuguo Joe; Zhang, Youjun.

In: GigaScience, Vol. 6, No. 5, gix018, 01.05.2017, p. 1-7.

Research output: Contribution to journalComment/debate

Xie, W, Chen, C, Yang, Z, Guo, L, Yang, X, Wang, D, Chen, M, Huang, J, Wen, Y, Zeng, Y, Liu, Y, Xia, J, Tian, L, Cui, H, Wu, Q, Wang, S, Xu, B, Li, X, Tan, X, Ghanim, M, Qiu, B, Pan, H, Chu, D, Delatte, H, Maruthi, MN, Ge, F, Zhou, X, Wang, X, Wan, F, Du, Y, Luo, C, Yan, F, Preisser, EL, Jiao, X, Coates, BS, Zhao, J, Gao, Q, Xia, J, Yin, Y, Liu, Y, Brown, JK, Zhou, XJ & Zhang, Y 2017, 'Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q', GigaScience, vol. 6, no. 5, gix018, pp. 1-7. https://doi.org/10.1093/gigascience/gix018
Xie W, Chen C, Yang Z, Guo L, Yang X, Wang D et al. Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q. GigaScience. 2017 May 1;6(5):1-7. gix018. https://doi.org/10.1093/gigascience/gix018
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 ; Luo, Chen ; Yan, Fengming ; Preisser, Evan L. ; Jiao, Xiaoguo ; Coates, Brad S. ; Zhao, Jinyang ; Gao, Qiang ; Xia, Jinquan ; Yin, Ye ; Liu, Yong ; Brown, Judith K ; Zhou, Xuguo Joe ; Zhang, Youjun. / Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q. In: GigaScience. 2017 ; Vol. 6, No. 5. pp. 1-7.
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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.",
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AU - Wang, Dan

AU - Chen, Ming

AU - Huang, Jinqun

AU - Wen, Yanan

AU - Zeng, Yang

AU - Liu, Yating

AU - Xia, Jixing

AU - Tian, Lixia

AU - Cui, Hongying

AU - Wu, Qingjun

AU - Wang, Shaoli

AU - Xu, Baoyun

AU - Li, Xianchun

AU - Tan, Xinqiu

AU - Ghanim, Murad

AU - Qiu, Baoli

AU - Pan, Huipeng

AU - Chu, Dong

AU - Delatte, Helene

AU - Maruthi, M. N.

AU - Ge, Feng

AU - Zhou, Xueping

AU - Wang, Xiaowei

AU - Wan, Fanghao

AU - Du, Yuzhou

AU - Luo, Chen

AU - Yan, Fengming

AU - Preisser, Evan L.

AU - Jiao, Xiaoguo

AU - Coates, Brad S.

AU - Zhao, Jinyang

AU - Gao, Qiang

AU - Xia, Jinquan

AU - Yin, Ye

AU - Liu, Yong

AU - Brown, Judith K

AU - Zhou, Xuguo Joe

AU - Zhang, Youjun

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N2 - 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.

AB - 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.

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