Location: Vegetable ResearchTitle: Estimation of the whitefly Bemisia tabaci genome size based on k-mer and flow cytometry analyses
|CHEN, WENBO - Boyce Thompson Institute|
|HASEGAWA, DANIEL - Boyce Thompson Institute|
|ARUMUGANATHAN, K - Benaroya Institute|
|Wintermantel, William - Bill|
|FEI, ZHANGJUN - Boyce Thompson Institute|
Submitted to: Insects
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/16/2015
Publication Date: 7/28/2015
Publication URL: http://doi:10.3390/insects6030704
Citation: Chen, W., Hasegawa, D., Arumuganathan, K., Simmons, A.M., Wintermantel, W.M., Fei, Z., Ling, K. 2015. Estimation of the whitefly Bemisia tabaci genome size based on k-mer and flow cytometry analyses. Insects. 6:704-715.
Interpretive Summary: Whitefly (Bemisia tabaci), one of important agricultural insect pests, causes serious economic losses to food, fiber and ornamental crops worldwide, largely due to its efficient transmission of a number of plant viruses. Surprisingly, there is little information about its genome sequence. To support our efforts in genome sequencing of whitefly B-biotype, accurate estimation of the genome size is necessary. In this report, genome size of a haploid whitefly was estimated to be around 690 Mb, using two independent technologies: k-mer analysis and flow cytometry measurement. Such accurate estimation of the whitefly genome size would offer solid baseline information for genome sequencing efforts on this and other related whitefly species.
Technical Abstract: Whiteflies, Bemisia tabaci (Hemiptera: Aleyrodidae), are one of the most important agricultural insect pests in the world. These phloem-feeding insects can colonize over 500 crop plants worldwide and inflict severe economic losses, mainly through the transmission of pathogenic viruses. Surprisingly, there is very little genomic information about whiteflies. As a starting point, here we report the accurate estimation of the genome size of the B. tabaci B biotype or Middle East-Asia Minor 1 (MEAM1) population. Using an isogenic whitefly colony, over 6,500 haploid male individuals were collected and used for genomic DNA extraction. Three paired-end genomic libraries with insert sizes of ~300 bp, 500 bp and 1 Kb were constructed and sequenced on an Illumina HiSeq 2500 system. A total of ~50 billion base pairs of high-quality cleaned sequences were obtained from each library. K-mer analysis using these sequences revealed that the genome size of whitefly is ~682.3 Mb. Additional flow cytometric analysis estimated the haploid genome size of whitefly to be ~690 Mb. Considering the congruency between both estimation methods, we predict the haploid genome size of B. tabaci to be ~680-690 Mb. Our data provide a baseline for ongoing efforts to assemble and annotate the B. tabaci genome, which will provide a valuable tool to address fundamental and practical questions regarding whitefly biology and management.