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Insects 2015, 6(3), 704-715; doi:10.3390/insects6030704

Estimation of the Whitefly Bemisia tabaci Genome Size Based on k-mer and Flow Cytometric Analyses

1
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
2
USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA
3
Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
4
USDA-Agricultural Research Service, Salinas, CA 93905, USA
5
USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Brian T. Forschler
Received: 5 May 2015 / Revised: 11 July 2015 / Accepted: 17 July 2015 / Published: 28 July 2015
View Full-Text   |   Download PDF [529 KB, uploaded 28 July 2015]   |  

Abstract

Whiteflies of the Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species complex are among the most important agricultural insect pests in the world. These phloem-feeding insects can colonize over 1000 species of plants worldwide and inflict severe economic losses to crops, mainly through the transmission of pathogenic viruses. Surprisingly, there is very little genomic information about whiteflies. As a starting point to genome sequencing, we report a new estimation of the genome size of the B. tabaci B biotype or Middle East-Asia Minor 1 (MEAM1) population. Using an isogenic whitefly colony with over 6500 haploid male individuals for genomic DNA, 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 sequences were obtained from each library. K-mer analysis using these sequences revealed that the genome size of the whitefly was ~682.3 Mb. In addition, the flow cytometric analysis estimated the haploid genome size of the whitefly to be ~690 Mb. Considering the congruency between both estimation methods, we predict the haploid genome size of B. tabaci MEAM1 to be ~680–690 Mb. Our data provide a baseline for ongoing efforts to assemble and annotate the B. tabaci genome. View Full-Text
Keywords: Bemisia tabaci; next-generation sequencing; flow cytometry; k-mer analysis Bemisia tabaci; next-generation sequencing; flow cytometry; k-mer analysis
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Chen, W.; Hasegawa, D.K.; Arumuganathan, K.; Simmons, A.M.; Wintermantel, W.M.; Fei, Z.; Ling, K.-S. Estimation of the Whitefly Bemisia tabaci Genome Size Based on k-mer and Flow Cytometric Analyses. Insects 2015, 6, 704-715.

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