title: Estimation of the Whitefly Bemisia tabaci Genome Size Based on k-mer and Flow Cytometric Analyses.
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.
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA. wc529@cornell.edu.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Chen
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA. alvin.simmons@ars.usda.gov.|USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. alvin.simmons@ars.usda.gov.
authors.forename: Daniel K
authors.initials: DK
authors.lastname: Hasegawa
authors.affiliation: Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA. karu@benaroyaresearch.org.
authors.forename: Kathiravetpillai
authors.initials: K
authors.lastname: Arumuganathan
authors.affiliation: USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. alvin.simmons@ars.usda.gov.
authors.forename: Alvin M
authors.initials: AM
authors.lastname: Simmons
authors.affiliation: USDA-Agricultural Research Service, Salinas, CA 93905, USA. Bill.wintermantel@ars.usda.gov.
authors.forename: William M
authors.initials: WM
authors.lastname: Wintermantel
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA. zf25@cornell.edu.|USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA. zf25@cornell.edu.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. kai.ling@ars.usda.gov.
authors.forename: Kai-Shu
authors.initials: KS
authors.lastname: Ling
keywords: Bemisia tabaci; flow cytometry; k-mer analysis; next-generation sequencing