Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q

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.

Minimum sample sizes for invasion genomics: Empirical investigation in an invasive whitefly

“…After deleting the low‐quality reads, a total of 142,621,503 enzyme reads were obtained (67.38% of the clean reads). These reads were aligned to the B. tabaci MEAM1 and MED genomes (Chen et al, ; Xie et al, ). An average of 94,386 unique tags were aligned to the genome sequence with an average depth of 19.…”

“…In N bases >8% and without restriction recognition sites, the filtered high‐quality sequences are referred to as enzyme reads. Then, mapping the enzyme reads to the B. tabaci MEAM1 and MED reference genomes using SOAP program (the parameter was set to ‐r0‐M4‐v2; Chen et al, ; Li et al, ; Xie et al, ) and the same reads cluster into Unique Tags. Finally, the SNP‐calling was performed using Maximum likelihood (ML) method (Fu et al, ).…”

Genome‐wide dissection of sex determination genes in the highly invasive whitefly species Bemisia tabaci Q/MED

“…Thirty candidate genes within the sex determination pathway were selected from the genes categorized as ‘sex determination (BSID: 492283)’ in the NCBI BioSystems database (http://www.ncbi.nlm.nih.gov/biosystems/) (Geer et al ., ) as well as genes previously reported in D. melanogaster and B. mori (Schütt and Nöthiger, ; Nagaraju et al ., ). The available candidate proteins from D. melanogaster , A. mellifera and B. mori were used as references to screen the B. tabaci Q genome (Xie et al ., ) using the tblastn algorithm with an e ‐value threshold of 10 −5 . The candidate B. tabaci SDGs were confirmed using the blastx algorithm against the nonredundant protein sequence (NR) database of GenBank.…”

“…The mechanism underlying sex determination in whiteflies is poorly understood. With a newly assembled B. tabaci Q/MED genome (Xie et al ., ), in this study, using the sex determination cascade of D. melanogaster as a reference, we (1) identified and annotated a comprehensive list of genes associated with sex determination in B. tabaci , (2) investigated the temporal expression profiles of these genes at different developmental stages and (3) explored the alternative splicing (AS) events of these genes in adult insects using our customized bioinformatics pipeline.…”

“… Figure S1. The computational pipeline used to identify SDGs and further analyse the alternative splicing of SDGs based on the Q B. tabaci genome (Xie et al ., ) and female and male transcriptomes. Figure S2.…”