Bemisia tabaci (Silverleaf whitefly, SSA1-SG1 Ng) Assembly and Gene Annotation

Bemisia tabaci Sub-Saharan Africa 1-Subgroup 1 Nigeria

Whiteflies of the Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) species complex are phloem-feeding insects and plant-virus vectors, some of which are widely regarded to be amongst the world’s worst agricultural pests. Outbreaks of B. tabaci cause significant crop losses and contribute to global food insecurity.

Two devastating diseases affecting cassava (Manihot esculenta), an important food security crop in sub-Saharan Africa, are spread by abundant populations of cassava whiteflies, most notably the cryptic species termed B. tabaci Sub-Saharan Africa 1-Subgroup 1 (SSA1-SG1) [1]. This species is currently widespread in East Africa and has recently been reported in eastern Nigeria [2], although populations there do not yet reach excessive numbers.

The genome described here was generated from a Nigerian population of B. tabaci SSA1-SG1, that was inbred in the laboratory to reduce heterozygosity.

The Bemisia tabaci cryptic species complex

Members of the B. tabaci species complex cause plant damage by feeding on plant-phloem sap, inducing phytotoxic disorders, depositing honeydew on which sooty moulds develop and by vectoring > 300 plant-virus species in the genera Begomovirus, Carlavirus, Crinivirus, Ipomovirus, Polerovirus and Torradovirus [3,4]. Diseases caused by these viruses often spread rapidly with devastating yield losses of up to 100% [5].

Bemisia tabaci sensu lato currently represents a relatively large group (>44) of mostly unresolved cryptic species, as inferred from phylogenetic species delimitation studies [6,7]. These morphologically indistinguishable species differ from one another not only in their genetic relatedness, but also in various biological traits such as plant host-range breadth, fecundity, insecticide resistance, and plant-virus transmission efficiencies.

Bemisia tabaci sensu lato are distributed globally, from tropical to temperate climatic zones and across all continents (except Antarctica) [6]. Most cryptic species in this complex, as currently understood, are geographically restricted, but two of them are highly invasive globally i.e., B. tabaci Middle East-Asia Minor 1 (MEAM1, also referred to as biotype B and Bemisia argentifolii) and B. tabaci Mediterranean (MED, also referred to as biotype Q) [6]. Bemisia tabaci sensu lato live predominantly on herbaceous plant hosts and have been recorded from an exceedingly broad range of host plants (>500 species) [8]. The documented host-plant range of most cryptic species within the complex remains largely incomplete.

Picture credit: Sharon van Brunschot.

Assembly

The Bemisia tabaci SSA1-SG1 Nigeria genome was produced by the genomics consortium of the African Cassava Whitefly Project, funded by the Bill & Melinda Gates Foundation (Grant Number OPP1058938).

A field-collected colony (Port Harcourt, Nigeria) was established, maintained and inbred (F8 generation) by Dr Joachim Nwezeobi at the quarantine insectary facilities of the Natural Resources Institute, University of Greenwich, United Kingdom.

High-molecular weight genomic DNA was isolated from a pooled sample of F8 inbred haploid male individuals (n=3000). PacBio Sequel library construction and sequencing (8 SMRT cells) was performed by the Centre for Genomic Research, The University of Liverpool (United Kingdom).

The current assembly of the B. tabaci SSA1 Nigeria genome was generated by Dr Lahcen Campbell at EMBL-EBI (Hinxton, UK). The assembly was generated using Canu v1.8. The length of the B. tabaci SSA1 Nigeria genome assembly was 656.2 Mb, housed in 4,493 scaffolds with a scaffold N50 of 458.2Kb. Total coverage within assembly input PacBio long reads was ~75X. The GC content of the assembly was 39.59%. Repeat content covered 39.1% of the overall genome, predominantly of transposable elements without complete classification. Of the identified transposable elements (TE), DNA type TE were the most widespread at 3.3% total coverage.

Annotation

RNA-Seq data utilized for genome annotation were deposited to the ENA under the accessions PRJEB35414, PRJEB28507, PRJEB36965, along with publicly available RNA-seq data from three independent short read Illumina PE datasets: SRR1523521 (PRJNA255988); SRR835869 (PRJNA79601); and SRR2001505 (PRJNA282156). Genomic annotation was generated with the Ensembl gene annotation system [9]. All transcript models were supported by RNA-seq experimental evidence derived from multiple whitefly life-stages. Gene model layering was supported with protein-to-genome alignment of experimentally verified proteins obtained from closely related Hemiptera: Uniprot (2019) and 570 experimentally verified protein genes from the published genome of Bemisia tabaci MEAM1 [10]. The Ensembl Gene Annotation pipeline then implemented transcript consensus filtration to remove unsupported alternate transcript isoform(s).

Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by examining genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.

lncRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

For a general in-depth overview of the Gene Annotation pipeline see here: detailed information on the genebuild.

References

1. Mugerwa et al. (2020) 'Whole-genome single nucleotide polymorphism and mating compatibility studies reveal the presence of distinct species in sub-Saharan Africa Bemisia tabaci whiteflies'. Insect Science. doi:10.1111/1744-7917.12881.
2. Nwezeobi et al. (2020). 'Cassava whitefly species in eastern Nigeria and the threat of vector-borne pandemics from East and Central Africa'. PLoS ONE, 15(5), e0232616. doi:10.1371/journal.pone.0232616.
3. Fiallo-Olivé et al. (2020) 'Transmission of begomoviruses and other whitefly-borne viruses: dependence on the vector species'. Phytopathology, 110(1), 10-17. doi:10.1094/phyto-07-19-0273-fi.
4. Gilbertson et al. (2015) 'Role of the insect supervectors Bemisia tabaci and Frankliniella occidentalis in the emergence and global spread of plant viruses'. Annual Review of Virology, 2, 67-93. doi:10.1146/annurev-virology-031413-085410.
5. Colvin et al. (2004) 'Dual begomovirus infections and high Bemisia tabaci populations: two factors driving the spread of a cassava mosaic disease pandemic.' Plant Pathology, 53(5), 577-584. doi: 10.1111/j.0032-0862.2004.01062.x
6. De Barro et al. (2011) 'Bemisia tabaci: a statement of species status.' Annual Review of Entomology, 56(1), 1-19. doi: 10.1146/annurev-ento-112408-085504.
7. Kanakala et al. (2019) 'Global genetic diversity and geographical distribution of Bemisia tabaci and its bacterial endosymbionts'. PLoS ONE, 14(3), e0213946. doi:10.1371/journal.pone.0213946.
8. Oliveira et al. (2001) 'History, current status, and collaborative research projects for Bemisia tabaci'. Crop Protection, 20(9), 709-723. doi:10.1016/S0261-2194(01)00108-9.
9. Aken et al. (2016) ‘The Ensembl gene annotation system’. Database, Volume 2016. doi:10.1093/database/baw093.
10. Chen et al. (2016) 'The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance'. BMC Biology 14, 110. doi:10.1186/s12915-016-0321-y.

More information

General information about this species can be found in Wikipedia