Abstract
“Candidatus Portiera aleyrodidarum” is the obligate primary endosymbiotic bacterium of whiteflies, including the sweet potato whitefly Bemisia tabaci, and provides essential nutrients to its host. Here we report two complete genome sequences of this bacterium from the B and Q biotypes of B. tabaci.
GENOME ANNOUNCEMENT
“Candidatus Portiera aleyrodidarum” is the obligate primary endosymbiotic bacterium hosted by whiteflies, including the sweet potato whitefly Bemisia tabaci, one of the most globally damaging insect pests in open fields and protected agricultural crops, causing annual losses estimated at 1 to 2 billion dollars. B. tabaci is one of the top 100 invasive species worldwide (5). Similar to other obligate bacteria living in sap-sucking insects, “Ca. Portiera aleyrodidarum” is thought to provide essential nutrients to whiteflies (2). B. tabaci is a species complex comprised of 11 high-level genetic groups that are well defined by DNA markers and at least 24 morphologically indistinguishable species (1, 4). The most predominant and damaging biotypes are B and Q, which differ considerably with regard to various fitness parameters: while B is defined by high fecundity and a wide host range, Q is known to develop higher resistance to insecticides (7). Despite these significant differences in their biology, nothing is known about the comparative genome sequences of the B and Q primary endosymbionts. Here we report the assembly and comparison of “Ca. Portiera aleyrodidarum” genomes from these two biotypes.
B and Q biotype whiteflies were collected in Israel, and each strain was interbred over 200 generations under standard laboratory conditions. High-quality DNA (>40 kb) was extracted from whole bodies of multiple pooled insect adults of each species. Paired-end libraries with 180-bp insertions and 5-kb mate-pair libraries were constructed and sequenced. Adaptors and low-quality reads were removed before assembly. ALLPATHS-LG (3) and Velvet (8) were used for de novo assembly. Based on the depth of coverage, paired-end connections (180 ± 10 bp), and 5-kb mate-pair connections, “Ca. Portiera aleyrodidarum” contigs were selected and linked into a closed circular molecule by customized scripts. We observed a limited number of short repeats/homopolymers that appear polymorphic and have taken the major allele in these cases as the consensus sequence. Over 1 million reads were mapped to each of the final assemblies. Assembly accuracy and the coverage (at least 25× coverage for each nucleotide) were manually curated. Annotation was done on the RAST annotation server (6).
The “Ca. Portiera aleyrodidarum” genome assembly is a 351-kb circular molecule. The “Ca. Portiera aleyrodidarum” genome from whitefly B (here referred to as WB) and the “Ca. Portiera aleyrodidarum” genome from whitefly Q (here referred to as WQ) share high similarity in sequence (99%). Both genomes are highly AT biased (73%) and have 36 RNA-coding genes. A total of 277 protein-coding genes were identified in the “Ca. Portiera aleyrodidarum” WB genome, and 281 were identified in the “Ca. Portiera aleyrodidarum” WQ genome. Similar to other genome-sequenced obligate endosymbionts from sap-feeding insects, enrichment for genes involved in essential amino acid biosynthesis was observed, while genes involved in processes such as membrane transport, cell wall/capsule, or motility were not found. These results support the hypotheses that primary endosymbionts primarily supply their hosts by amino acids. Comparing “Ca. Portiera aleyrodidarum” genome sequences from the B and Q biotypes showed a number of regions that have diverged between the two genomes. Such divergence might play a differential role in “Ca. Portiera aleyrodidarum” interactions with their whitefly host.
Nucleotide sequence accession numbers.
The complete chromosome sequences have been deposited in the NCBI GenBank database under accession numbers CP003867 (for “Ca. Portiera aleyrodidarum” WQ) and CP003868 (for “Ca. Portiera aleyrodidarum” WB).
ACKNOWLEDGMENTS
This research was partially supported by grant IS-4062-07 from the United States-Israel Binational Agricultural Research and Development Fund (BARD) and by research grant 887/07 from the Israel Science Foundation to M.G. We also thank the Chicago Center for Systems Biology for a Research Experiences for Undergraduates (REU) fellowship (NIH P50 GM081892) to K.W.J.
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