Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase

Abstract

High-throughput genome sequencing techniques have now reached vector biology with an emphasis on those species that are vectors of human pathogens. The first mosquito to be sequenced was Anopheles gambiae, the vector for Plasmodium parasites that cause malaria. Further mosquitoes have followed: Aedes aegypti (Yellow fever and Dengue fever vector) and Culex pipiens (lymphatic filariasis and West Nile fever). Species that are currently in sequencing include the body louse Pediculus humanus (Typhus vector), the triatomine Rhodnius prolixus (Chagas disease vector) and the tick Ixodes scapularis (Lyme disease vector). The motivations for sequencing vector genomes are to further understand vector biology, with an eye on developing new control strategies (for example novel chemical attractants or repellents) or understanding the limitations of current strategies (for example the mechanism of insecticide resistance); to analyse the mechanisms driving their evolution; and to perform an exhaustive analysis of the gene repertory. The proliferation of genomic data creates the need for efficient and accessible storage. We present VectorBase, a genomic resource centre that is both involved in the annotation of vector genomes and act as a portal for access to the genomic information (http://www.vectorbase.org).

Genetics and evolution of triatomines: from phylogeny to vector control

“…Whereas several microsatellite markers have been identified in major triatomine species such as T. infestans, T. dimidiata or R. prolixus, molecular markers are lacking for many other species. Also, genome-wide single-nucleotide polymorphism genotyping approaches, which are now popular in other insect vector species (Megy et al, 2009;Horton et al, 2010;Li et al, 2010), have not yet been developed in triatomines. In that respect, the ongoing sequencing of the R. prolixus genome (Megy et al, 2009) will provide a very valuable tool to further understand triatomine biology and genetics.…”

“…Also, genome-wide single-nucleotide polymorphism genotyping approaches, which are now popular in other insect vector species (Megy et al, 2009;Horton et al, 2010;Li et al, 2010), have not yet been developed in triatomines. In that respect, the ongoing sequencing of the R. prolixus genome (Megy et al, 2009) will provide a very valuable tool to further understand triatomine biology and genetics. Nonetheless, additional triatomine genomes will be required, particularly from the Triatoma genus, and major vector species such as T. infestans or T. dimidiata would be excellent candidates for future genome sequencing.…”

CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus

“…Wikel.IscaW1.fa.gz (dataset downloaded from VectorBase (Lawson et al, 2009) (DFCI IscGI) sequences were searched using tBLASTx at an expected value of 1e-05 206 to uniref100, and orthologous sequences were determined for those alignments that 207 had greater than or equal to 60% R. microplus sequence coverage and an amino acid 208 conservation greater than or equal to 30%. Transcript alignments were also made 209 using BLAT (Kent, 2002) to a comparative species with 70% identity and a length 210 greater than 100 bp.…”

“…Only 58 BES aligned with greater than 80% BES coverage and 80% 304 PID. The number of BES found in comparative searches at specified thresholds were: 305 2,418 (23%) at an expected alignment value (e-value) of 1e-05 to the NCBI protein 306 non-redundant (nr) database, 416 (4%) at an e-value 1e-20 to I. scapularis proteins 307 (Lawson et al, 2009;Megy et al, 2009), 2,559 (24%) BES at an e-value 1e-20 to R. 308 microplus gene indices (Guerrero et al, 2005), and 134 (1.2%) to the I. scapularis 309 gene index (Ribeiro et al, 2006) at an e-value of 1e-20. The protein functional 310 analyses by Gene Ontology (GO) classification are presented in Supplementary Table 311 S2 and Supplementary Fig.…”

A set of ontologies to drive tools for the control of vector-borne diseases

“…This is about 683 more than what the insecticide resistance section in VectorBase carried, the only repository for data of this kind. In addition to databases that are driven by ontologies in an increasing fashion (see for example databases using the ontology-depending schema Chado 25 , such as FlyBase 26, 27 and VectorBase 28,29 , ontologies are ideal tools for the design of intelligent decision support systems. In cases such as vectorborne diseases, whose control is also hampered by weak infrastructure in endemic countries, these DSSs can be used by medical workers and health agencies in remote areas, either for ongoing studies or in cases that need immediate attention 30,31 .…”