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Phlebotomus papatasi

Image: 
Phlebotomus papatasi
Community contact: 
Mary Ann McDowell
Body: 

The sandfly Phlebotomus papatasi is the main vector of the Old World cutaneous leishmaniasis. It is distributed from Morocco to the Indian subcontinent and from southern Europe to central and eastern Africa.

Short Name: 
ppapatasi
Organism taxonomy: 

Anopheles albimanus

Image: 
Anopheles albimanus
Body: 

Range

Anopheles albimanus it is one of the main vectors of malaria in Central America, northern South America and the Caribbean. On the Atlantic coast it is found from Texas to Venezuela, on most of the Caribbean islands and on the Pacific coast, from Mexico to northern Peru.

Habitat

The larval sites used by An. albimanus are characterised across its range as open, sunlit and containing clear water. The species can be found in natural and man-made habitats where these characteristics exist. For example, it occurs in recently planted rice fields, or in older fields with sunlit areas in between the rice plants. The larvae tolerate a wide variation in water chemistry and are able to exploit diverse food sources enabling them to survive in both fresh water (e.g. irrigation channels, small ponds, marshes, slow flowing streams and river margins) and brackish water (e.g. mangrove swamps).

Behaviour

An. albimanus is predominantly exophagic with exophilic resting behaviour, however there is some indication that in the northern reaches of its distribution (Mexico, Central America), this species exhibits a preference for resting indoors after feeding. An. albimanus bites in the evening and during the night. It appears to show a tendency for zoophily, but some reports have indicated anthropophillic activity.

Vectorial capacity

An. albimanus is considered to be a dominant malaria vector species.

This text was modified from Sinka ME et al. (2010) The dominant Anopheles vectors of human malaria in the Americas: occurrence data, distribution maps and bionomic précis Parasites & Vectors 3:72.

Short Name: 
aalbimanus
Organism taxonomy: 

Anopheles freeborni

Image: 
Anopheles freeborni
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Anopheles freeborni, the Western malaria mosquito, is found in western Canada and in the United States. This species is the principal malaria vector in the arid and semiarid western U.S. (Carpenter and LaCasse 1955).

Short Name: 
afreeborni
Organism taxonomy: 

Anopheles quadrimaculatus

Image: 
Anopheles quadrimaculatus
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Anopheles quadrimaculatus belongs to the Maculipennis group and Quadrimaculatus subgroup, often mis-reported as a complex. Its distribution includes the eastern half of the United States, south eastern Canada and northeastern Mexico. A. quadrimaculatus was a capable malaria vector in the United states where malaria occurred.

Short Name: 
aquadrimaculatus
Organism taxonomy: 

MOZ2

Although photographs of the BAC in situ hybridizations have been archived, the initial physical mapping of scaffolds was based on the assignment of BAC clones to lettered subdivisions in the polytene chromosome complement. This resulted in some ambiguity in physical map assignments and in orientation, particularly of the shorter scaffolds. In the initial MOZ1 assembly, 30 of the largest scaffolds (187,844,042 bp) were mapped and oriented and an additional 112 scaffolds were mapped but not oriented (45,266,526 bp), for a total of 84% of the assembly sequence having a formal map assignment. In some instances, more than one small scaffold mapped to the same lettered subdivision, in which case order and possibly orientation were assigned arbitrarily. The remaining 8845 unmapped scaffolds were arbitrarily assigned to an 'unmapped chromosome.' The MOZ1 assembly was the subject of the initial genome annotation described in Holt et al. (2002), and the assembly and associated annotation were displayed on the EBI/Sanger Ensembl Genome Browser on 29 May 2002.

The first update to the MOZ1 assembly, MOZ2 involved the results of a concerted effort to correct some of the ambiguities in scaffold map locations and orientations by manual analysis of the archived BAC chromosome hybridization photographs and by the hybridization of a small number of new BAC clones selected to resolve questions of scaffold orientation. The new AGP file, and early draft of which was first displayed on the A. gambiae genome poster published in the 4 October 2002 issue of Science, formed the basis of a new annotation and gene build displayed on 1 October 2003 (MOZ2) (Mongin et al. 2004). This assembly was also 278 Mb. The automated Ensembl gene-building system was used, repeated sequence elements and regions of low complexity were masked, coding regions were identified using BLAST and ESTs were mapped to the genome.

Assembly name: 
MOZ2
Release date: 
Wednesday, October 1, 2003

PEST

The Anopheles gambiae PEST strain was chosen for genome sequencing because it had both a fixed, standard chromosomal arrangement and a sex-linked pink eye mutation that could readily be used as an indicator of cross-colony contamination. The pink eye mutation originated in a colony called A. gambiae LPE established in 1951 at the London School of Hygiene and Tropical Medicine from mosquitoes collected in Lagos, Nigeria.

Scaffold count: 
8 987
Assembly status: 
Deprecated
Sequencing method: 
Sanger shotgun
Assembly software: 
Celera Assembler
Average depth of coverage: 
10.2X
Finishing status: 
chromosomes
Genome Size (bp): 
278,000,000

Newsletter 12 (Nov 2011)

Release Date: 
November, 2011
News: 
  • Genome projects approved
    VectorBase has been informed that the NIH/NIAID vector genome working group has approved two new projects. One will sequence the mite vector of scrub typhus, Leptotrombidium deliense, and provide additional genome and transcriptome sequencing of Ixodes scapularis and related ticks. The second will target genomes of 11 Simulium (black fly) species, including the major S. damnosum siblings, S. woodii, S. ochraceum and S. vittatum.
    Data: 
    • Pre-sites
      To provide faster access to upcoming genomes, we have recently introduced preliminary sites, called “pre-sites”. These contain preliminary gene annotations, transcriptome and proteome alignments and represent a snap shot of the annotation process at a given time. The rationales for presenting such data are to give more frequent updates on the annotation and to engage the community much earlier in the process. Releases are data-driven, rather than time-driven, and as such pre-sites, are updated independently of the bi-monthly release cycle. Because these data are preliminary, they are not archived and non-searchable. While we strongly encourage the community to use them, we advise not to rely on the identifiers, as these will not be tracked.
      To date, we have been providing pre-sites for two species: Rhodnius prolixus and Glossina morsitans.
      • Rhodnius prolixus pre-site
        The 0.5 gene set has been released for R. prolixus; it was built using the Ensembl annotation pipeline. It is accessible via the new Rhodnius prolixus species page. Additional features such as RNA-seq and protein similarities, ab initio predictions and EST-build genes are also available in the genome browser accessible from the species page.
      • Glossina morsitans pre-site
        The 0.5 gene set has been released for G. morsitans and is our first annotation using the MAKER pipeline (Cantarel et al., 2008), rather than the more traditional Ensembl pipeline. It is currently undergoing some analysis from the Glossina community so we only provide gene models via BLAST and the Glossina morsitans species page. We welcome any help from the community, so please contact us if you would like to be involved in the manual annotation process!
    Tools: 
    • Unified population data
      During the summer, VectorBase unveiled its “beta” population biology web resource. Our aim is to bring together all population-based studies (field or lab) into one database so that geographic, experimental, phenotypic and genotypic characteristics can be queried, analysed and visualised. For now, it is possible to browse the mosquito field samples that were originally made available in VectorBase’s IRBase and AgPopGenBase resources, along with 60 samples from the Neafsey et al. SNP-chip paper. Comments and suggestions from the community are welcome at any stage in the development of this resource.
    Community: 
    • Meetings
      • Attending TropMed Philly?
        Visit us in the exhibits area at the ASTMH 60th Annual Meeting in Philadelphia, December 4-8, 2011. Representatives of VectorBase will be part of a shared exhibit along with several other NIH/NIAID Bioinformatics Resource Centers. VectorBase representatives will answer questions, demo VectorBase, help with queries and distribute materials.
    • Workshops
      • VectorBase workshops
        Our staff will be running a 2-day VectorBase workshop at the Liverpool School of Tropical Medicine (Liverpool, UK) in November. This event is now fully subscribed, but we invite other labs and institutes to host VectorBase workshops. You are free to select the topics you would like us to cover. If you are interested, please contact us at info@vectorbase.org for more details.
    • Networks
    Contact us: 

    To (un)subscribe to the newsletter visit the Mailman admin page for this list.

    Top tip: 

    VectorBase Top Tip : Switch on a genome browser track via email It is now possible to send a link via email which will turn on a specified track in the recipient’s genome browser. This saves explaining to your colleagues and collaborators how to “Configure this page...”. Simply mouse-over the track name and then the chain-link icon in the popup. Then copy the URL (right mouse-click menu in most web browsers). Here is the (shortened) link from the graphic below (goo.gl/WL1pf) to prove that it works.

    Updated on February 2014: The above tip corresponds to an older version of VectorBase genome browser. In the current version you can click on the share icon highlighted below.

    12
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    Attached or inlined images: 

    Newsletter 13 (Sep 2012)

    Release Date: 
    September, 2012
    News: 

    New website coming soon!

    The VectorBase developers have been busy creating a new website with improved search and navigation, as well as a more consistent look and feel. During the transition period of several months, both new and old sites will run in parallel. Your feedback is very welcome at any time.
    Data: 

    New data for Rhodnius prolixus

    An enhanced gene build for Rhodnius prolixus has been included as part of the VB-2012-04 release. The high number of trascripts has been reduced. At the present time, the following data are available: repeats, EST alignments, RNA-seq alignments, peptide alignments, full lenght cDNAs, Lagerblad gene models (clustered 454 sequences), consensus set with 16,122 genes and 16,134 trascripts, Genscan models, SNAP models, ncRNAs and pseudogenes. Note that VectorBase provides a BLAST service to compare your sequence against the R. prolixus supercontigs, trascripts and peptides.
    Tools: 

    VectorBase Expression Map

    VectorBase stores many high-throughput microarray (a.k.a. DNA chip) datasets which measure the relative amounts of thousands of Anopheles gambiae and Aedes aegypti gene product with respect to various experimental factors, such as tissues/organs, developmental stages and pathogens. Each experiment provides a wealth of information but, until now, a big picture "all genes, all factors" analysis has not been readly available. Such a holistic, or "systems", view of gene expression could greatly accelerate knowledge discovery and hypothesis generation from mosquito gene expression data. In our updated VectorBase Expression Map (MacCallum et al. 2011, BMC Genomics. Dec: 12:620) each A. gambiae and A. aegypti gene is assigned to one of 500 clusters. Because genes within a cluster have similar expression profiles, and the clusters are arranged on a rectangular grid, this resource is a powerful visualization tool for casual exploration and knowledge discovery. For example, we show in the figure below a query asking: Which genes are highly expressed in A. gambiae shortly after ingestion of a blood meal?

    Two regions of the map are highlighted in red. Examination of the clusters soon reveals that one region is dominated by high levels of expression in late embryonic development (green highlighting) and also genes involved in cuticle formation (yellow symbols). Thus in just a few minutes we can begin to hypothesize that one response to the blood meal is to remodel the cuticle in order to accomodate the large increse in volume. The map shows two further modes of behavior for cuticle genes: they are either constitutively expressed (in all experiments performed so far) or are expressed in the ovaries (blue highlighting).
    Community: 

    Outreach

    VectorBase workshops We invite labs and institutes to host VectorBase 1-2 day workshops. You are free to select the topics you would like us to cover. If you are interested, please contact us at info@vectorbase.org for more details.
    Contact us: 
    Post your comments, questions, suggestions or tweets! To (un)subscribe to the newsletter visit the Mailman admin page for this list.
    Top tip: 

    New search engine at VectorBase

    Searching via the box at the top of all pages now lets you find more than just genes! Most site content is now searchable.

    Updated on February 2014: This tip and its image corresponds to the old (or Classic) VectorBase search. If you would like to learn how to use search in the new website please follow this link: www.vectorbase.org/tutorials/search. There you will find two tutorials, one for “Search” and one for “Advanced search”.

    Top tip image: 
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    Attached or inlined images: 

    PEST

    The Anopheles gambiae PEST strain was chosen for genome sequencing because it had both a fixed, standard chromosomal arrangement and a sex-linked pink eye mutation that could readily be used as an indicator of cross-colony contamination (Holt et al 2002: PMID 12364791). The pink eye mutation originated in a colony called A. gambiae LPE established in 1951 at the London School of Hygiene and Tropical Medicine from mosquitoes collected in Lagos, Nigeria. In 1986, this mutation was introduced into a colony of A. gambiae from Asembo Bay western Kenya by crossing males of the LPE strain with female offspring of wild caught Kenyan A. gambiae (the Savanna form), selecting males from the F2 of this cross and then crossing them again with additional female offspring of wild caught Kenyan A. gambiae. From the F2 offspring of this second outcross to Kenyan mosquitoes, a strain was selected that was fixed for pink eye. This outcrossing scheme was repeated one more time in 1987 producing a pink eye strain with a genetic composition largely constituted of the western Kenya Savanna cytogenetic form. In each of these crosses, several hundred female offspring of at least 20 wild caught mosquitoes were used in the cross. This strain, designated A. gambiae PE (Pink Eye), was polymorphic for the inversions 2La (32%) and 2Rbc (19%). The 2Rbc inversion is characteristic of the Mopti chromosomal form, indicating that the original LPE strain from Nigeria was the Mopti form, which is the M molecular form. This inversion was apparently balanced by the uninverted form, because no 2Rbc/bc individuals were detected in the colony. Mukabayire and Besansky selected from this PE strain a set of 9 families whose female parent and at least 20 female offspring were fixed for the standard chromosome karyotype. The progeny of these nine families were pooled to form the A. gambiae PEST strain (Pink Eye STandard). This strain clearly had some Mopti-derived DNA, as the standard karyotype is shared by Mopti and Savanna and the original PE strain did have the 2Rbc inversion rather than 2Rb that is typical of Savanna. Clones from two different PEST strain BAC (Bacterial Artificial Chromosome) libraries had already been end sequenced and physically mapped. When tested, this colony was fully susceptible to P. falciparum from western Kenya. DNA preparation and library construction methods were conducted following standard protocols, and the sequencing method was whole-genome Sanger sequencing. Subsequent to sequencing, the PEST strain was found to be polymorphic for molecular markers diagnostic of the A. gambiae M and S molecular forms. The last known isolate of the A. gambiae PEST colony was lost in about 2005.

    Strain name: 
    PEST
    Sort weight: 
    0
    Ensembl organism name: 
    Anopheles_gambiae

    Pimperena

    The A. gambiae S Pimperena colony was established from blood-fed adult females collected in the village of Pimperena, Mali in November 2005. Approximately 5 isofemale families molecularly identified as A. gambiae S form were used to establish the colony.

    Strain name: 
    Pimperena
    Sort weight: 
    10
    Ensembl organism name: 
    Anopheles_gambiaeS
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