Update of the Anopheles gambiae PEST genome assembly.

Update of the Anopheles gambiae PEST genome assembly. Research Abstract Details 

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Update of the Anopheles gambiae PEST genome assembly. Abstract Text:

Maria V Sharakhova,Martin P Hammond,Neil F Lobo,Jaroslaw Krzywinski,Maria F Unger,Maureen E Hillenmeyer,Robert V Bruggner,Ewan Birney,Frank H Collins,

BACKGROUND: The genome of Anopheles gambiae, the major vector of malaria, was sequenced and assembled in 2002. This initial genome assembly and analysis made available to the scientific community was complicated by the presence of assembly issues, such as scaffolds with no chromosomal location, no sequence data for the Y chromosome, haplotype polymorphisms resulting in two different genome assemblies in limited regions and contaminating bacterial DNA. RESULTS: Polytene chromosome in situ hybridization with cDNA clones was used to place 15 unmapped scaffolds (sizes totaling 5.34 Mbp) in the pericentromeric regions of the chromosomes and oriented a further 9 scaffolds. Additional analysis by in situ hybridization of bacterial artificial chromosome (BAC) clones placed 1.32 Mbp (5 scaffolds) in the physical gaps between scaffolds on euchromatic parts of the chromosomes. The Y chromosome sequence information (0.18 Mbp) remains highly incomplete and fragmented among 55 short scaffolds. Analysis of BAC end sequences showed that 22 inter-scaffold gaps were spanned by BAC clones. Unmapped scaffolds were also aligned to the chromosome assemblies in silico, identifying regions totaling 8.18 Mbp (144 scaffolds) that are probably represented in the genome project by two alternative assemblies. An additional 3.53 Mbp of alternative assembly was identified within mapped scaffolds. Scaffolds comprising 1.97 Mbp (679 small scaffolds) were identified as probably derived from contaminating bacterial DNA. In total, about 33% of previously unmapped sequences were placed on the chromosomes. CONCLUSION: This study has used new approaches to improve the physical map and assembly of the A. gambiae genome.

Update of the Anopheles gambiae PEST genome assembly. Publishing Authors By Initials

MV Sharakhova,MP Hammond,NF Lobo,J Krzywinski,MF Unger,ME Hillenmeyer,RV Bruggner,E Birney,FH Collins,

For similar biological phenomena, cell phenomena, and immunity: immunity: antibody specificity: species specificity research abstracts see: biological phenomena, cell phenomena, and immunity: immunity: antibody specificity: species specificity research

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Update of the Anopheles gambiae PEST genome assembly. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Genome biology

VOLUME: 8

Page Numbers: R5

Journal Abbreviation: Genome Biol.

ISSN: 1465-6914

DAY: 3

MONTH: 12

YEAR: 2007

Update of the Anopheles gambiae PEST genome assembly. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 100960660

Update of the Anopheles gambiae PEST genome assembly. Keywords Mesh Terms:

KEYWORDS: Species Specificity

MESH TERMS: genetics

Chemical & Substance for Abstract: Update of the Anopheles gambiae PEST genome assembly. Information

Substance Name: Euchromatin

Registry Number: 0

Grant and Affiliation Information for Update of the Anopheles gambiae PEST genome assembly.

AFFILIATION: Center for Global Health and Infectious Diseases, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN 46556-0369, USA. msharakh@vt.edu

Country: England

AGENCY: United States NIAID

GRANT: U01 AI 48846

ACRONYM: AI

MEDLINETA: Genome Biol

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