ArticleGenome biology2007
Update of the Anopheles gambiae PEST genome assembly.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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88 citing papers in PubMed, 154 citations in OpenAlex.
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- A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes.Communications biology · 2024Article
- The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes.BMC biology · 2024Article
- Chromosome-level genome of the poultry shaft louse Menopon gallinae provides insight into the host-switching and adaptive evolution of parasitic lice.GigaScience · 2024Article
- A chromosomal reference genome sequence for the malaria mosquito,Wellcome open research · 2024Article
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- A chromosomal reference genome sequence for the malaria mosquito,Wellcome open research · 2024Article
- Genomic advances in the study of the mosquito vector during avian malaria infection.Parasitology · 2023Review
- In silico SNP prediction of selected protein orthologues in insect models for Alzheimer's, Parkinson's, and Huntington's diseases.Scientific reports · 2023Article
- Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.eLife · 2023Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundThe 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.
resultsPolytene 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.
conclusionThis study has used new approaches to improve the physical map and assembly of the A. gambiae genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.