Update of the Anopheles gambiae PEST genome assembly.
Update of the Anopheles gambiae PEST genome assembly.
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DOI：
10.1186/gb-2007-8-1-r5
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Collins, Frank H
中科院分区：
文献类型：
--
作者：
Sharakhova, Maria V;Hammond, Martin P;Lobo, Neil F;Krzywinski, Jaroslaw;Unger, Maria F;Hillenmeyer, Maureen E;Bruggner, Robert V;Birney, Ewan;Collins, Frank H
冈比亚按蚊PEST基因组组装的更新将约33%的先前未定位的序列置于染色体上。冈比亚按蚊是疟疾的主要传播媒介，其基因组已于2002年测序和组装。这种最初的基因组组装和分析提供给科学界是复杂的组装问题的存在，如支架没有染色体位置，没有Y染色体的序列数据，单倍型多态性导致两个不同的基因组组装在有限的区域和污染的细菌DNA。多线染色体原位杂交与cDNA克隆被用来放置15个未映射的支架（大小总计5.34 Mbp）在染色体的着丝粒周围区域，并定向进一步9支架。通过细菌人工染色体（BAC）克隆的原位杂交的附加分析将1.32Mbp（5个支架）置于染色体的常染色质部分上的支架之间的物理间隙中。Y染色体序列信息（0.18 Mbp）在55个短支架中保持高度不完整和片段化。BAC末端序列分析表明，BAC克隆跨越了22个支架间缺口。还将未映射的支架与计算机模拟的染色体组装体进行比对，鉴定了总计8.18 Mbp（144个支架）的区域，这些区域可能在基因组计划中由两个替代组装体表示。在映射的支架内鉴定了另外3.53 Mbp的替代组装。包含1.97 Mbp的支架（679个小支架）被鉴定为可能来源于污染的细菌DNA。总的来说，大约33%的先前未定位的序列被放置在染色体上。本研究采用了新的方法来改进A.冈比亚基因组。
An update on the Anopheles gambiae PEST genome assembly places about 33% of previously unmapped sequences on the chromosomes. 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. 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. This study has used new approaches to improve the physical map and assembly of the A. gambiae genome.