A de novo expression profiling of Anopheles funestus, malaria vector in Africa, using 454 pyrosequencing.
A de novo expression profiling of Anopheles funestus, malaria vector in Africa, using 454 pyrosequencing.
复制标题
DOI：
10.1371/journal.pone.0017418
复制
发表时间：
2011-02-25
期刊：
影响因子：
3.7
通讯作者：
Wondji CS
中科院分区：
文献类型：
--
作者：
Gregory R;Darby AC;Irving H;Coulibaly MB;Hughes M;Koekemoer LL;Coetzee M;Ranson H;Hemingway J;Hall N;Wondji CS
funestus按蚊是非洲主要的疟疾媒介之一，但与Anopheles相比，很少有针对该物种的基因组工具。冈比亚按蚊。为了缩小这一知识差距，我们对An进行了测序。利用来自马里的拟除虫菊酯抗性实验室菌株和拟除虫菊酯敏感田间菌株的cDNA文库进行研究。使用每个菌株的生命阶段池（蛹，幼虫，成虫：雌性和雄性），454测序产生375,619个reads（平均长度为182 bp）。De novo组装产生18,103个contigs，平均长度为253 bp。这些组合的平均覆盖深度为8.3。与参考数据库相比，总共有20.8%的阅读是新颖的。田间菌株的测序产生204,758个reads，而耐杀虫剂实验室菌株的测序产生170,861个reads。耐药菌株中差异最大的基因组属于P450基因家族和表皮基因，这与以往的研究表明这两个基因家族与拟除虫菊酯耐药有关。对6个contigs进行qPCR分析表明，这些ESTs可用于基因表达研究，如微阵列研究。据估计，31,000个位点含有单核苷酸多态性（snp），对来自20个contigs的snp的分析表明，这些snp中的大多数可能是真正的snp。基因保守分析证实了这两种植物的亲缘关系。funestus和An。冈比亚按蚊。本研究代表了一项重大进展的遗传学和基因组学的安。因为它提供了一套广泛的表达序列标签（est）和SNP，可以很容易地用于设计新的基因组工具，如微阵列或SNP平台。
Anopheles funestus is one of the major malaria vectors in Africa and yet there are few genomic tools available for this species compared to An. gambiae. To start to close this knowledge gap, we sequenced the An. funestus transcriptome using cDNA libraries developed from a pyrethroid resistant laboratory strain and a pyrethroid susceptible field strain from Mali. Using a pool of life stages (pupae, larvae, adults: females and males) for each strain, 454 sequencing generated 375,619 reads (average length of 182 bp). De novo assembly generated 18,103 contigs with average length of 253 bp. The average depth of coverage of these contigs was 8.3. In total 20.8% of all reads were novel when compared to reference databases. The sequencing of the field strain generated 204,758 reads compared to 170,861 from the insecticide resistant laboratory strain. The contigs most differentially represented in the resistant strain belong to the P450 gene family and cuticular genes which correlates with previous studies implicating both of these gene families in pyrethroid resistance. qPCR carried out on six contigs indicates that these ESTs could be suitable for gene expression studies such as microarray. 31,000 sites were estimated to contain Single Nucleotide Polymorphisms (SNPs) and analysis of SNPs from 20 contigs suggested that most of these SNPs are likely to be true SNPs. Gene conservation analysis confirmed the close phylogenetic relationship between An. funestus and An. gambiae. This study represents a significant advance for the genetics and genomics of An. funestus since it provides an extensive set of both Expressed Sequence Tags (ESTs) and SNPs which can be readily adopted for the design of new genomic tools such as microarray or SNP platforms.
登录
查看更多内容
影响因子：
1.9
作者：
Hunt, RH;Brooke, BD;Coetzee, M
通讯作者：
Coetzee, M
影响因子：
2.6
作者：
Morlais, I;Severson, DW
通讯作者：
Severson, DW
影响因子：
4.4
作者：
Zagrobelny M;Scheibye-Alsing K;Jensen NB;Møller BL;Gorodkin J;Bak S
通讯作者：
Bak S
影响因子：
64.8
作者：
Margulies, M;Egholm, M;Rothberg, JM
通讯作者：
Rothberg, JM
影响因子：
9.8
作者：
Turner TL;Hahn MW;Nuzhdin SV
通讯作者：
Nuzhdin SV