Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes.
Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes.
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DOI：
10.1186/1471-2164-11-407
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发表时间：
2010-06-25
期刊：
影响因子：
4.4
通讯作者：
Salzet M
中科院分区：
文献类型：
--
作者：
Macagno ER;Gaasterland T;Edsall L;Bafna V;Soares MB;Scheetz T;Casavant T;Da Silva C;Wincker P;Tasiemski A;Salzet M
药用水蛭是研究神经系统结构、功能、发育、再生和修复的重要模式动物。它也是目前被批准用于医疗程序的独特物种，例如在某些外科手术后清除汇集的血液。它是当前和潜在的未来医学上有用的分子因子的来源，例如抗凝剂和抗菌肽，其可能是由于其寄生于大型哺乳动物（包括人类）而进化的。尽管对该系统的研究有广泛的关注，但在基因组或转录组水平上做得很少，并且公开可用的序列数据很少。为了开始解决这个问题，我们构建了整个胚胎和成年中枢神经系统（CNS）EST文库，并创建了一个可供科学界使用的水蛭转录组聚类序列数据库。从两个定向克隆的cDNA文库（一个是从几个发育阶段的整个胚胎的mRNA中构建的，另一个是从成年CNS索中构建的）中总共获得约133，000个EST克隆，由三个不同的小组进行单向或双向测序：Genoscope（法国国家测序中心），爱荷华州大学测序设施和DOE联合基因组研究所。使用phrap软件包将这些组装成31，232个独特的重叠群和单体，平均长度为827 nt。然后将组装的转录物在所有六个框架中进行翻译，并与NCBI的非冗余（NR）和基因本体（GO）蛋白质序列数据库中的蛋白质进行比较，导致NR中11，236个蛋白质的15，565个匹配和GO中8，073个蛋白质的13，935个匹配。在数据库中搜索与脊椎动物和其他无脊椎动物先天免疫反应相关的基因同源的转录本，得到了一组近100个进化上保守的序列，代表了所有已知的参与这些重要功能的途径。水蛭转录本获得的序列代表了在这个重要的模型系统中表达的基因的第一个主要数据库。翻译的开放阅读框架（ORF）与其他公开可用的水蛭数据集，Helobdella robusta的基因组和转录组的比较，显示在氨基酸水平的平均同一性为58%的匹配序列。有趣的是，与其他可用的Lophotrochozoans比较显示出类似的高水平的氨基酸同一性，其中序列匹配，例如，64%与Capitella capitata（多毛类动物）和56%与Aparasia californica（软体动物）以及58%与Schistosoma mansoni（一种扁平蠕虫）。本文描述的水蛭转录组数据库中存在的推定水蛭先天免疫应答基因的系统发育比较显示与相应的哺乳动物基因的强烈相似性，表明这种重要的生理应答可能具有比先前提出的更古老的起源。
The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions. The sequences obtained for Hirudo transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of Helobdella robusta, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with Capitella capitata (a polychaete) and 56% with Aplysia californica (a mollusk), as well as 58% with Schistosoma mansoni (a platyhelminth). Phylogenetic comparisons of putative Hirudo innate immune response genes present within the Hirudo transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.
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影响因子：
5.3
作者：
Briggman, Kevin L.;Kristan, William B., Jr.
通讯作者：
Kristan, William B., Jr.
DOI：
10.1016/0167-5699(92)90198-g
发表时间：
1992-01-01
期刊：
IMMUNOLOGY TODAY
影响因子：
--
作者：
JANEWAY, CA
通讯作者：
JANEWAY, CA
影响因子：
64.5
作者：
Denes, Alexandru S.;Jekely, Gaspar;Arendt, Detlev
通讯作者：
Arendt, Detlev
影响因子：
64.8
作者：
BAPTISTA, CA;GERSHON, TR;MACAGNO, ER
通讯作者：
MACAGNO, ER
影响因子：
4.8
作者：
Chopin, V;Salzet, M;Malecha, J
通讯作者：
Malecha, J