Lazzari Barbara, Mariani Valentina, Malinverni Roberto, Caprera Andrea, Giuffra Elisabetta
Parco Tecnologico Padano, CERSA, Via Einstein, 26900 Lodi, Italy.
Mar Genomics. 2008 Mar;1(1):15-21. doi: 10.1016/j.margen.2008.04.002. Epub 2008 May 2.
Sturgeons are archaic fishes phylogenetically distinct from Teleosts. They represent an important niche for aquaculture, particularly for the production of caviar and high quality fillets, while many natural populations in various world areas are today threatened by extinction. Knowledge of the sturgeon genome is limited, as it is the case of many other species of interest for fishery, aquaculture and conservation. Sequences from non-normalized libraries of skin and spleen of the American sturgeon (A. transmontanus) produced in our laboratories were analysed via a bioinformatic procedure, and compared to similar resources available for three Teleost species. Data collected during the analyses were stored in a database - the Sturgeon database (db) - that can be queried via a web interface. The Sturgeon db contains a total of 16,404 sequences from Acipenser transmontanus, Ictalurus punctatus, Salmo salar and Takifugu rubripes, each specie being represented by expressed sequence tags (ESTs) from skin and spleen. Data contained in the database are the results of a number of analyses that mostly focus on sequence annotation and intra- and inter-species comparison. Putative SNP sites, tandem repeats, and sequences matching known protein patterns and motifs were also identified. The Sturgeon db is by now the only online resource dedicated to the analysis of A. transmontanus EST sequences, and represents a starting point for the investigation of the genome of sturgeons from a physiological perspective; it will be used to identify polymorphic markers to study, for example, fish pathologies or to survey fish disease resistance, and to produce gene expression arrays. Introduction of sequences from other species in the analysis pipeline allowed inter-species comparisons of transcripts distribution in Gene Ontology categories, as well as orthologs identification, despite the high sturgeon phylogenetic distance from other fish species. As a result of the EST analysis procedure, 1058 sturgeon novel unigenes were identified.
鲟鱼是在系统发育上与硬骨鱼不同的古老鱼类。它们是水产养殖的一个重要细分领域，特别是在鱼子酱和优质鱼片的生产方面，然而如今世界各地区的许多自然种群都面临灭绝的威胁。与许多其他对渔业、水产养殖和保护具有重要意义的物种一样，人们对鲟鱼基因组的了解有限。我们实验室对美国鲟（A. transmontanus）皮肤和脾脏的非标准化文库中的序列进行了生物信息学分析，并与三种硬骨鱼物种的类似资源进行了比较。分析过程中收集的数据存储在一个数据库——鲟鱼数据库（db）中，该数据库可通过网络界面进行查询。鲟鱼数据库总共包含来自美国白鲟、斑点叉尾鮰、大西洋鲑和红鳍东方鲀的16404条序列，每个物种都由皮肤和脾脏的表达序列标签（EST）代表。数据库中的数据是大量分析的结果，这些分析主要集中在序列注释以及种内和种间比较。还鉴定了推定的单核苷酸多态性（SNP）位点、串联重复序列以及与已知蛋白质模式和基序匹配的序列。鲟鱼数据库目前是唯一专门用于分析美国白鲟EST序列的在线资源，从生理学角度来看，它是研究鲟鱼基因组的起点；它将用于识别多态性标记，例如研究鱼类病理学或调查鱼类抗病性，并用于生产基因表达阵列。尽管鲟鱼与其他鱼类物种在系统发育上距离较远，但在分析流程中引入其他物种的序列可以对转录本在基因本体论类别中的分布进行种间比较，以及鉴定直系同源基因。通过EST分析程序，共鉴定出1058个鲟鱼新单基因。
