title: De novo assembly and analysis of crow lungs transcriptome.
abstract: The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.
authors: a High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal-462021, Madhya Pradesh, India.
authors: Periyasamy
authors: P
authors: Vijayakumar
authors: Ashwin Ashok
authors: AA
authors: Raut
authors: Pushpendra
authors: P
authors: Kumar
authors: Deepak
authors: D
authors: Sharma
authors: Anamika
authors: A
authors: Mishra
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics; D002645:Chickens / Q000235:genetics; D046368:Crows / Q000235:genetics* / Q000378:metabolism; D046369:Finches / Q000235:genetics; D020869:Gene Expression Profiling; D063990:Gene Ontology; D005819:Genetic Markers; D055633:Immune System Phenomena / Q000235:genetics; D008168:Lung / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D030161:Avian Proteins; D005819:Genetic Markers
keywords: 454 pyrosequencing; Corvus macrorhynchos; corbeau à gros bec; jungle crow; polymorphismes mononucléotidiques; pyroséquençage 454; simple sequence repeats; single nucleotide polymorphisms; séquences simples répétées; transcriptome