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De novo assembly and analysis of crow lungs transcriptome.

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Title De novo assembly and analysis of crow lungs transcriptome.
Not Available
 
Creator Vijayakumar P.
Raut A.A.
Kumar P.
Sharma D.
Mishra A.
 
Subject Jungle crow
Corvus macrorhynchos
Transcriptome
454 pyrosequencing
Single nucleotide polymorphisms
Simple sequence repeats
 
Description Not Available
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.
Not Available
 
Date 2018-03-22T07:50:20Z
2018-03-22T07:50:20Z
2014-09-01
 
Type Research Paper
 
Identifier Vijayakumar P, Raut AA, Kumar P, Sharma D, Mishra A.(2014). De novo assembly and analysis of crow lungs transcriptome. Genome. 2014 Sep;57(9):499-506.
0831-2796
http://krishi.icar.gov.in/jspui/handle/123456789/5986
 
Language English
 
Relation Not Available;
 
Publisher CSP Publishing Services