Summary
Publication
Yuan, Z. , Fang, Y. , Zhang, T. , Fei, Z. , Han, F. , Liu, C. , Liu, M. , Xiao, W. , Zhang, W. , Wu, S. , Zhang, M. , Ju, Y. , Xu, H. , Dai, H. , Liu, Y. , Chen, Y. , Wang, L. , Zhou, J. , Guan, D. , Yan, M. , Xia, Y. , Huang, X. , Liu, D. , Wei, H. and Zheng, H. (2018), The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology. Plant Biotechnol J, 16: 1363-1374. doi:10.1111/pbi.12875 https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12875
Name
Punica granatum - Reference Genome
Resource Type
Genome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Punica granatum

Published in the 22 December 2017 in Biotechnology, a 274-Mb genome sequence which covered approximately 81.5% of the genome. From the 274-Mb genome sequence, 2177 scaffolds with a N50 size of 1.7-Mb and containing 30,903 genes. The assembly also contains 7088 contigs with an N50 of 97 kb. The cleaned reads were assembled de novo using ALLPATTHS-LG, and the mate-pair reads were then used to construct scaffolds using SSPACE2.0. GapCloser, provided by SOAPdenovo2, was used to fill in gaps. The scaffolds were compared against the Genbank nt databases using megablast, scaffolds were also compared to known microbial proteins using BLASTX. Scaffolds that were classified as microbial sequences, unanchored rDNA, mitochondrion, chloroplast, and repeated sequences were removed from the final assembly, as well as those <1 kb.

Source: https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12875

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Details
Program, Pipeline, Workflow or Method Name
allpaths-LG
Program Version
1.0 [03-10-2019]
Date Performed
Wednesday, December 5, 2018 - 14:37
Data Source
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