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Title: rup : Reconstructing ancestral genotype from environmental genomes and metagenomes      
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ID:
PRJEB3221
description:
Earth crust contains estimated 600,000 tons of hexachlorocycloheane (HCH), nearly half of the terrestrial organochlorine pesticide. Using paired end sequenced (~100X) genome and HCH dumpsite metagenome (~1.6Gbp) data we have reconstructed the last common ancestor (3128 genes) of two representative HCH degrading subspecies (average nucleotide identity = >98%); Sphingobium indicum B90A and Sphingobium japonicum UT26. We find metagenomic evidences of large scale horizontal gene transfer (> 20%) in the subspecies, unexpectedly; lindane degradation upper pathway (linA, linB and linC) as transposon mediated genetic import. Anthranilate degradation is a strain specific trait for Sphingobium japonicum UT26; acquired from the ancestor but absent in its subspecies and lineages in situ. In contrast, homogentisate degradation is an environment specific trait as it’s absent in the predicted ancestor and subspecies but fairly present across dumpsite microbiota. Cross validated (replicates) dumpsite metagenome showed enrichment for genotypes (strains) of the genus Sphingobium. Using tetraESOM and graph based clustering on genome and metagenome sequence data, we have reassembled one draft secondary chromosome, 2 near complete plasmids and 8 complete transposons (corresponding to lin genes; IS6 family-IS6100) enriched at dumpsite. Reconstructed, pangenomic structural variants were validated in situ (coverage ~13X). Together, our results reveals yet unknown evolutionary dynamics of the specialised (xenobiotic degradation) genus, at one of the world’s most polluted HCH open sink.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJEB3221
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dateReleased:
11-05-2012
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject