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Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data

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dc.contributor.authorSoorni, Aboozaren
dc.contributor.authorHaak, David C.en
dc.contributor.authorZaitlin, Daviden
dc.contributor.authorBombarely, Aurelianoen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2018-01-05T12:23:59Zen
dc.date.available2018-01-05T12:23:59Zen
dc.date.issued2017-01-07en
dc.description.abstractBackground The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. Results We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Conclusion Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBAen
dc.description.versionPublished versionen
dc.format.extent8 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Genomics. 2017 Jan 07;18(1):49en
dc.identifier.doihttps://doi.org/10.1186/s12864-016-3412-9en
dc.identifier.issn1471-2164en
dc.identifier.orcidHaak, D [0000-0002-3692-3152]en
dc.identifier.orcidBombarely, A [0000-0001-6257-8914]en
dc.identifier.urihttp://hdl.handle.net/10919/81542en
dc.identifier.volume18en
dc.language.isoenen
dc.publisherBiomed Centralen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000391335400003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBiotechnology & Applied Microbiologyen
dc.subjectGenetics & Heredityen
dc.subjectChloroplasten
dc.subjectMitochondriaen
dc.subjectPacBioen
dc.subjectOrganelle Genome Assemblyen
dc.subjectMECHANISMSen
dc.subjectGENESen
dc.subjectREADSen
dc.titleOrganelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing dataen
dc.title.serialBMC Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Horticultureen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Plant Pathology, Physiology, & Weed Scienceen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Fralin Affiliated Facultyen

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