An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

BMC Genomics
Marco FerrariniDaniel J Sargent

Abstract

Second generation sequencing has permitted detailed sequence characterisation at the whole genome level of a growing number of non-model organisms, but the data produced have short read-lengths and biased genome coverage leading to fragmented genome assemblies. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality containing fewer gaps and longer contigs. However, these advantages come at a much greater cost per nucleotide and with a perceived increase in error-rate. In this investigation, we evaluated the performance of the PacBio RS sequencing platform through the sequencing and de novo assembly of the Potentilla micrantha chloroplast genome. Following error-correction, a total of 28,638 PacBio RS reads were recovered with a mean read length of 1,902 bp totalling 54,492,250 nucleotides and representing an average depth of coverage of 320× the chloroplast genome. The dataset covered the entire 154,959 bp of the chloroplast genome in a single contig (100% coverage) compared to seven contigs (90.59% coverage) recovered from an Illumina data, and revealed no bias in coverage of GC rich region...Continue Reading

References

Apr 5, 2002·Genome Research·W James Kent
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Jan 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·R Kolodner, K K Tewari
Feb 28, 2007·BMC Bioinformatics·Daniel D SommerMihai Pop
Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
Oct 28, 2008·Bioinformatics·Jason R MillerGranger Sutton
Nov 22, 2008·Science·John EidStephen Turner
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Nov 10, 2009·Nature Biotechnology·Carl W FullerDmitri V Vezenov
Dec 15, 2010·The New England Journal of Medicine·Chen-Shan ChinMatthew K Waldor
Apr 8, 2011·Bioinformatics·Leena Salmela, Jan Schröder
Jul 29, 2011·The New England Journal of Medicine·David A RaskoMatthew K Waldor
Dec 20, 2011·Nature Biotechnology·Hugo Y K LamMichael Snyder
Jul 4, 2012·Nature Biotechnology·Sergey Koren Adam M Phillippy
Jul 26, 2012·Journal of Biomedicine & Biotechnology·Lin LiuMaggie Law
Sep 6, 2012·International Journal of Cancer. Journal International Du Cancer·Ben TranJanet E Dancey
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach

❮ Previous
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Citations

Feb 4, 2016·Nature Nanotechnology·Stephanie J Heerema, Cees Dekker
May 31, 2015·Briefings in Bioinformatics·David LaehnemannAlice Carolyn McHardy
Nov 7, 2015·Genomics, Proteomics & Bioinformatics·Anthony Rhoads, Kin Fai Au
Oct 21, 2015·Genomics Data·Jonas Korlach
Mar 5, 2015·Scientific Reports·Yu-Chieh LiaoHsin-Hung Lin
Sep 22, 2015·Genomics·Kazuharu Misawa, Ryo Ootsuki
Sep 18, 2015·BMC Bioinformatics·Kai Bernd StadermannDaniela Holtgräwe
Jun 7, 2014·Cytopathology : Official Journal of the British Society for Clinical Cytology·W D Mojica, R Bassey
Jun 13, 2015·BMC Genomics·John F WoltersHeather L Fiumera
Apr 19, 2015·BMC Genomics·Funda Orkunoglu-SuerTravis J O'Brien
Jan 13, 2015·Journal of Microbiological Methods·Mikang Sim, Jaebum Kim
Nov 16, 2014·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Martine Schroyen, Christopher K Tuggle
Jun 25, 2016·Genome Biology·Henry DaniellWan-Jung Chang
Aug 3, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Peter M HollingsworthAlex D Twyford
Aug 16, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Beibei XiangYong Wang
Sep 3, 2016·Bioinformatics·Ehsan HaghshenasCedric Chauve
Jan 24, 2017·The Plant Journal : for Cell and Molecular Biology·Julian Tonti-FilippiniIan Small
Dec 1, 2017·Frontiers in Cellular and Infection Microbiology·Kenneth Siu-Sing LeungWing-Cheong Yam
Apr 4, 2019·PloS One·Juliana Andrea Pérez Di GiorgioNormand Brisson
Apr 11, 2020·Microbiology Resource Announcements·Bianca FrommerBernd Weisshaar
Aug 25, 2020·Annals of Laboratory Medicine·Yiming ZhongMarilyn M Li
Jul 25, 2019·BMC Genomics·Jordan PattersonGane Ka-Shu Wong

❮ Previous
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Datasets Mentioned

BETA
PRJEB4540
JF345175
DQ317523
AC093544
HQ336405
AP008956
AM087200

Methods Mentioned

BETA
PCR
Illumina
454 sequencing
electrophoresis

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