Abstract:
BACKGROUND: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. RESULTS: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 regions. Post-assembly the data were largely concordant with the Illumina data generated and allowed 187 ambiguities in the Illumina data to be resolved. The additional read length also permitted small differences in the two inverted repeat regions to be assigned unambiguously. CONCLUSIONS:This is the first report to our knowledge of a chloroplast genome assembled de novo using PacBio sequence data. The PacBio RS data generated here were assembled into a single large contig spanning the P. micrantha chloroplast genome, with a higher degree of accuracy than an Illumina dataset generated at a much greater depth of coverage, due to longer read lengths and lower GC bias in the data. The results we present suggest PacBio data will be of immense utility for the development of genome sequence assemblies containing fewer unresolved gaps and ambiguities and a significantly smaller number of contigs than could be produced using short-read sequence data alone.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Ferrarini M,Moretto M,Ward JA,Šurbanovski N,Stevanović V,Giongo L,Viola R,Cavalieri D,Velasco R,Cestaro A,Sargent DJdoi
10.1186/1471-2164-14-670subject
Has Abstractpub_date
2013-10-01 00:00:00pages
670issn
1471-2164pii
1471-2164-14-670journal_volume
14pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repet...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1436-1
更新日期:2015-04-10 00:00:00
abstract:BACKGROUND:Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a powerhouse of numerous degradation functions, due to their ability to metabolize a wide range of organ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4965-6
更新日期:2018-08-06 00:00:00
abstract:BACKGROUND:We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we transferred this respiratory phenotype in the presence of up to 50 g/L glucose to a yeast strai...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-365
更新日期:2008-07-31 00:00:00
abstract:BACKGROUND:The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific tr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-161
更新日期:2010-03-09 00:00:00
abstract:BACKGROUND:Reliable indicators for the onset of flowering are not available for most perennial monocarpic species, representing a drawback for crops such as bamboo, agave and banana. The ability to predict and control the transition to the reproductive stage in A. tequilana would represent an advantage for field manage...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5808-9
更新日期:2019-06-10 00:00:00
abstract:BACKGROUND:Bulbs of the ornamental flower Lilium pumilum enter a period of dormancy after flowering in spring, and require exposure to cold for a period of time in order to release dormancy. Previous studies focused mainly on anatomical, physiological and biochemical changes during dormancy release. There are no dorman...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4536-x
更新日期:2018-03-14 00:00:00
abstract:BACKGROUND:Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) tes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6481-8
更新日期:2020-01-28 00:00:00
abstract:BACKGROUND:Ras-related proteins in brain (Rab)-family proteins are key members of the membrane trafficking pathway in cells. In addition, these proteins have been identified to have diverse functions such as cross-talking with different kinases and playing a role in cellular signaling. However, only a few Rab proteins ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3145-9
更新日期:2016-10-10 00:00:00
abstract:BACKGROUND:Gene expression analysis by reverse transcription quantitative PCR (qPCR) is the most widely used method for analyzing the expression of a moderate number of genes and also for the validation of microarray results. Several issues are crucial for a successful qPCR study, particularly the selection of internal...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-648
更新日期:2014-08-04 00:00:00
abstract:BACKGROUND:Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression prof...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-262
更新日期:2011-05-24 00:00:00
abstract:BACKGROUND:Auxin plays important roles in hormone crosstalk and the plant's stress response. The auxin-responsive Gretchen Hagen3 (GH3) gene family maintains hormonal homeostasis by conjugating excess indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acids (JAs) to amino acids during hormone- and stress-rel...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-297
更新日期:2013-05-02 00:00:00
abstract:BACKGROUND:Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the combinatorial epigenetic patterns or "epigenetic code", none of them has explicitly addressed the r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3764-9
更新日期:2017-05-12 00:00:00
abstract:BACKGROUND:Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S9
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Most members of the serpin family of proteins are potent, irreversible inhibitors of specific serine or cysteine proteinases. Inhibitory serpins are distinguished from members of other families of proteinase inhibitors by their metastable structure and unique suicide-substrate mechanism. Animal serpins exert...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-449
更新日期:2012-09-04 00:00:00
abstract:BACKGROUND:Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1752-5
更新日期:2015-07-16 00:00:00
abstract:BACKGROUND:Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-318
更新日期:2014-04-28 00:00:00
abstract:BACKGROUND:Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-488
更新日期:2010-09-07 00:00:00
abstract:BACKGROUND:Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-989
更新日期:2014-11-18 00:00:00
abstract:BACKGROUND:5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous cop...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2084-1
更新日期:2015-10-23 00:00:00
abstract:BACKGROUND:Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinical complications of this pathological condition. Several reports have focused on the identification o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-388
更新日期:2009-08-21 00:00:00
abstract:BACKGROUND:The papaya Y chromosome has undergone a degenerative expansion from its ancestral autosome, as a consequence of recombination suppression in the sex determining region of the sex chromosomes. The non-recombining feature led to the accumulation of repetitive sequences in the male- or hermaphrodite-specific re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-335
更新日期:2014-05-04 00:00:00
abstract:BACKGROUND:The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or very low temperatures. Being able to accurately predict this based on a genomic sequence, would thu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S7-S3
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Ophiocordyceps sinensis is an important traditional Chinese medicine for its comprehensive active ingredients, such as cordycepin, cordycepic acid, and Cordyceps polysaccharide. O. sinensis zjut, a special strain isolated from O. sinensis, has similar pharmacological functions to wild O. sinensis. Currently,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07298-z
更新日期:2020-12-11 00:00:00
abstract:BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-120
更新日期:2012-03-28 00:00:00
abstract:BACKGROUND:The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to ide...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-55
更新日期:2006-03-16 00:00:00
abstract:BACKGROUND:Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. RESULTS:Here we report a novel nanowell-based single-cell RNA...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3893-1
更新日期:2017-07-07 00:00:00
abstract:BACKGROUND:Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and he...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2928-3
更新日期:2016-08-09 00:00:00
abstract:BACKGROUND:The origin and importance of exon-intron architecture comprises one of the remaining mysteries of gene evolution. Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons an...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-47
更新日期:2009-01-24 00:00:00
abstract:BACKGROUND:Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play a role in obesity associated traits, the genetic architecture that underlies the natural variation ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-297
更新日期:2010-05-11 00:00:00
abstract::The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial de...
journal_title:BMC genomics
pub_type:
doi:10.1186/1471-2164-10-S2-I1
更新日期:2009-07-14 00:00:00