Applications and challenges of next-generation sequencing in Brassica species

Wei, Lijuan; Xiao, Meili; Hayward, Alice; Fu, Donghui

doi:10.1007/s00425-013-1961-6

Cited by 25 publications

(11 citation statements)

References 113 publications

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“…Unlike other approaches, our algorithm strives to maintain the relationships between factors such as to co-evolving sites and recombinant breakpoints within the underlying transcripts. VTBuilder has the potential to increase the usability of transcript sequences generated from read data across a wide range of research areas including; the detection of drug resistant variants within viruses and other disease causing parasites, where co-evolving sites confers resistance to particular classes of drugs [ 60 - 62 ]; the monitoring of disease progression, where variation across a range of sites can be indicative of progression and pathological outcome [ 50 , 63 - 68 ]; plant biology, where it has proven difficult to reconstruct full length transcripts representing complex transcript populations derived from genomes where polyploidy is present [ 69 , 70 ]; and reconstructing accurate evolutionary relationships on phylogenetic trees, and in detecting recombinant breakpoints, where the usage of long non-chimeric transcripts is essential. We have made the source code for VTBuilder available from https://code.google.com/p/vt-builder/ where researchers from a wide range of backgrounds can access and develop it for their own requirements.…”

Section: Discussionmentioning

confidence: 99%

VTBuilder: a tool for the assembly of multi isoform transcriptomes

et al. 2014

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BackgroundWithin many research areas, such as transcriptomics, the millions of short DNA fragments (reads) produced by current sequencing platforms need to be assembled into transcript sequences before they can be utilized. Despite recent advances in assembly software, creating such transcripts from read data harboring isoform variation remains challenging. This is because current approaches fail to identify all variants present or they create chimeric transcripts within which relationships between co-evolving sites and other evolutionary factors are disrupted. We present VTBuilder, a tool for constructing non-chimeric transcripts from read data that has been sequenced from sources containing isoform complexity.ResultsWe validated VTBuilder using reads simulated from 54 Sanger sequenced transcripts (SSTs) expressed in the venom gland of the saw scaled viper, Echis ocellatus. The SSTs were selected to represent genes from major co-expressed toxin groups known to harbor isoform variants. From the simulated reads, VTBuilder constructed 55 transcripts, 50 of which had a greater than 99% sequence similarity to 48 of the SSTs. In contrast, using the popular assembler tool Trinity (r2013-02-25), only 14 transcripts were constructed with a similar level of sequence identity to just 11 SSTs. Furthermore VTBuilder produced transcripts with a similar length distribution to the SSTs while those produced by Trinity were considerably shorter. To demonstrate that our approach can be scaled to real world data we assembled the venom gland transcriptome of the African puff adder Bitis arietans using paired-end reads sequenced on Illumina’s MiSeq platform. VTBuilder constructed 1481 transcripts from 5 million reads and, following annotation, all major toxin genes were recovered demonstrating reconstruction of complex underlying sequence and isoform diversity.ConclusionUnlike other approaches, VTBuilder strives to maintain the relationships between co-evolving sites within the constructed transcripts, and thus increases transcript utility for a wide range of research areas ranging from transcriptomics to phylogenetics and including the monitoring of drug resistant parasite populations. Additionally, improving the quality of transcripts assembled from read data will have an impact on future studies that query these data. VTBuilder has been implemented in java and is available, under the GPL GPU V0.3 license, from http:// http://www.lstmed.ac.uk/vtbuilder.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0389-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

VTBuilder: a tool for the assembly of multi isoform transcriptomes

et al. 2014

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“…Next-generation sequencing (NGS) technology produces numerous short DNA reads at relatively low cost and in a short period of time. NGS has a wide range of applications and has revolutionized the use of genomic data for crop improvement (Wei et al 2013). The combination of TD with NGS technology allows the use of different high copy mTE families to detect insertion polymorphism among accessions.…”

Section: Transposon Display (Td) For Mtesmentioning

confidence: 99%

Miniature Transposable Elements (mTEs): Impacts and Uses in the Brassica Genome

Sampath

Lee

Cheng

et al. 2015

Compendium of Plant Genomes

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Transposable elements occupy large portions of eukaryotic genomes and play an important role in genome evolution. Terminal repeat retrotransposons in miniature (TRIMs), short interspersed elements (SINEs) and miniature inverted-repeat transposable elements (MITEs) are representative forms of so-called miniature transposable elements (mTEs), which are present in very high-copy numbers, stable, widely distributed and in close association with genic regions in plant genomes. These features make mTEs useful for applications such as developing marker systems, functional characterization of associated genes, and elucidating the contribution of TEs to gene evolution. Here, we summarize the characteristics, copy numbers and distribution patterns of five TRIM families, 14 short interspersed elements (SINE) families and 20 MITE families in the Brassica rapa genome. We also show the comparative distribution pattern of paralogous mTE family members in Brassica oleracea and 11 B. rapa accessions. In addition, we describe putative roles for mTEs in the evolution of the triplicated Brassica genome and discuss the utility of mTEs for analysis of genome evolution and for developing practical marker systems.

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“…Complex polyploid crop genomes such as that of B. napus pose a significant challenge for genome assembly, with resolution of homeologous and duplicated sequences often difficult with short-read sequence assemblies (Feuillet et al 2011;Edwards et al 2013). Current genome sequencing approaches also do not allow easy resolution of many genome features of interest, including tandem repeats, centromeres, transposable elements and regulatory features such as short non-coding repeats (Feuillet et al 2011;Wei et al 2013). These elements are predicted to play a significant role in genome evolution and possibly even in crop phenotypes (Fu et al 2015), and hence our understanding of polyploidisation processes cannot be complete without deep insight into their organisation and evolution in newly arising genomes.…”

Section: Towards the Species Pan-genome The Role Of Rearrangements Amentioning

confidence: 99%

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

Mason

Snowdon

2016

Plant Biol J

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Oilseed rape (Brassica napus) is one of our youngest crop species, arising several times under cultivation in the last few thousand years and completely unknown in the wild. Oilseed rape originated from hybridisation events between progenitor diploid species B. rapa and B. oleracea, both important vegetable species. The diploid progenitors are also ancient polyploids, with remnants of two previous polyploidisation events evident in the triplicated genome structure. This history of polyploid evolution and human agricultural selection makes B. napus an excellent model with which to investigate processes of genomic evolution and selection in polyploid crops. The ease of de novo interspecific hybridisation, responsiveness to tissue culture, and the close relationship of oilseed rape to the model plant Arabidopsis thaliana, coupled with the recent availability of reference genome sequences and suites of molecular cytogenetic and high-throughput genotyping tools, allow detailed dissection of genetic, genomic and phenotypic interactions in this crop. In this review we discuss the past and present uses of B. napus as a model for polyploid speciation and evolution in crop species, along with current and developing analysis tools and resources. We further outline unanswered questions that may now be tractable to investigation.

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Applications and challenges of next-generation sequencing in Brassica species

Cited by 25 publications

References 113 publications

VTBuilder: a tool for the assembly of multi isoform transcriptomes

VTBuilder: a tool for the assembly of multi isoform transcriptomes

Miniature Transposable Elements (mTEs): Impacts and Uses in the Brassica Genome

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

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