Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

Thành, Nguyễn Minh; Jung, Hyungtaek; Lyons, Russell E.; Njaci, Isaac; Yoon, Byoung-Ha; Chand, Vincent; Tuan, Nguyen Viet; Thu, Vo Thi Minh; Mather, Peter B.

doi:10.1016/j.margen.2015.05.001

Cited by 14 publications

(11 citation statements)

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“…While de novo assembly of short reads without a known reference remains a challenging task for non-model species such as M . rosenbergii , a number of recent studies have demonstrated the utility of transcriptome assembly using Illumina [ 3 , 11 , 29 ] and Ion-Torrent short read NGS platforms [ 30 , 31 ], in particular, by combining paired-end read sequencing technology to facilitate the assembly.…”

Section: Discussionmentioning

confidence: 99%

“…Despite this fact, results indicate that Trans-ABySS and Trinity were clearly inferior to CLC for assembly of long transcriptome sequences, indicating the strength of CLC for generating an assembly with better contiguity. In addition, a single type of assembler and/or sequencing platform is not sufficient for the assembly of long and reliable contigs in de novo transcriptome sequencing with short read NGS platforms like Illumina or Ion-Torrent [ 31 , 33 ]. While the current combined dataset (454 FLX + Ion-Torrent) was helpful in extending genomic resources of M .…”

Section: Discussionmentioning

confidence: 99%

“…According to our previous research on teleost species [ 30 , 31 ], our initial assumption was the current short single-end reads (113 bp) from Ion-Torrent with limited tissue samples might not be enough to improve the quality of de novo assembly performance. Thus, the hybrid assembly approach was solely considered from the beginning of this study with a hope that the longer 454 FLX data could be helpful in increasing overall assembly quality.…”

Section: Discussionmentioning

confidence: 99%

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Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction

Jung

Yoon

Kim

et al. 2016

IJMS

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The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction

Jung

Yoon

Kim

et al. 2016

IJMS

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“…In fish, the platform has been applied to develop microsatellite markers in Indian carp (Catla catla) (Sahu et al 2014), in the transcriptome assembly of striped catfish (Pangasianodon hypophthalmus) (Thanh et al 2015), for complete sequencing of the Sea bass (Dicentrarchus labrax) genome (Bertolini et al 2016) and in the genome sequencing of the Aeromonas veronii Ae52 strain isolated in fish (Carassius auratus) (Jagoda et al 2017).…”

Section: Next-generation Sequencing-third Generationmentioning

confidence: 99%

Application of molecular tools to elucidate the microbiota of seafood

2018

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The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result. Two methodologies can be employed for this purpose, dependent and independent cultures. However, the dependent culture has certain limitations that can be solved through the independent cultivation techniques, such as PCR, PFGE and NGS, especially through the sequencing of the 16S rRNA region, providing a complete view of microbial diversity. These have revolutionized microbiological knowledge, mainly because they allow for the identification of uncultivable micro-organisms, which represent a substantial portion of total micro-organisms, making it possible to elucidate not yet described taxa which may display pathogenic potential, besides quantifying microbial communities, microbiota genetics, translated proteins and produced metabolites. In addition, transcriptomic and metabolomic techniques also allow for the evaluation of possible impacts that microbial communities may create in their environment, as well as the determination of potential pathogenicity to humans.

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“…In fact, previous studies had shown that Trinity is able to generate more 211 assembled contigs than the CLC assembler when applied on the same dataset. It is also known 212 that assembled contigs from Trinity are shorter than those assembled by CLC but provided similar 213 proportion of significant hits to the nr database [42].…”

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confidence: 99%

A de novo approach to disentangle partner identity and function in holobiont systems

Meng

Marchet

Corre

et al. 2017

Preprint

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Abstract. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/221424 doi: bioRxiv preprint first posted online Nov. 17, 2017; 2 Background Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept. ResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method.We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partner's transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic RadiolariaDinophyta system forming widespread symbiotic association for which our knowledge is limited. ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations. Keywordsholobiont; transcriptomic; de novo assembly; marine; plankton; k-mer based similarity Background. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/221424 doi: bioRxiv preprint first posted online Nov. 17, 2017; 3 In its scientific acceptation, symbiosis is defined as the living together of unlike organisms 1 whatever the nature of their relationship [1], ranging from parasitism to mutualism. Symbiosis is a...

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Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

Cited by 14 publications

References 102 publications

Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction

Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction

Application of molecular tools to elucidate the microbiota of seafood

A de novo approach to disentangle partner identity and function in holobiont systems

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