Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, <i>Paralichthys olivaceus</i>

Wang, Wenji; Wang, Jing; You, Feng; Ma, Liman; Yang, Xiangdong; Gao, Jinling; He, Yan; Qi, Jie; Yu, Haiyang; Wang, Zhigang; Wang, Xubo; Wu, Zhihao; Zhang, Quanqi

doi:10.1534/g3.114.012138

Cited by 28 publications

(10 citation statements)

References 25 publications

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“…In O. cruralis the 550,871 transcripts clustered into 422,999 unigenes. This difference in number is likely because of alternatively spliced isoforms derived from paralogous genes ( Wang et al, 2014 ). However, this will need to be confirmed with new amphibian genomes as they become available.…”

Section: Resultsmentioning

confidence: 99%

A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

Montero‐Mendieta

Grabherr²,

Lantz³

et al. 2017

PeerJ

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Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

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Section: Resultsmentioning

confidence: 99%

A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

Montero‐Mendieta

Grabherr²,

Lantz³

et al. 2017

PeerJ

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“…Briefly, the first strand cDNA was synthesized from 1 μg of RNA using M-MLV reverse transcriptase (RNase H-) (TaKaRa) and random primers according to the manufacturer’s instructions. A positive fragment (1100 bp) sharing high identities with Epinephelus coioides sox3 and Larimichthys crocea sox3 was found by searching the de novo transcriptome sequencing data of P. olivaceus [ 46 ]. Primer pair sox3-core-Fw/Rv was designed to verify the core fragment and ensure sequence accuracy.…”

Section: Methodsmentioning

confidence: 99%

Molecular Cloning, Promoter Analysis and Expression Profiles of the sox3 Gene in Japanese Flounder, Paralichthys olivaceus

Gao

Zhang

et al. 2015

IJMS

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Sox3, which belongs to the SoxB1 subgroup, plays major roles in neural and gonadal development. In the present study, Japanese flounder Paralichthys olivaceus sox3 gene (Posox3) and its promoter sequence were isolated and characterized. The deduced PoSox3 protein contained 298 amino acids with a characteristic HMG-box domain. Alignment and phylogenetic analyses indicated that PoSox3 shares highly identical sequence with Sox3 homologues from different species. The promoter region of Posox3 has many potential transcription factor (TF) binding sites. The expression profiles of Posox3 in different developmental stages and diverse adult tissues were analyzed by quantitative real-time RT-PCR (qRT-PCR). Posox3 mRNA was maternally inherited, and maintained at a considerably high expression level between the blastula stage and the hatching stage during embryonic development. Posox3 was abundantly expressed in the adult brain and showed sexually dimorphic expression pattern. In situ hybridization (ISH) was carried out to investigate the cellular distribution of Posox3 in the ovary, and results showed the uniform distribution of Posox3 throughout the cytoplasm of oogonia and stage I–III oocytes. These results indicate that Posox3 has potentially vital roles in embryonic and neural development and may be involved in the oogenesis process. Our work provides a fundamental understanding of the structure and potential functions of Sox3 in Paralichthys olivaceus.

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“…As important economically animals, fishes should be investigated for AS regulation in the immune system as well, which might contribute to the disease control in aquaculture. In this context, AS of Japanese flounder ( Paralichthys olivaceus ) has been recently detected by using RNA sequencing 9 , which lays a foundation for functional genomics studies in fishes.…”

mentioning

confidence: 99%

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)

Wan

2015

Sci Rep

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Characterization of the transcriptomic response to infection is an effective approach to understanding the immune mechanisms. Herein we challenged grass carp (Ctenopharyngodon idella) with grass carp reovirus (GCRV) and sequenced four cDNA libraries obtained from head-kidney and spleen by using Illumina Miseq. As a result, we gained a total of 21.52 Gb clean data with 107.96 million reads, and de novo assembled 55,199 unigenes with an average length of 1,470 bp. Comparative transcriptome analysis reveals that 217 unigenes are differentially expressed (fold-change of at least 4) between resistant and susceptible fish in both head-kidney and spleen, and of which 36 unigenes were validated by RT-qPCR experiment. The expression profile of immune-related genes demonstrates that the immune response of spleen is more intense than that of head-kidney. Remarkably, 11,811 unigenes contain multiple transcripts, of which 322 unigenes possess notably differentially expressed transcripts between the four transcriptomic datasets. Furthermore, the splicing transcripts of IL-12p40 and IL-1R1 are firstly found to play diverse roles in the antiviral response of fishes. This study provides a complete transcriptome dataset of C. idella, which is valuable for the studies of immune complexity and, moreover, throws light on the regulatory role of AS in antiviral immunity.

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Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus

Cited by 28 publications

References 25 publications

A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

A practical guide to buildde-novoassemblies for single tissues of non-model organisms: the example of a Neotropical frog

Molecular Cloning, Promoter Analysis and Expression Profiles of the sox3 Gene in Japanese Flounder, Paralichthys olivaceus

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)

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