Correction to: De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Carruthers, Madeleine; Yurchenko, Andrey A.; Augley, Julian J.; Adams, Colin E.; Herzyk, Paweł; Elmer, Kathryn R.

doi:10.1186/s12864-018-4840-5

Cited by 4 publications

(3 citation statements)

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“…Many of these have already been identified owing to transcriptome assembly in the brown trout (Carruthers et al, 2018) and consolidate resources to address this challenging key task. While the number of markers cannot be considered sufficient to accurate phylogeny estimation (Pyron, 2015) and their nature may lead to conflicting results (e.g., Reddy et al, 2017), results by Collins and Hrbek (2018) suggest good performance of SNP data coming from restriction-site-associated DNA (RAD) analysis to address relatively recent and shallow phylogenies.…”

Section: The Futurementioning

confidence: 99%

Brown trout phylogenetics: A persistent mirage towards (too) many species

Guinand

Oral

Tougard

2021

Journal of Fish Biology

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Section: The Futurementioning

confidence: 99%

Brown trout phylogenetics: A persistent mirage towards (too) many species

Guinand

Oral

Tougard

2021

Journal of Fish Biology

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“…(2019) Transcriptomics (RNA-seq, cDNA arrays, microarrays) Assembly of transcriptomic profiles Oncorhynchus mykiss; Salmo salar; Salmo trutta, Salvelinus alpinus, Coregonus lavaretus; Oncorhynchus tshawytscha Yes Salem et al. (2015) ; Carruthers et al. (2018) ; Christensen et al.…”

Section: Introductionmentioning

confidence: 99%

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Delgado

Ruzzante

2020

iScience

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Summary Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.

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“…Next-generation sequencing (NGS; i.e., Illumina RNA sequencing) can generate digital data on gene expression without the limits of predesigned probes [6], and has been conducted not only to create the reference genomes such as in Arabidopsis [7], rice [8], maize [9], but also provides the de-novo assembly for many organisms in the past including animals and plants [10, 11]. The results of incomplete (ranging between 1 and 2 kb, including a methylated cap at the 5′ end and poly-A tails at the 3′ end) and low-quality transcripts obtained through Illumina RNA sequencing limit the scope of analysis of alternative splicing variants and corrected annotation [12].…”

Section: Introductionmentioning

confidence: 99%

A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis

et al. 2019

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Background Ricinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis at the transcriptional level are limited. Results In this study, we combined PacBio single-molecule long read isoform and Illumina RNA sequencing to identify the alternative splicing (AS) events, novel isoforms, fusion genes, long non-coding RNAs (lncRNAs) and alternative polyadenylation (APA) sites to unveil the transcriptomic complexity of castor beans and identify critical genes related to ricinoleic acid biosynthesis. Here, we identified 11,285 AS-variants distributed in 21,448 novel genes and detected 520 fusion genes, 320 lncRNAs and 9511 (APA-sites). Furthermore, a total of 6067, 5983 and 4058 differentially expressed genes between developing beans of the R. communis lines 349 and 1115 with extremely different oil content were identified at 7, 14 and 21 days after flowering, respectively. Specifically, 14, 18 and 11 DEGs were annotated encoding key enzymes related to ricinoleic acid biosynthesis reflecting the higher castor oil content of 1115 compared than 349. Quantitative real-time RT-PCR further validated fifteen of these DEGs at three-time points. Conclusion Our results significantly improved the existed gene models of R. communis , and a putative model of key genes was built to show the differences between strains 349 and 1115, illustrating the molecular mechanism of castor oil biosynthesis. A multi-transcriptome database and candidate genes were provided to further improve the level of ricinoleic acid in transgenic crops. Electronic supplementary material The online version of this article (10.1186/s12864-019-5832-9) contains supplementary material, which is available to authorized users.

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Correction to: De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Cited by 4 publications

References 1 publication

Brown trout phylogenetics: A persistent mirage towards (too) many species

Brown trout phylogenetics: A persistent mirage towards (too) many species

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis

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