Dataset Information

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast.

ABSTRACT: Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).

SUBMITTER: Dittami SM

PROVIDER: S-EPMC5695246 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Publications

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp <i>Saccharina japonica</i> using Taxoblast.

Dittami Simon M SM Corre Erwan E

PeerJ 20171117

Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp <i>Saccharina japonica</i>. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as ...[more]

PMID: 29158994

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Project description:BackgroundBrown macroalgae dominate temperate coastal ecosystems, and their productivity is typically limited by nitrate availability. As an economically important kelp, Saccharina japonica is the most productive farmed seaweed and needs to be supplemented with sufficient nitrate throughout the cultivation process. However, molecular characterization of genes involved in nitrogen assimilation has not been conducted in brown macroalgae.ResultsHere, we described the identification of the nitrate reductase (NR) gene from S. japonica (SjNR). Using two different cloning methods for SjNR, i.e. rapid amplification of cDNA ends (RACE) and cDNA cloning alone, a single fragment was obtained respectively. According to results of sequence analysis between these two fragments, the tentative coding sequence in two clones, SjNR-L and SjNR-S, were suggested to represent two transcripts of the single copy SjNR, and the ATG of SjNR-S was located inside the third exon of SjNR-L. In the 5' upstream sequence of each transcript, promoter core elements, response elements, especially multiple N response elements which occurred in microalgal NR, were all predicted. Further sequence analysis revealed that both transcripts encoded all five domains conserved in eukaryotic plant NRs. RT-qPCR results showed that the transcription level of SjNR in juvenile sporophytes could be significantly induced by nitrate and inhibited by ammonium, which was in line with plant NRs. The recombinant SjNR-L and SjNR-S were all proved to have NR activity, suggesting that the single-copy gene SjNR might be regulated on transcription level based on alternative promoters and multiple transcriptional start sites. Moreover, both NADH and NADPH were found to be able to act as electron donors for SjNR alone, which is the first confirmation that brown algal NR has a NAD(P)H-bispecific form.ConclusionThese results will provide a scientific basis for understanding the N demand of kelp in various stages of cultivation and evaluating the environmental remediation potential of kelp in eutrophic sea areas.

Project description:BackgroundIn brown algae, dioicy is the prevalent sexual system, and phenotypic differences between male and female gametophytes have been found in many dioicous species. Saccharina japonica show remarkable sexual dimorphism in gametophytes before gametogenesis. A higher level of phenotypic differentiation was also found in female and male gametes after gametogenesis. However, the patterns of differential gene expression throughout gametophyte development and how these changes might relate to sex-specific fitness at the gamete stage in S. japonica are not well known.ResultsIn this study, differences in gene expression between male and female gametophytes in different developmental stages were investigated using comparative transcriptome analysis. Among the 20,151 genes expressed in the haploid gametophyte generation, 37.53% were sex-biased. The abundance of sex-biased genes in mature gametophytes was much higher than that in immature gametophytes, and more male-biased than female-biased genes were observed in the mature stage. The predicted functions of most sex-biased genes were closely related to the sex-specific characteristics of gametes, including cell wall biosynthesis, sperm motility, and sperm and egg recognition. In addition, 51 genes were specifically expressed in males in both stages, showing great potential as candidate male sex-determining region (SDR) genes.ConclusionsThis study describes a thorough investigation into differential gene expression between male and female gametophytes in the dioicous kelp S. japonica. A large number of sex-biased genes in mature gametophytes may be associated with the divergence of phenotypic traits and physiological functions between female gametes (eggs) and male gametes (sperm) during sexual differentiation. These genes may mainly come from new sex-biased genes that have recently evolved in the S. japonica lineage. The duplication of sex-biased genes was detected, which may increase the number of sex-biased genes after gametogenesis in S. japonica to some extent. The excess of male-biased genes over female-biased genes in the mature stage may reflect the different levels of sexual selection across sexes. This study deepens our understanding of the regulation of sex development and differentiation in the dioicous kelp S. japonica.

Dataset Information

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast.

Publications

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp <i>Saccharina japonica</i> using Taxoblast.

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