High-throughput transcriptome analysis of barley (Hordeum vulgare) exposed to excessive boron

Tombuloğlu, Güzin; Tombuloğlu, Hüseyin; Sakcali, Mehmet Serdal; Ünver, Turgay

doi:10.1016/j.gene.2014.12.012

Cited by 54 publications

(22 citation statements)

References 60 publications

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“…Clean data were obtained by removing reads containing adapter, ploy-N and low quality reads from raw data through in-house perl scripts, and assembled into contigs using Trinity [19,20]. Q20, Q30 and GC-content of data were calculated for downstream analyses.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth

Gao

Bao

et al. 2017

PLoS ONE

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The sea cucumber (Apostichopus japonicus) is an economically important aquaculture species in China. However, the serious individual growth variation often caused financial losses to farmers and the genetic mechanisms are poorly understood. In the present study, the extensively analysis at the transcriptome level for individual growth variation in sea cucumber was carried out. A total of 118946 unigenes were assembled from 255861 transcripts, with N50 of 1700. Of all unigenes, about 23% were identified with at least one significant match to known databases. In all four pair of comparison, 1840 genes were found to be expressed differently. Global hypometabolism was found to be occurred in the slow growing population, based on which the hypothesis was raised that growth retardation in individual growth variation of sea cucumber is one type of dormancy which is used to be against to adverse circumstances. Besides, the pathways such as ECM-receptor interaction and focal adhesion were enriched in the maintenance of cell and tissue structure and communication. Further, 76645 SSRs, 765242 SNPs and 146886 ins-dels were detected in the current study providing an extensive set of data for future studies of genetic mapping and selective breeding. In summary, these results will provides deep insight into the molecular basis of individual growth variation in marine invertebrates, and be valuable for understanding the physiological differences of growth process.

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Section: Methodsmentioning

confidence: 99%

Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth

Gao

Bao

et al. 2017

PLoS ONE

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show abstract

“…In this concept, we performed a transcriptome-based analysis of barley ( Hordeum vulgare ) exposed to excess Boron (B) (Tombuloglu 2014, Tombuloglu et al 2015. Totally, 256,874 unigenes were generated and assigned to known peptide databases: Gene Ontology (GO), Swiss-Prot, Clusters of Orthologous Groups (COG), and the Kyoto Encyclopedia of Genes and Genomes (KEGG), as determined by BLASTx search (Fig.…”

Section: Fig 122mentioning

confidence: 99%

Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

Sablok¹,

Kumar²,

Ueno³

et al. 2015

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“…DGE analysis was performed to identify the genes involved in excess B. Most of them were involved in the cell wall, stress response, membrane, protein kinase, and transporter mechanisms (Tombuloglu et al 2013(Tombuloglu et al , 2015.…”

Section: Reads (Sample 2)mentioning

confidence: 99%

High-Throughput Transcriptome Analysis of Plant Stress Responses

Tombuloğlu

2015

Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

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High-throughput transcriptome analysis of barley (Hordeum vulgare) exposed to excessive boron

Cited by 54 publications

References 60 publications

Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth

Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth

Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches

High-Throughput Transcriptome Analysis of Plant Stress Responses

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