Investigation of friction conditions of a microtome

Ventsel, S. V.; Kryuchkov, V. Ya.; Нестеренко, Вадим Анатольевич

doi:10.1007/bf00561688

Cited by 2 publications

(2 citation statements)

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“…Transcripts were compared against the NCBI databases Non-redundant protein sequences (Nr, diamond v0.8.36) (Li, Jaroszewski & Godzik, 2002), NCBI non-redundant nucleotide sequences (Nt, ncbi-blast-2.7.1+), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG, diamond v0.8.36) (Kanehisa et al, 2004) and Clusters of Orthologous Groups of proteins database (COG, diamond v0.8.36) (Tatusov et al, 2003) by BLASTX v2.2.31 with an E-value cut-off of 10 −5 . HMMER 3.1 was used to compare amino acid sequence transcripts against the Pfam database for Pfam annotation (Ventsel, Kriuchkov & Nesterenko, 1973). Gene Ontology (GO) were determined based on the protein annotation results of the Pfam database (Ashburner et al, 2000).…”

Section: Gene Function Analysismentioning

confidence: 99%

SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera

Chen

Kang

et al. 2020

PeerJ

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The white-backed planthopper Sogatella furcifera is an economically important rice pest distributed throughout Asia. It damages rice crops by sucking phloem sap, resulting in stunted growth and plant virus transmission. We aimed to obtain the full-length transcriptome data of S. furcifera using PacBio single-molecule real-time (SMRT) sequencing. Total RNA extracted from S. furcifera at various developmental stages (egg, larval, and adult stages) was mixed and used to generate a full-length transcriptome for SMRT sequencing. Long non-coding RNA (lncRNA) identification, full-length coding sequence prediction, full-length non-chimeric (FLNC) read detection, simple sequence repeat (SSR) analysis, transcription factor detection, and transcript functional annotation were performed. A total of 12,514,449 subreads (15.64 Gbp, clean reads) were generated, including 630,447 circular consensus sequences and 388,348 FLNC reads. Transcript cluster analysis of the FLNC reads revealed 251,109 consensus reads including 29,700 high-quality reads. Additionally, 100,360 SSRs and 121,395 coding sequences were identified using SSR analysis and ANGEL software, respectively. Furthermore, 44,324 lncRNAs were annotated using four tools and 1,288 transcription factors were identified. In total, 95,495 transcripts were functionally annotated based on searches of seven different databases. To the best of our knowledge, this is the first study of the full-length transcriptome of the white-backed planthopper obtained using SMRT sequencing. The acquired transcriptome data can facilitate further studies on the ecological and viral-host interactions of this agricultural pest.

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Section: Gene Function Analysismentioning

confidence: 99%

SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera

Chen

Kang

et al. 2020

PeerJ

View full text Add to dashboard Cite

show abstract

“…Transcripts were compared against the NCBI databases Non-redundant protein sequences (Nr, diamond v0.8.36) (Li et al 2002), NCBI non-redundant nucleotide sequences (Nt, ncbi-blast-2.7.1+), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG, diamond v0.8.36) (Kanehisa et al 2004) and Clusters of Orthologous Groups of proteins database (COG, diamond v0.8.36) (Tatusov et al 2003) by BLASTX v2.2.31 with an E-value cut-off of 10 −5 . HMMER 3.1 was used to compare amino acid sequence transcripts against the Pfam database for Pfam annotation (Ventsel et al 1973). Gene Ontology (GO) were determined based on the protein annotation results of the Pfam database (Ashburner et al 2000).…”

Section: Gene Function Analysismentioning

confidence: 99%

Peer Review #3 of "SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera (v0.1)"

Hosmani¹

2020

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Investigation of friction conditions of a microtome

Cited by 2 publications

References 0 publications

SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera

SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera

Peer Review #3 of "SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera (v0.1)"

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