PconsFam: An Interactive Database of Structure Predictions of Pfam Families

Lamb, John; Jarmolinska, Aleksandra I.; Michel, Mirco; Menéndez-Hurtado, David; Sułkowska, Joanna I.; Elofsson, Arne

doi:10.1016/j.jmb.2019.01.047

Cited by 18 publications

(28 citation statements)

References 30 publications

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“…Annotation information on the obtained nonredundant transcript sequences was based on BLAST in the following databases [66]: NR; Pfam [66]; KOG [67]; COG; swiss-Prot [68]; KEGG [69]; and GO [70].…”

Section: Functional Annotationmentioning

confidence: 99%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

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Background: Caucasian clover (Trifolium ambiguum M.Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analyzed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs)from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene specific to T5. WGCNA cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analyzed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant upregulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

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Section: Functional Annotationmentioning

confidence: 99%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…We investigated the transcript expression levels in the five tissues, and T1 had the highest number of expressed genes (76,124), followed by T4 (75.978), T2 (75,885), T3 (74,396) and T2 (74,327) (Additional file 4: Figure S3a). The number of genes co-expressed in each tissue was 68,241.…”

Section: Expression Of Specific Genes and Statistics Ofdifferentiallymentioning

confidence: 99%

“…Four computational approaches include CPC [72]/CNCI/CPAT [73]/Pfam [74] were combined to sort nonprotein-coding RNA candidates from putative protein-coding RNAs among the transcripts. Putative protein-coding RNAs were filtered using a minimum length and exon number threshold.…”

Section: Detection Of Ssr Orfs As and Lncrnamentioning

confidence: 99%

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Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant up-regulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

show abstract

“…With the rapid development of contact-assisted ab initio modelling methods, several groups have given thought to producing structure predictions to cover protein sequence space, using Pfam (El-Gebali et al, 2018) as a convenient definition of protein families. Prominent among these are the GREMLIN database (Ovchinnikov et al, 2017), which contains representatives of 614 Pfam families resulting from sophisticated iterative modelling with Rosetta, and the PconsFam database (Lamb et al, 2019), which covers a much larger number of protein families, 13 617, but with more rapidly obtained models. Since these models represent Pfam families, often with thousands of members, they provide a degree of structural information for many proteins: for example, the GREMLIN authors calculate that their models with predicted TM-scores of >0.65 (where a TM-score of >0.5 is taken as a correct fold prediction; Zhang & Skolnick, 2004a;Xu & Zhang, 2010) cover almost half a million sequences in UniRef100 (Suzek et al, 2007).…”

Section: Introductionmentioning

confidence: 99%