MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models

Nastou, Katerina C.; Tsaousis, Georgios N.; Παπανδρεου, Νικολαοσ; Hamodrakas, Stavros J.

doi:10.1016/j.bbapap.2016.03.015

Cited by 23 publications

(16 citation statements)

References 62 publications

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“…All non-redundant transcripts were subjected to Basic Local Alignment Search Tool (BLASTx) [37] searches (E-value < 10 −5 ) against public protein databases, including the NCBI non-redundant (nr) [38], the Swissprot protein (Swiss-Prot) [39], the Gene Ontology (GO) [40], the Clusters of Orthologous Groups (COGs) [41], KOG [42] (the database of Clusters of Protein homology), eggNOG4.5 (a database of orthologous groups of genes), [43] and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases [44]. The predicted amino acid sequences of the unigenes were then annotated using HMMER [45]. GO analysis was used to assign putative gene functions to the uncharacterized sequences.…”

Section: Methodsmentioning

confidence: 99%

Deep Sequencing and Analysis of Transcriptomes of Pinus koraiensis Sieb. & Zucc.

Shi

Yan

Zhao

et al. 2020

Forests

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The objective of this research was to study the differences in endogenous hormone levels and the genes related to reproductive development in Chinese pinenut (Pinus koraiensis) trees of different ages. The apical buds of P. koraiensis were collected from 2-, 5-, 10-, 15-, and 30-year-old plants and also from grafted plants. There were three replicates from each group used for transcriptome sequencing. After assembly and annotation, we identified the differentially expressed genes (DEGs) and performed enrichment analysis, pathway analysis, and expression analysis of the DEGs in each sample. The results showed that unigenes related to reproductive development, such as c64070.graph_c0 and c68641.graph_c0, were expressed at relatively low levels at young ages, and that the relative expression gradually increased with increasing plant age. In addition the highest expression levels were reached around 10 and 15 years of age, after which they gradually decreased. Moreover, some unigenes, such as c61855.graph_c0, were annotated as abscisic acid hydroxylase genes, and the expression of c61855.graph_c0 gradually declined with increasing age in P. koraiensis.

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Section: Methodsmentioning

confidence: 99%

Deep Sequencing and Analysis of Transcriptomes of Pinus koraiensis Sieb. & Zucc.

Shi

Yan

Zhao

et al. 2020

Forests

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“…The statistical enrichment of DEGs in the KEGG pathways were tested using KOBAS 2.0 (Xie et al, 2011). Unigenes were also aligned against the Pfam (Finn et al, 2014) database using HMMER (Nastou et al, 2016). The E-value cut-offs of BLAST and HMMER were <10 À5 and <10 À10 , resulting in 122 325 annotated unigenes (Table S5).…”

Section: Data Analysesmentioning

confidence: 99%

Resource allocation strategies among vegetative growth, sexual reproduction, asexual reproduction and defense during growing season of Aconitum kusnezoffii Reichb.

et al. 2020

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Natural plants must actively allocate their limited resources for survival and reproduction. Although vegetative growth, sexual reproduction, asexual reproduction and defense are all basic processes in the life cycle of plants, the strategies used to allocate resources between these processes are poorly understood. These processes are conspicuous in naturally grown Aconitum kusnezoffii Reichb., which makes it a suitable study subject. Here, the morphology, dry matter, total organic carbon, total nitrogen and aconitum alkaloid levels of shoot, principal root (PR) and lateral roots were measured throughout the growing season. Then, transcriptome and metabolite content analyses were performed. We found that vegetative growth began first. After vegetative growth ceased, sexual development began. Flower organ development was accompanied by increased photosynthesis and the PR consumed temporarily stored resources after flower formation. Asexual propagule development initiated earlier than sexual reproduction and kept accumulating resources after that. Development was slow before flower formation, mainly manifesting as increasing length; then, after flower formation it accelerated via enhanced material transport and accumulation. Defense compounds were maintained at low levels before flowering. In particular, the turnover of defense compounds was enhanced before and after flower bud emergence, providing resources for other processes. After flower formation, defense compounds were accumulated. The pattern found herein provides a vivid example for further studies on resource allocation strategies. The exciting finding that the PR, as a more direct storage site for photosynthate, is a buffer unit for resources, and that defense compounds can be reused for other processes, suggests a need to explore potential mechanisms.

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“…Unigenes were screened against the NR and Swiss-Prot databases using BLAST software (Deng et al, 2006;Coordinators, 2016;UniProt Consortium, 2016). The predicted amino acid sequences of the unigenes were screened against the Pfam database using HMMER software to gain annotation information (Nastou et al, 2016;Finn et al, 2013). The functional annotations of the unigenes were screened against the Clusters of Orthologous Groups (COGs; http://www.ncbi.nlm.nih.gov/COG), Gene Ontology (GO; http://www.geneontology.org/), and the Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg) databases.…”

Section: Quality Control Assembly and Functional Annotationmentioning

confidence: 99%

Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves

Yuan

Sun

Guo

et al. 2020

PeerJ

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Leaf senescence is a complex organized developmental stage limiting the yield of crop plants, and alfalfa is an important forage crop worldwide. However, our understanding of the molecular mechanism of leaf senescence and its influence on biomass in alfalfa is still limited. In this study, RNA sequencing was utilized to identify differentially expressed genes (DEGs) in young, mature, and senescent leaves, and the functions of key genes related to leaf senescence. A total of 163,511 transcripts and 77,901 unigenes were identified from the transcriptome, and 5,133 unigenes were differentially expressed. KEGG enrichment analyses revealed that ribosome and phenylpropanoid biosynthesis pathways, and starch and sucrose metabolism pathways are involved in leaf development and senescence in alfalfa. GO enrichment analyses exhibited that six clusters of DEGs are involved in leaf morphogenesis, leaf development, leaf formation, regulation of leaf development, leaf senescence and negative regulation of the leaf senescence biological process. The WRKY and NAC families of genes mainly consist of transcription factors that are involved in the leaf senescence process. Our results offer a novel interpretation of the molecular mechanisms of leaf senescence in alfalfa.

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MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models

Cited by 23 publications

References 62 publications

Deep Sequencing and Analysis of Transcriptomes of Pinus koraiensis Sieb. & Zucc.

Deep Sequencing and Analysis of Transcriptomes of Pinus koraiensis Sieb. & Zucc.

Resource allocation strategies among vegetative growth, sexual reproduction, asexual reproduction and defense during growing season of Aconitum kusnezoffii Reichb.

Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves

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