Preparation and Characterization of Enzymic Milk Protein Hydrolysates from an Ultrafiltration Reactor

Bard, C.; Gauthier, Sylvie F.

doi:10.1016/s0315-5463(89)70537-x

Cited by 4 publications

(4 citation statements)

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“…The updated collection of homologous protein sets of prokaryotes and eukaryotes is expected to be used for functional annotation of newly sequenced genomes, including those complex eukaryotes, as well as genome-wide evolutionary studies (Tatusov et al, 2003). Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes (Ashburner et al, 2000). In SMRT sequencing of the full-length transcriptome of the R. ferrugineus, a total of 27,707 FL transcripts were annotated into the GO database, most of which were biological processes, followed by cellular components and molecular functions.…”

Section: Discussionmentioning

confidence: 99%

“…Transcripts function was annotated based on the following databases:NR (NCBI non-redundant protein sequences) (Deng et al, 2006), NT (NCBI non-redundant nucleotide sequences), Pfam (Protein family) (Finn et al, 2014), KOG (Clusters of Orthologous Groups of proteins) (Koonin et al, 2004), Swiss-Prot (A manually annotated and reviewed protein sequence database) (Apweiler et al, 2004), KEGG (Kyoto Encyclopedia of Genes and Genomes) (Kanehisa et al, 2004) and GO (Gene Ontology) (Ashburner M, 2000). The BLAST software with E-value ≤1e-5 was used for NT database analysis.…”

Section: Functional Annotation Of Transcriptsmentioning

confidence: 99%

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Peer Review #2 of "SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) (v0.1)"

2020

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Background. Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods. In this study, we used PacBio Iso-Seq and Illumina RNAseq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results. A total of 63,801 nonredundant fulllength transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.

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Section: Discussionmentioning

confidence: 99%

Section: Functional Annotation Of Transcriptsmentioning

confidence: 99%

Peer Review #2 of "SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) (v0.1)"

2020

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“…The Gene Ontology database (Ashburner et al, 2000;Sherlock, 2009) (GO: http://geneontology.org/, last access: 9 May 2021) is a structured, standard biological annotation system built in 2000 by an organization (Gene Ontology Consortium), and it aims at establishing a standard vocabulary systematic knowledge of genes and their products. The Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa et al, 2004;Teber et al, 2009) (https://www.kegg.jp/, last access: 9 May 2021) is a database resource for understanding high-level functions and utilities of the biological system, including the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.…”

Section: Go and Kegg Pathway Enrichment Analysismentioning

confidence: 99%

Transcriptomic profile of leg muscle during early growth and development in Haiyang yellow chicken

Yin

Zhang

et al. 2021

Arch. Anim. Breed.

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Abstract. Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. This study aimed to identify candidate genes involved in chicken growth and development and to investigate the potential regulatory mechanisms of early growth in Haiyang yellow chicken. RNA sequencing was used to compare the transcriptomes of chicken muscle tissues at four developmental stages. In total, 6150 differentially expressed genes (DEGs) (|fold change| ≥ 2; false discovery rate (FDR) ≤ 0.05) were detected by pairwise comparison in female chickens. Functional analysis showed that the DEGs were mainly involved in the processes of muscle growth and development and cell differentiation. Many of the DEGs, such as MSTN, MYOD1, MYF6, MYF5, and IGF1, were related to chicken growth and development. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were significantly enriched in four pathways related to growth and development: extracellular matrix (ECM)–receptor interaction, focal adhesion, tight junction, and insulin signalling pathways. A total of 42 DEGs assigned to these pathways are potential candidate genes for inducing the differences in growth among the four development stages, such as MYH1A, EGF, MYLK2, MYLK4, and LAMB3. This study identified a range of genes and several pathways that may be involved in regulating early growth.

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“…To investigate the function of genes, we used BLAST (version 2.2.26) (Altschul et al, 1997), HMMER 3.1 (Eddy, 1998), and KOBAS 3.0 (Xie et al, 2011) to search the NR (Li et al, 2002), Nt (Li et al, 2002), KOG (Koonin et al, 2004), COG (Tatusov et al, 2003), Swiss-prot (Amos and Rolf, 2000), KEGG (Minoru et al, 2004), GO (Ashburner et al, 2000), and protein family (Pfam) (Finn et al, 2016) databases. CPC v0.9 (Kong et al, 2007), CNCI v2 (Sun et al, 2013), PLEK v1.2 (Aimin et al (2014), and Pfam-scan (Finn et al, 2016) were used to identify lncRNAs from the Iso-Seq data (Chao et al, 2018).…”

Section: Identification and Functional Annotation Of Lncrnasmentioning

confidence: 99%

Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response

Fang

et al. 2020

Front. Genet.

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Long non-coding RNAs (lncRNAs) regulate plant responses to abiotic stresses. However, the short reads produced by second-generation sequencing technology make it difficult to accurately explore full-length transcripts, limiting the study of lncRNAs. In this study, we used third-generation long-read sequencing technology with the PacBio Sequel and Illumina platform to explore the role of lncRNAs in the heat stress response of Populus x canadensis Moench trees. We using 382,034,416 short reads to correct 4,297,179 long reads by resulted in 66,657 full-length transcripts, representing 33,840 genes. Then, 753 putative lncRNAs were identified, including 658 sense lncRNAs (87.38%), 41 long intervening/intergenic non-coding RNAs (lincRNAs) (5.44%), 12 antisense lncRNAs (1.59%), and 42 sense intronic lncRNAs (5.58%). Using the criteria | log 2 FC| ≥ 1 and q-value < 0.05, 3,493 genes and 78 lncRNAs were differentially expressed under the heat treatment. Furthermore, 923 genes were detected as targets of 43 differently expressed lncRNAs by cis regulation. Functional annotation demonstrated that these target genes were related to unfolded protein binding, response to stress, protein folding, and response to stimulus. Lastly, we identified a lncRNA-gene interaction network consisting of four lncRNAs and six genes [Heat Shock Protein 82 (HSP82), HSP83, Disease Resistance Protein 27 (DRL27), DnaJ family protein (DNJH), and two other predicted protein-coding genes], which showed that lncRNAs could regulate HSP family genes in response to heat stress in Populus. Therefore, our third-generation sequencing has improved the description of the P. canadensis transcriptome. The potential lncRNAs and HSP family genes identified here present a genetic resource to improve our understanding of the heat-adaptation mechanisms of trees.

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Preparation and Characterization of Enzymic Milk Protein Hydrolysates from an Ultrafiltration Reactor

Cited by 4 publications

References 0 publications

Peer Review #2 of "SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) (v0.1)"

Peer Review #2 of "SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae) (v0.1)"

Transcriptomic profile of leg muscle during early growth and development in Haiyang yellow chicken

Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response

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