Amino Acid Compositions of 27 Food Fishes and Their Importance in Clinical Nutrition

Proteins and amino acids are important biomolecules which regulate key metabolic pathways and serve as precursors for synthesis of biologically important substances; moreover, amino acids are building blocks of proteins. Fish is an important dietary source of quality animal proteins and amino acids and play important role in human nutrition. In the present investigation, crude protein content and amino acid compositions of important food fishes from different habitats have been studied. Crude protein content was determined by Kjeldahl method and amino acid composition was analyzed by high performance liquid chromatography and information on 27 food fishes was generated. The analysis showed that the cold water species are rich in lysine and aspartic acid, marine fishes in leucine, small indigenous fishes in histidine, and the carps and catfishes in glutamic acid and glycine. The enriched nutrition knowledge base would enhance the utility of fish as a source of quality animal proteins and amino acids and aid in their inclusion in dietary counseling and patient guidance for specific nutritional needs

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Not AvailableEnzyme β-galactosidase (EC 3.2.1.23) is known to influence vascular differentiation during early vegetative growth of plants, but its role in hypocotyl development is not yet fully understood. We generated the hypocotyl transcriptome data of a hypocotyl-defect jute (Corchorus capsularis L.) mutant (52,393 unigenes) and its wildtype (WT) cv. JRC-212 (44,720 unigenes) by paired-end RNA-seq and identified 11 isoforms of β-galactosidase,using a combination of sequence annotation, domain identification and structural-homology modeling. Phylogenetic analysis classified the jute β-galactosidases into six subfamilies of glycoside hydrolase-35 family, which are closely related to homologs from Malvaceous species. We also report here the expression of a β- galactosidase of glycoside hydrolase-2 family that was earlier considered to be absent in higher plants. Comparative analysis of domain structure allowed us to propose a domain-centric evolution of the five classes of plant β-galactosidases. Further, we observed 1.8–12.2-fold higher expression of nine β-galactosidase isoforms in the mutant hypocotyl, which was characterized by slower growth, undulated shape and deformed cell wall. In vitro and in vivo β-galactosidase activities were also higher in the mutant hypocotyl. Phenotypic analysis supported a significant (P≤0.01) positive correlation between enzyme activity and undulated hypocotyl. Taken together, our study identifies the complete set of β-galactosidases expressed in the jute hypocotyl, and provides compelling evidence that they may be involved in cell wall degradation during hypocotyl development.Not Availabl

Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in jute (Corchorus olitorius L.)

<p>We performed individual-based restriction site-associated DNA (RAD) sequencing to discover single-nucleotide polymorphisms (SNPs) across a diverse set of 225 fibre-type lines in jute (<i>Corchorus olitorius </i>L., Malvaceae s. l.) <i></i>and identified a set of 1115 polymorphic RAD-SNP markers (SNP containing RADseq loci), each supporting a single SNP with >0.05 minor allele frequency (MAF). Based on multilocus RAD-SNP genotypes of 221 lines (four lines were excluded due to >50 % missing genotypes) with a call rate of >0.95, we examined the geographic patterns of genetic diversity across nine predefined populations, viz. AFR1 (Kenya and Sudan), AFR2 (Tanzania), CI (central India), EI (east India), NI (north India), SI (south India), NPPK (Nepal and Pakistan), ESEA (China, Myanmar, Indonesia and Thailand) and RoW (Australia, Brazil, Germany and Russia) and determined their genetic relatedness by assessing the <i>F</i>_ST, AMOVA, <i>N</i>_mand PCA at the population level. Using five assignment tests with different statistical bases (<i>k</i>-means clustering, STRUCTURE, sNMF, DAPC and frequency-based assignment test), the most exhaustive yet to our knowledge, we inferred how these geographic populations are structured. We further applied subpopulation-based <i>F</i>_ST- (LOSITAN and BayeScan) and <i>G</i>_ST-outlier (HacDivSel) tests and an individual-based global approach (PCAdapt) based on principal component analysis (PCA) to detect putative RAD-SNP loci under selection. Instead of BLAST alone, we employed a serial approach based on BLAST, Blast2GO mapping, protein domain annotation (DoMosaics) and REViGO semantic analysis to identify candidate genes and retrieve the overrepresented gene ontology (GO) terms associated with the outlier RAD-SNP loci putatively involved in local adaptation.</p><p> </p><p> </p><p><br></p

Genomics for augmenting bast fibre yield and quality improvement in jute

<p>Jute (<i>Corchorus capsularis </i>L. and <i>C. olitorius</i> L., Malvaceae s. l.) is an important ligno-cellulosic bast fibre crop (2n = 2<i>x</i> = 14), with diversified industrial uses of textiles. We initiated genomics research in jute, with an objective to implement genomics-assisted breeding approaches for bast fibre yield and quality improvement. Here, we present a few important genomic resources and tools made available for jute over the past few years.</p

Development and validation of SSR and InDel markers in jute (Corchorus olitorius L.) using next-generation sequencing

We used next-generation sequencing based on Illumina NextSeq (Illumina, San Diego, CA), with 2 x 150 bp chemistry, to assemble <i>de novo</i> the whole genome shotgun (WGS) sequence of <i>Corchorus olitorius</i> cv. Sudan Green and identified genomic SSR and InDel markers. Of 13,814 SSRs identified, the number of di-, tri- and tetra-nucleotide repeat classes were 10,078, 2,388 and 1,348, respectively. Although a total of 5,471 InDels were detected at various positions, we could only identify 44 InDel markers based on stringent parameters. A total of 1,000 SSR (956) and InDel (44) markers were successfully validated in <i>Corchorus</i> spp

The draft genome of Corchorus olitorius cv. JRO-524 (Navin)

Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000)