Search

Bos indicus cattle breeds have been naturally selected for thousands of years for disease resistance and thermo-tolerance. However, the genetic mechanisms underlying these specific inherited characteristics must be elucidated. Hence, in this study, a whole-genome comparative analysis ofthe Bos indicus cattle breeds Kangayam, Tharparkar, Sahiwal, Red Sindhi, and Hariana of the Indian subcontinent was conducted. Genetic variant identification analysis revealed 155 851 012 SNPs and 10 062 805 InDels in the mapped reads across all Bos indicus cattle breeds. The functional annotation of 17252 genes that comprised both SNPs and InDels, with high functional impact on proteins, was carried out. The functional annotation results revealed the pathways involved in the innate immune response, including toll-like receptors, retinoic acid-inducible gene I-like receptors, NOD-like receptors, Jak-STAT signaling pathways, and non-synonymous variants in the candidate immune genes. We also identified several pathways involved in the heat shock response, hair and skin properties, oxidative stress response, osmotic stress response, thermal sweating, feed intake, metabolism, and non-synonymous variants in the candidate thermo-tolerant genes. These pathways and genes directly or indirectly contribute to the disease resistance and thermo-tolerance adaptations of Bos indicus cattle breeds. Key words: Bos indicus, disease resistance, thermo-tolerance, SNPs, InDels. Les races de bovins appartenant a l'espece Bos indicus ont ete selectionnees naturellement au cours de milliers d'annees pour leur resistance aux maladies et leur tolerance a la chaleur. Cependant, le mecanisme genetique expliquant ces caracteres hereditaires n'a pas encore ete decrit. Dans ce travail, les auteurs ont realise une analyse comparee pan-genomique de cinq races du Bos indicus qui sont presentes sur le sous-continent indien (Kangayam, Tharparkar, Sahiwal, Red Sindhi et Hariana). Au total, 155 851 012 SNP et 10 062 805 InDels ont ete identifies a partir des lectures alignees parmi les cinq races. Les auteurs ont realise l'annotation fonctionnelle des 17 252 genes qui comprenaient des SNP ou des InDels dont on a predit qu'ils auraient un impact fonctionnel important sur les proteines. Les resultats de l'annotation fonctionnelle ont revele des sentiers impliques dans les reponses immunitaires innees, comme les recepteurs de type Toll, les recepteurs du type de l'acide retinoique, des recepteurs de type NOD, les sentiers de signalisation Jak-STAT et des variants nonsynonymes dans des genes candidats du systeme immunitaire. De plus, les auteurs ont egalement identifie plusieurs sentiers impliques dans la reponse au choc thermique, lies aux caracteristiques des poils et de la peau, a la reponse aux stress oxydatifs, a la reponse au stress osmotique, la sudation, la prise alimentaire, le metabolisme et des variants non-synonymes dans des genes candidats pour le thermo-tolerance. Ces sentiers et genes pourraient contribuer directement ou indirectement a la resistance aux maladies et aux adaptations liees a la thermo-tolerance chez les races bovines de Bos indicus. [Traduit par la Redaction] Mots-cles: Bosindicus, resistance aux maladies, thermo-tolerance, SNP, InDel., Introduction Bos indicus cattle breeds (Zebu cattle) are characterized by a hump at the withers, pendulous skin in the dewlap and navel, draught ability, fertility at higher temperatures, maintenance of [...]

Domestic ducks (Anas platyrhynchos domesticus) are resistant to most of the highly pathogenic avian influenza virus (HPAIV) infections. In this study, we characterized the lung proteome and phosphoproteome of ducks infected with the HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala) at 12 h, 48 h, and 5 days post-infection. A total of 2082 proteins were differentially expressed and 320 phosphorylation sites mapping to 199 phosphopeptides, corresponding to 129 proteins were identified. The functional annotation of the proteome data analysis revealed the activation of the RIG-I-like receptor and Jak-STAT signaling pathways, which led to the induction of interferon-stimulated gene (ISG) expression. The pathway analysis of the phosphoproteome datasets also confirmed the activation of RIG-I, Jak-STAT signaling, NF-kappa B signaling, and MAPK signaling pathways in the lung tissues. The induction of ISG proteins (STAT1, STAT3, STAT5B, STAT6, IFIT5, and PKR) established a protective anti-viral immune response in duck lung tissue. Further, the protein–protein interaction network analysis identified proteins like AKT1, STAT3, JAK2, RAC1, STAT1, PTPN11, RPS27A, NFKB1, and MAPK1 as the main hub proteins that might play important roles in disease progression in ducks. Together, the functional annotation of the proteome and phosphoproteome datasets revealed the molecular basis of the disease progression and disease resistance mechanism in ducks infected with the HPAI H5N1 virus. [ABSTRACT FROM AUTHOR]

A better understanding of the biology of lactation, both in terms of gene expression and the identification of candidate genes for the production of milk and its components, is made possible by recent advances in RNA seq technology. The purpose of this study was to understand the synthesis of milk components and the molecular pathways involved, as well as to identify candidate genes for milk production traits within whole mammary transcriptomic datasets. We performed a meta-analysis of publically available RNA seq transcriptome datasets of mammary tissue/milk somatic cells. In total, 11 562 genes were commonly identified from all RNA seq based mammary gland transcriptomes. Functional annotation of commonly expressed genes revealed the molecular processes that contribute to the synthesis of fats, proteins, and lactose in mammary secretory cells and the molecular pathways responsible for milk synthesis. In addition, we identified several candidate genes responsible for milk production traits and constructed a gene regulatory network for RNA seq data. In conclusion, this study provides a basic understanding of the lactation biology of cows at the gene expression level. Keywords: cow, mammary transcriptome, meta-analysis, pathways, candidate genes, milk synthesis. Une meilleure connaissance de la biologie de la lactation, tant en ce qui concerne l'expression des genes que l'identification des genes candidats pour la production du lait et de ses composantes, est rendue possible par les recentes avancees en matiere de technologie RNA-seq. Le but de cette etude etait de comprendre la synthese des composantes du lait et les sentiers moleculaires impliques ainsi que d'identifier des genes candidats pour la production laitiere au sein de jeux de donnees transcriptomiques pour les tissus mammaires. Les auteurs ont realise une meta-analyse des donnees RNA-seq disponibles pour les tissus mammaires et les cellules somatiques du lait. Au total, 11 562 genes etaient partages au sein de tous les transcriptomes de la glande mammaire. Une annotation fonctionnelle des genes exprimes communement a contribue a une comprehension des processus moleculaires contribuant a la synthese des lipides, des proteines et du lactose au sein des cellules secretrices mammaires et des sentiers moleculaires responsables de la synthese du lait. De plus, les auteurs ont identifie plusieurs genes candidats controlant la production du lait et ont construit un reseau de regulation genique a partir des donnees RNA-seq. En conclusion, cette etude contribue a une meilleure comprehension de la lactation chez les vaches au niveau de l'expression genique. [Traduit par la Redaction] Mots-cles : vache, transcriptome des tissus mammaires, meta-analyse, sentiers, genes candidats, synthese du lait., Introduction Cow milk is an important source of dietary food and provides essential nutrients like energy, fats, proteins, calcium, magnesium, selenium, riboflavin, vitamin B12, and pantothenic acid to infant mammals [...]

The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1510 303 high-quality sequence reads with 581198 230 bases was de novo assembled into 22 169 isotigs (isotig represents an individual transcript) and 784 009 singletons. Using these isotigs and 581681 length-filtered (greater than 300 bp) singletons, 20 010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46 604 (70.29%) and 51 642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20 599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species. Key words: jungle crow, Corvus macrorhynchos, transcriptome, 454 pyrosequencing, single nucleotide polymorphisms, simple sequence repeats. Le corbeau a gros bec (Corvus macrorhynchos) est un oiseau qui appartient a l'ordre des Passeriformes et qui est important pour les etudes en ecologie et en genetique evolutive. Cependant, il existe peu de donnees transcriptomiques pour cette espece. Dans le present travail, les auteurs rapportent la caracterisation du transcriptome pulmonaire du corbeau a gros bec a l'aide d'un appareil GS FLX Titanium XLR70. Au total, 1 510 303 sequences de haute qualite, totalisant 581 198 230 bases, ont ete assemblees de novo pour former 22 169 isotigs (chaque isotig representant un transcrit individuel) et 784 009 singletons. En analysant ces isotigs et 581 681 singletons retenus (mesurant au moins 300 nucleotides), 20 010 genes codant pour des proteines ont ete identifies par analyse BLASTx contre une base de donnees non-redondante (nr) de sequences proteiques. Des analyses comparatives ont revele que 46 603 (70,29 %) et 51 642 (72,48%) des transcrits assembles presentaient respectivement une similarite significative avec des proteines RefSeq du diamant mandarin et du poulet. Au terme d'une annotation GO et d'une cartographie des sentiers KEGG, l'annotation fonctionnelle de ces unigenes a mis en evidence plusieurs fonctions et processus biologiques. Des transcrits vraisemblablement impliques dans la reponse immunitaire ont ete identifies. De plus, 20 599 polymorphismes mononucleotidiques (SNP) et 7525 sequences simples repetees (SSR) ont ete identifies au sein du transcriptome assemble. Cette ressource devrait constituer une assise importante pour de futures etudes genetiques en ecologie, en evolution et en conservation chez cette espece et des especes apparentees. [Traduit par la Redaction] Mots-cles : corbeau a gros bec, Corvus macrorhynchos, transcriptome, pyrosequencage 454, polymorphismes mononucleotidiques, sequences simples repetees., Introduction Over the past two decades, nearly all aspects of avian biology from behaviour to systematics had benefited from the application of molecular methods (Lerner and Fleischer 2010). Genomic approaches [...]

Author(s): Mohammed Fawaz[sup.1] , Periyasamy Vijayakumar[sup.1] , Anamika Mishra[sup.1] , Pradeep N. Gandhale[sup.1] , Rupam Dutta[sup.1] , Nitin M. Kamble[sup.1] , Shashi B. Sudhakar[sup.1] , Parimal Roychoudhary[sup.2] , Himanshu Kumar[sup.3] [...]