Agri Gene最新文献

Numerous environmental reservoirs contribute to the problem of acquired antibiotic resistance of human pathogens. One environmental reservoir of particular importance is the intestinal bacteria of poultry. Antibiotics are often used to prevent sickness and improve production in chicken farms. Hence, the intestinal microbial community of chickens as a reservoir for antibiotic resistance genes (ARGs) has received increasing attention. Therefore, the aim of this study was to investigate the occurrence, diversity, and abundance of ARGs and mobile genetic elements (MGEs), and the distribution of plasmids in layer and broiler feces using Illumina high-throughput sequencing. Metagenomic analysis showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were predominate in chicken feces. At the genus level, Escherichia coli may be predominant in chicken feces with a relative abundance of plasmids. Sequencing reads revealed differences in the distribution of plasmids in microbial communities between layer and broiler feces. Genes coding for antibiotic resistance were identified in both communities. BLAST analysis against the Antibiotic Resistance Genes Database (ARDB) further revealed that layer and broiler feces contained various ARGs with high abundances, among which vancomycin (van) was the most abundant, accounting for > 36% of all reads of ARGs. Beta-lactam resistance genes (bl) were highly enriched in the broiler feces, among which bl2e_cbla was the most abundant, but was absent in layer feces. Over 20 types of insertion sequences were detected in each fecal sample. These results highlight the prevalence of ARGs, plasmids, and MGEs in chicken feces, which warrants further studies to better elucidate the risk to public health.

Small RNA sequencing in the copepod ectoparasite Caligus rogercresseyi was conducted to evidence putative roles of non-coding RNAs during the sea louse ontogeny. Here, differentially expressed miRNAs and mRNAs for each developmental stage were analyzed in parallel with bioinformatic gene target predictions. Based on sequence analysis, C. rogercresseyi miRNome comprises 673 conserved miRNAs, including precursors, 5′ and 3′ isomiRs. The conserved miRNAs include 40 families found in twelve different arthropods species. The results also showed that C. rogercresseyi miRNome exhibit stage-specific expression patterns, with miRNA-996-4 and miRNA-124 displaying sex-biased expression. Target prediction of these miRNAs identifies possible silencing mechanism of sex-related genes. Furthermore, bantam isomiRs were highly transcribed during the infective stage of copepodid and target prediction using differentially expressed genes in Atlantic salmon infested with sea lice, suggests a putative role of these miRNAs in the host-pathogen interaction. This is the first study reporting a miRNA repertoire in a marine copepod ectoparasite that affects the salmon aquaculture worldwide.

Drought is the most serious abiotic stress that limits crop production in rain-fed environments. In this study genetic diversity of SNAC1 gene investigated in a collection of 83 diverse rice accessions from different geographical origins. Amplification of SNAC1 gene exons was performed by combined hot start-touchdown PCR protocol. The average number of alleles was 9.5 alleles. A total of 6 rare alleles were identified from exons of SNAC1. The average gene diversity index, PIC (Polymorphism information content) and Shannon value were 0.8518, 0.8343 and 2.0469, respectively. Evolutionary study based on Ewens-Watterson test showed that exon 1 of SNAC1 gene was probability under genetic drift. To identify potential SSR markers in SNAC1 gene sequence, SSR distributions within rice SNAC1 gene sequence were mined. Totally 15 microsatellite loci were detected which tri-nucleotide motifs (8) was being most abundant, followed by di- (6) and tetra-nucleotide (1) motifs. Maximum loci were found in 3′ UTR (5) (Untranslated regions), followed by in 5′ UTR (4) and coding sequences (3 for each exon). The present study revealed genetic divergence of SNAC1 gene coding regions and also mined SSR distributions within SNAC1 gene sequence and introduced an optimized PCR method. This information can be used for the development of drought tolerant rice varieties.

Long non-coding RNAs (lncRNAs), endogenous RNAs with restricted or null coding potential, are emerging as key regulators of multiple biological processes in several species. Despite the importance of these transcripts, few studies have characterized marine crustacean lncRNAs or the modulation of these in response to chemical exposure. Therefore, the present study mainly focused on identifying lncRNAs in the sea louse Caligus rogercresseyi, an ectoparasite of primary concern to the Chilean salmon industry. A bioinformatics pipeline for lncRNAs discovery was designed, revealing 1835 putative lncRNA sequences in the C. rogercresseyi transcriptome. Furthermore, C. rogercresseyi lncRNAs evidenced features classical of lncRNAs, such as lower values of GC content, length, transcription activity, and minimum free energy as compared with coding transcripts. Furthermore, since developed resistance against delousing drugs is a major threat to the management and control of sea lice, the transcriptional modulation of C. rogercresseyi lncRNAs during exposure to delousing drugs was also evaluated. Unlike coding transcripts, lncRNAs were mainly downregulated after exposure to either deltamethrin or azamethiphos, showing transcription patterns similar to other, better studied non-coding RNAs in arthropods. Finally, a subset of lncRNAs exhibited a strong transcriptional correlation to genes commonly associated with the drug response, such as ABC transporters, cytochrome p450, and glutathione S-transferase, among others. Our findings provide one of the first comprehensive lncRNA characterizations in a crustacean, contributing towards understandings on the regulatory role of lncRNAs during the drug response in Caligus rogercresseyi.

Mitochondrial DNA provides useful tools for inferring population genetic structure within a species and phylogenetic relationships between species. The complete mitogenome sequences were assembled from strains of the cowpea aphids, Aphis craccivora, from the old (15,308 bp) and new world (15,305 bp) using shotgun Illumina HiSeq 2500 sequence reads. The A. craccivora mitogenomes have 13 protein coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs in the same order and orientation found among Insecta. The two A. craccivora mitogenomes do not contain long intergenic repeats as found in other members of the family Aphididae. Comparisons between strains indicated a 99.7% sequence identity, wherein 57 and 11 substitutions were respectively predicted among reads from new and old world strains. Among these substitutions, 31 and 2 were in PCGs of new world and old world aphids, respectively, and out of which 28 and 2 were nonsynonymous. A majority of the substitutions were in NADH Dehydrogenase subunit 1. Phylogenetic analysis of full mitogenomes sequences predicted that Aphididae as monophyletic and clustered with Pterocommatinae and Aphidinae at subfamily level.

Germin-like protein (GLP) genes in plants constitute a multigene family that functions in a variety of biological processes, such as plant growth and development and respond to abiotic and biotic stresses. Available genome sequences of foxtail millet (Setaria italica) have facilitated the identification and delineation of the GLP gene family, which is perhaps the first report in any millet crop. A total of 20 SiGLP genes were mapped in six of the nine foxtail millet chromosomes. The majority of these SiGLP genes, except six, clustered into five known germin (GER) groups and revealed group-specific variations in their gene structure and conserved protein motifs. The SiGLP genes shared homologous relationship within and across plant genomes as per their syntenic chromosomal regions, indicating gene duplication and expansion in course of plant evolution. Gene expression dynamics revealed four out of the 20 SiGLP genes having a putative functional role in different tissues. The presence of diverse cis-acting regulatory elements in the putative SiGLP promoter sequences and homology-based 3-D protein structure predictions revealed their possible functional diversity. The present work encompasses a molecular insight into the organization and functions of SiGLP gene family members. This may serve as a platform for functional analysis and their efficient utilizations in genetic improvement of foxtail millet and other related crops.

Cichorium intybus commonly known as chicory, is an important medicinal plants having different therapeutic properties. Several studies have been done on plant miRNAs for understanding their role in biological functions. However, no miRNAs are reported in miRBase for the genus C. intybus. In the present study, we used a homology based search and in-silico approach for identifying miRNA in C. intybus. Twenty eight potential miRNA families were predicted. Out of 28 predicted miRNA families, 17 were found to regulate 349 target transcripts and play important role in different biological, cellular and metabolic process. To understand the miRNA mediated gene regulatory control and to validate predicted miRNA targets, a biological network was also constructed. Further study of C. intybus miRNA regulation mechanisms may help us to know more about the important roles of miRNAs in C. intybus.

Ever-increasing demands of mungbean consumption, wide eco-geographical variations and inadequate achievements through conventional breeding necessitate comprehensive assessment of genetic variability coupled with population patterning. In the present work 30 mungbean landraces of the Odisha State of India representing four different geographical regions (populations) along with some Indian genotypes were used for elucidation of genetic diversity and population structure analysis using 52 SCoT (gene-targeted) and 45 RAPD (arbitrary) markers. SCoT markers proved to be more effective than RAPD in ascertaining genetic diversity at genotype level (% polymorphism, Rp, PIC, EMR, MI, GI and I) and population level (Na, Ne, H, I, Ht and Hs). Unique bands (23 RAPD and 47 SCoT) were generated which enabled identification of 16 and 25 genotypes respectively. Genetic diversity parameters of East Odisha revealed high genetic variability compared to other populations. AMOVA revealed > 95% variation within the populations which is further supported by high gene flow and low level of genetic differentiation. UPGMA dendrogram and population structure grouped genotypes into 8 major clusters irrespective of their geographical affiliations. However, genotypes belonging to certain clusters exhibited significant geographical and morphological preferences using the cumulative strategy. The study illustrated the importance of combined marker analysis, which uses complementary information from two distinct and analogous markers and in the process, offers accurate and reliable results. Further, the applicability of in silico analysis in performing a high resolution patterning of genetic divergence and population structure was demonstrated.

Schizothorax prenanti (Cypriniformes, Cyprinidae, Schizothoracinae) is an endemic, valuable fish in the southwest of China. Although a series of studies concerning the genetic and endocrine control of feeding and growth in S. prenanti have been examined in our laboratory, the mechanism is still unclear. To better understand these mechanisms, complete coding sequences of the eukaryotic initiation factor 4E binding proteins (4E-BP1, 4E-BP2 and 4E-BP3) were isolated in S. prenanti and their mRNA distributions examined in different tissues. S. prenanti 4E-BP1, 4E-BP2 and 4E-BP3 consisted of 120, 113 and 111 amino acids and exhibited a quite high degree of amino acid identity, respectively, to their cyprinid fish homologs. Phylogenetic analysis of the 4E-BPs sequences showed three main branches of vertebrate 4E-BPs. However, it was of interest that teleost 4E-BP1 clustered with vertebrate 4E-BP3, while the tetrapod 4E-BP1 formed a distinct clade. The mRNAs of all 4E-BPs were ubiquitously expressed in S. prenanti tissues, including brain, pituitary, eye, heart, gut, hepatopancreas, kidney, spleen, gonad, muscle, skin and gill. The widespread distributions suggest that 4E-BPs might have distinct physiological actions in S. prenanti, in particular on the brain, pituitary, gut, hepatopancreas and muscle, which involved feeding and growth regulation. This preliminary study opens the way for further functional studies on the mechanisms of the regulation of feeding and growth in S. prenanti and other teleost.

The dominance effect is important for mastitis, which is the major source of economic loss in dairy herds. The objective of this study was to evaluate dominance effects of CXCR1 gene for clinical mastitis and production traits in Holstein dairy cattle using the selective genotyping method. Records of 305-day lactation were obtained for production traits and for the number of cases of clinical mastitis per lactation. Cows were selected based on extreme values (highest and lowest CMR values) for clinical mastitis residuals (CMR) from mixed model analyses. Each of the two extreme groups of cowswas genotyped for CXCR1 gene and then, associations between genotypes and CMR and also breeding values for traits of interest were estimated by applying logistic regression analyses. Allele G of CXCR1 gene was associated with fewer cases for clinical mastitis (CM), and showed desired effects on production traits, especially on milk, protein and fat yield. Effects of dominance ranged from − 0.03 SD to 0.55 SD for the production traits and CM. For milk production traits, positive values for dominance indicated a surplus in these traits. Result showed that CXCR1 gene may be a valuable candidate gene for improvement of mastitis resistance as well as production traits in dairy cattle herds and the dominance effects may not be negligible.