Honey comb Microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1281392 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR34261851.fastq.gz | Fastqsanger.gz |
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Project description:Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype. After conducting a genome-wide association study (GWAS), a 36.5-kb candidate genomic region (chromosome 19:757,754-794,200) related to the Antler-comb phenotype was identified, which wholly and partially encompassed heat shock factor 5 (HSF5) and ring finger protein 43 (RNF43), respectively. HSF5 was ectopically expressed and RNF43 was up-regulated in Antler-comb chickens at embryo ages 7 and 9 (E7 and E9). We further genotyped the most significant single-nucleotide polymorphism (SNP) site, Chr19:794200, across 222 chickens of 16 breeds. We found that the major allele G in Antler-comb chickens remained highly significant across different breeds, and each Antler-comb chicken harbored an allele G. Whole-genome re-sequencing (WGS) involving 10 Hetian Antler-comb and 10 Wildtype-comb chickens reaffirmed the 36.5-kb candidate genomic region, and revealed a genomic duplication, which was 15.7 kb in length and pertained to the 5’-untranslated region and 5’-flanking region of HSF5 (Chr19:784,335-800,034), suggesting its possible role in inducing ectopic expression of HSF5 and altering expression of RNF43 during comb development (E7 and E9). The present study furthers our understanding of this novel chicken comb phenotype, and likely gives another example regarding interactions between genetic variation and phenotype.
2023-12-31 | GSE145948 | GEO
Project description:Dongxiang blue-shelled chicken, an indigenous chicken breed in China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The recent selection has also resulted in a significant difference in egg production. The red comb line (RCL) chicken produces significantly higher number of eggs than that by the dark comb line (DCL) chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. We performed genome-wide association study to identify candidate genes associated with chicken comb color using SNP array data, and we conducted selective sweep analysis to identify putative regions of selection harboring pleiotropic genes affecting both comb color and egg production.
2019-06-04 | GSE124906 | GEO
Project description:This experiment examines gene expression profiles in the brains of adult honey bee workers (Apis mellifera) performing different behavioral tasks in the hive. The different behavioral groups examined were nurse, comb builder, guard, undertaker, and forager. The comb builder, guard, and undertaker behavioral groups perform their respective tasks over a relatively short time scale (typically 1 day), while nursing and foraging are longer duration (lasting > 1 week). The purpose of this study was to examine whether behaviors that persist over different time scales are associated with differences in the extent of gene expression changes in the brain.
2005-01-21 | E-MEXP-252 | biostudies-arrayexpress
Project description:In this study, RNA sequencing (RNA-seq) was employed to compare the whole transcriptomic differences between six Partridge Shank chickens that are divergent in comb sizes and divided into two groups. A total of 563 differentially expressed genes (DEGs) were found in the two groups. Among these DGEs, 277 were up-regulated and 286 were down-regulated in the big comb group. According to the animal QTL database, eight DEGs including BMP2 and CHADL matched the QTLs associated with the chicken comb traits. Functional annotation analysis revealed that the DEGs were involved in cell communication and calcium signaling. Protein-protein interaction network analysis showed that STK32A, PI3KR1, EDN1, HSPA5 and HSPA8 might have great impact on comb growth. Moreover, potential alternative splicing (AS) events and single nucleotide polymorphisms (SNP) were also identified.
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Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos.
2015-07-09 | GSE66183 | GEO
Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos. Genomic binding/occupancy profiling of Scm, Pc and E(z) by high throughput sequencing
2015-07-09 | E-GEOD-66183 | biostudies-arrayexpress
Project description:Transcriptome sequencing has become the main methodology for analyzing the relationship between genes and characteristics of interests, particularly those associated with diseases and economic traits. Because of its functional superiority, commercial royal jelly (RJ) and its production are major areas of focus in the field of apiculture. Multiple lines of evidence have demonstrated that many factors affect RJ output by activating or inhibiting various target genes and signaling pathways to augment their efficient replication. The coding sequences made available by the Honey Bee Genome Sequencing Consortium have permitted a pathway-based approach for investigating the development of the hypopharyngeal glands (HGs). In the present study, 3573941, 3562730, 3551541, 3524453, and 3615558 clean reads were obtained from the HGs of five full-sister honey bee samples using Solexa RNA sequencing technology. These reads were then assembled into 18378, 17785, 17065, 17105, and 17995 unigenes, respectively, and aligned to the DFCI Honey Bee Gene Index database. The differentially expressed genes (DEGs) data were also correlated with detailed morphological data for HGs acini. The results identify areas that warrant further study, including those that can be used to improve honey bee breeding techniques and help ensure stable yields of RJ with high quality traits. The 5 samples at given time (d3, d6, d9, d12, d16 after adult worker bees emergence from the comb) are in the critical stage of the RJ secretion and HGs developments indicated (triggered) the further caste differentiation (worker bees and queen) and task switch (nurse bees and foragers). 30 pooled heads of each samples were
2014-05-20 | E-GEOD-47136 | biostudies-arrayexpress
Project description:Fungus-cultivating termite comb metagenome Targeted loci
| PRJNA604886 | ENA
Project description:Our molecular understanding of honey bee cellular stress responses is incomplete. Previously, we sought to identify and began functional characterization of the components of the UPR in honey bees. We observed that UPR stimulation resulted in induction of target genes upon and IRE1 pathway activation, as assessed by splicing of Xbp1 mRNA. However, were not able to determine the relative role of the various UPR pathways in gene activation. Our understanding of honey bee signal transduction and transcriptional regulation has been hampered by a lack of tools. After using RNAseq to expand the known UPR targets in the bee, we use the Drosophila melanogaster S2 cell line and honey bee trans and cis elements to investigate the role of the IRE-1 pathway in the transcriptional activation of one of these targets, the honey bee Hsc70-3 gene. Using a luciferase reporter, we show that honey bee hsc70 promoter activity is inducible by UPR activation. In addition, we show that this activation is IRE1-dependent and relies on specific cis regulatory elements. Experiments using exogenous honey bee or fruit fly XBP1S proteins demonstrate that both factors can activate the Hsc70-3 promoter and further support a role for the IRE-1 pathway in control of its expression in the honey bee. By providing foundational knowledge about the UPR in the honey bee and demonstrating the usefulness of a heterologous cell line for molecular characterization of honey bee pathways, this work stands to improve our understanding of this critical species.
2020-03-28 | GSE139368 | GEO