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ABSTRACT: Termitomyces fungus-comb and surrounding environment metagenome sequencing

PROVIDER: PRJNA672331 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12959732_1.fastq.gz	Fastqsanger.gz
	SRR12959732_2.fastq.gz	Fastqsanger.gz
	SRR12959733_1.fastq.gz	Fastqsanger.gz
	SRR12959733_2.fastq.gz	Fastqsanger.gz
	SRR12959734_1.fastq.gz	Fastqsanger.gz

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Genome-wide association analysis and genome resequencing reveal a genomic duplication possibly concerning a novel chicken comb morphology

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.

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Project description:Microbiota of degrading fungus comb of Odontotermes obesus

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Project description:Mycobiota of degrading fungus comb of Odontotermes obesus

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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.

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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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