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Bolinopsis mikado

ABSTRACT: Ctenophore comb plate project

PROVIDER: PRJDB8655 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	DRR189212_1.fastq.gz	Fastqsanger.gz
	DRR189212_2.fastq.gz	Fastqsanger.gz
	DRR189213_1.fastq.gz	Fastqsanger.gz
	DRR189213_2.fastq.gz	Fastqsanger.gz
	DRR189214_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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Regeneration in the Ctenophore Mnemiopsis leidyi: A Transcriptomic Analysis

Project description:Ctenophores’ amazing capacity of regeneration has fascinated biologists for centuries. The morphological features of ctenophore regeneration have been documented, but the molecular and cellular components behind this phenomenon have remained a mystery. Here, next generation sequencing technologies and transcriptomic analysis are used to investigate the regeneration dynamics in the ctenophore Mnemiopsis leidyi. The resulting data identify multiple signaling pathways that might be involved in ctenophore regeneration. These include evolutionarily conserved pathways, such as Ca2+-dependent and MAP-kinase signaling pathways, that are up regulated during regeneration, as well as genes involved in energetics and cytoskeleton function. The data also show evidence for involvement of dozens of ctenophore specific secretory molecules, their receptors and processing components that are important signal messengers in regeneration. A unique subset of transcription factors were also found to be involved in regeneration which may be upstream regulators of those signaling pathways. In summary, our data indicate that the strategies which ctenophores employ to regenerate use a unique combination of evolutionarily conserved and ctenophore specific signaling components. These data provide novel insights into the mechanisms of regeneration in the earliest branching taxa in Metazoa.

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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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