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Granulosa cells provide transcriptomic information on ovarian follicle dynamics in southern white rhinoceros

ABSTRACT: Granulosa cells provide transcriptomic information on ovarian follicle dynamics in southern white rhinoceros

PROVIDER: PRJNA1084856 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28247409_1.fastq.gz	Fastqsanger.gz
	SRR28247409_2.fastq.gz	Fastqsanger.gz
	SRR28247410_1.fastq.gz	Fastqsanger.gz
	SRR28247410_2.fastq.gz	Fastqsanger.gz
	SRR28247411_1.fastq.gz	Fastqsanger.gz

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Granulosa cells provide transcriptomic information on ovarian follicle dynamics in southern white rhinoceros

Project description:Much remains unknown about the reproductive physiology of southern white rhinoceros (SWR) and the effect of ovarian stimulation prior to ovum pickup (OPU) have not been fully elucidated. Granulosa cells (GC) provide valuable insight into follicle growth and oocyte maturation status. The goals of this study were to evaluate transcriptomic changes in GC from three stages of follicle development and to identify biomarkers possibly associated with follicular growth and maturation as a result of ovarian stimulation. GC collected from SWRs following OPU were assigned stages based upon follicle size. Total RNA was isolated, and cDNA libraries were prepared and sequenced on a NovaSeq 6000. All bioinformatics analyses were performed utilizing the Galaxy web platform. Reads were aligned to CerSimCot1.0, and the manual curation was performed with EquCab3.0. Overall, 39,455 transcripts (21,612 genes) were identified across follicle stages, and manual curation yielded a 61% increase in gene identification from the original annotation. Granulosa cells from preovulatory follicles expressed the highest number of unique transcripts. The following seven biomarkers were determined based upon cluster analysis and patterns of expression: COL1A1, JMY, FBXW11, NRG1, TMPO, MACIR and COL4A1. These data can be used to potentially evaluate the effects of different ovarian stimulation protocols on follicle dynamics, improve OPU results, and support conservation efforts in this species.

2024-08-25 | GSE261038 | GEO

Granulosa cells provide transcriptomic information on ovarian follicle dynamics in southern white rhinoceros

Project description: Not available

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A preliminary analysis of the southern white rhinoceros granulosa cell transcriptome (Ceratotherium simum simum)

Project description:In vivo-collected granulosa cells (GC) from the southern white rhinoceros (SWR) provide a non-invasive assessment of the developmental status of oocytes prior to in vitro culture, which will aid in the development of assisted reproductive technologies (ART). Our study aimed to investigate gene expression in SWR granulosa cells (GC), collected in vivo and gain preliminary insight into the transcriptional activity occurring within the cells during various stages of oocyte development. It was hypothesized there would be similarities between the SWR GC transcriptome and cattle and humans, two species for which well-annotated genomes are available and ART are commonly used. GC were collected from SWR following ovum pickup (OPU) and pooled from all aspirated follicles. Total RNA was isolated, libraries prepared and sequencing performed using an Illumina NextSeq 500. Reads were aligned and annotated to CerSimCot1.0. Databases for cattle and human were acquired for comparison. This study identified 37,407 transcripts present in GC of SWR. It was determined that cattle and human transcriptomes are valuable resources with a homology of 45% with the SWR. In conclusion, these data provide preliminary, novel insights into the transcriptional activity of GC in the SWR that can be used to enhance ART in this species.

2023-05-11 | GSE216035 | GEO

Mapping the follicle-specific regulation of extracellular vesicle-mediated microRNA transport in the southern white rhinoceros (Ceratotherium simum simum)

Project description:Efforts to implement effective assisted reproductive technologies (ART) to extricate the northern white rhinoceros (NWR; Ceratotherium simum cottoni) from extinction, could be unconventionally offset from studies carried out using the southern white rhinoceros (Ceratotherium simum simum) as a relative model species. The bi-directional communication and critical transport of regulatory molecules controlling follicular growth and oocyte development are in part mediated through extracellular vesicles (EVs), which encompass a highly conserved and advanced paracrine signaling mechanism important in shuttling unique cargo such as microRNAs (miRNAs). In this study, critical miRNAs for follicular development were identified, proposing novel approaches using EV-mediated miRNA to possibly improve the in vitro technologies outcome in a multitude of species.

2024-05-30 | GSE246260 | GEO

A preliminary analysis of the southern white rhinoceros granulosa cell transcriptome (Ceratotherium simum simum)

Project description:A preliminary analysis of the southern white rhinoceros granulosa cell transcriptome (Ceratotherium simum simum)

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Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

Project description:Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus which has been used as a biocontrol agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. Here, chronically infected beetles were collected from the Philippines, Fiji, PNG and the Solomon Islands (SI). RNAseq was performed to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the SI and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as gp034, lef-8, lef-4 and vp91. We found limited evidence of variation in viral gene expression among geographic populations. Only a few genes such as gp01, gp022 and gp107 were differentially expressed among different strains. Additionally, small RNA sequencing from SI population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.

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