Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20830 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1974840.fastq.gz | Fastqsanger.gz | |||
| ERR1974840_1.fastq.gz | Fastqsanger.gz | |||
| ERR1974840_2.fastq.gz | Fastqsanger.gz | |||
| ERR1974833_1.fastq.gz | Fastqsanger.gz | |||
| ERR1974833_2.fastq.gz | Fastqsanger.gz |
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Project description:Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing about one million infections globally each year. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large MAT locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with two MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the origin and evolution of pathogenesis, as well as the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species. In this study, we sequenced, assembled, and annotated the genomes of two C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the two C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Also, bioinformatics and ChIP-seq analyses showed that C. amylolentus has regional centromeres that are enriched with species-specific transposable and repetitive elements, similar to the centromeric structures in the pathogenic Cryptococcus species. Additionally, we found that while neither of the P/R and HD loci in C. amylolentus is physically linked to its centromere, both MAT loci exhibit centromere linkage in meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the inter MAT-CEN regions. Furthermore, genomic comparison between C. amylolentus and pathogenic Cryptococcus species provides evidence that chromosomal rearrangements mediated by intercentromeric recombination have occurred after the two lineages split from their common ancestor. We propose a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by repetitive elements located within the centromeric regions and shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and was followed by chromosomal rearrangements that resulted in the two MAT loci becoming physically linked and eventually fused to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species.
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Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
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