Small RNAs from 11 Drosophila species

Description: Summary from the GEO: "Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment."

Overall design from the GEO: "Small RNA samples from 11 Drosophila species."

Abstract Summary: "To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution."

Subject of Study

Drosophila ananassae

Drosophila erecta

Drosophila grimshawi

Drosophila mojavensis

Drosophila persimilis

Drosophila pseudoobscura

Drosophila sechellia

Drosophila simulans

Drosophila virilis

Drosophila willistoni

Subject(s)

RNA, Small Untranslated

RNA, Untranslated

Access via GEO
Plain Text files of Non-coding RNA profiling by high throughput sequencing
Accession #: GSE98013

Access via SRA
ncRNA sequencing of 56 samples.
Accession #: SRP104403

Access via BioProject
Additional information about the overall inititative.
Accession #: PRJNA383669
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Mohammed J, Flynt A, Panzarino A, et al. Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Research. 2018; 28(1):52-65.
Data Type: Genomic
Equipment Used: AB SOLiD System
Platform for genomic sequencing

Illumina Genome Analyzer II
The Genome Analyzer supports a wide range of applications, including whole-genome and candidate region resequencing, transcriptome analysis, small RNA discovery, methylation profi ling, and protein-nucleic acid interaction analysis at a genome-wide scale.

Illumina HiSeq 2000
High throughput gene sequencing system
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): Plain Text, SRA, TAR
Data Tool(s): RNA Seq
Dataset Size: 900.8 MB (TAR of TXT), 65 datasets ranging from 0.01-2.3 Gb (SRA)

Data Catalog Record Updated: 2023-12-07