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Series GSE148762 Query DataSets for GSE148762
Status Public on Apr 17, 2020
Title Small RNAs in monocots
Organisms Colocasia esculenta; Acorus calamus; Lemna gibba; Oryza glaberrima; Setaria viridis; Sorghum bicolor; Zea mays; Cyperus alternifolius; Ananas comosus; Canna indica; Cocos nucifera; Zostera marina; Anomochloa marantoidea; Phyllostachys edulis; Streptochaeta angustifolia; Liriope muscari; Phoenix dactylifera; Kniphofia uvaria; Elaeis guineensis; Phalaenopsis equestris; Hemerocallis lilioasphodelus; Sagittaria montevidensis; Pharus parvifolius; Nymphaea colorata; Echinodorus uruguayensis; Musa acuminata var. zebrina; Musa ABB Group; Musa acuminata AAA Group; Freycinetia cumingiana; Tradescantia fluminensis; Raddia brasiliensis; Goudaea ospinae; Prosthechea radiata
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary In monocots other than the cereals maize and rice, the repertoire and diversity of microRNAs (miRNAs) and the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly characterized. To remedy this, we sequenced small RNAs (sRNAs) from vegetative and dissected inflorescence tissue in 28 phylogenetically diverse monocots and from several early-diverging angiosperm lineages, as well as publicly available data from 10 additional monocot species. We annotated miRNAs, siRNAs and phasiRNAs across the monocot phylogeny, identifying miRNAs apparently lost or gained in the grasses relative to other monocot families, as well as a number of tRNA fragments misannotated as miRNAs. Using our miRNA database cleaned of these misannotations, we identified conservation at the 8th, 9th, 19th and 3’ end positions that we hypothesize are signatures of selection for processing, targeting, or Argonaute sorting. We show that 21-nt reproductive phasiRNAs are far more numerous in grass genomes than other monocots. Based on sequenced monocot genomes and transcriptomes, DICER-LIKE 5 (DCL5), important to 24-nt phasiRNA biogenesis, likely originated via gene duplication before the diversification of the grasses. This curated database of phylogenetically diverse monocot miRNAs, siRNAs, and phasiRNAs is the largest collection to date, and should facilitate continued exploration of small RNA diversification in flowering plants.
 
Overall design Small RNA (sRNA) sequencing for 28 phylogenetically diverse monocots
 
Contributor(s) Meyers BC, Mathioni S
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Submission date Apr 16, 2020
Last update date Sep 09, 2020
Contact name Blake C. Meyers
E-mail(s) bmeyers@danforthcenter.org
Phone 314-587-1422
Organization name Donald Danforth Plant Science Center
Lab Meyers lab
Street address 975 N Warson Road
City St. Louis
State/province MO
ZIP/Postal code 63132
Country USA
 
Platforms (34)
GPL9361 Illumina Genome Analyzer II (Zea mays)
GPL13371 Illumina Genome Analyzer II (Oryza glaberrima)
GPL17628 Illumina HiSeq 2500 (Zea mays)
Samples (195)
GSM4478439 Acorus_ant_r1
GSM4478440 Acorus_pis_r1
GSM4478441 Acorus_spadix_r1
Relations
BioProject PRJNA625703
SRA SRP256576

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE148762_RAW.tar 9.7 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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