TY - JOUR
T1 - High-throughput sequencing of Arabidopsis microRNAs
T2 - Evidence for frequent birth and death of MIRNA genes
AU - Fahlgren, Noah
AU - Howell, Miya D.
AU - Kasschau, Kristin D.
AU - Chapman, Elisabeth J.
AU - Sullivan, Christopher M.
AU - Cumbie, Jason S.
AU - Givan, Scott A.
AU - Law, Theresa F.
AU - Grant, Sarah R.
AU - Dangl, Jeffery L.
AU - Carrington, James C.
PY - 2007/2/14
Y1 - 2007/2/14
N2 - In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana. 48 non-conserved MIRNA families, nearly all of which were represented by single genes, were identified. Sequence similarity analyses of miRNA precursor foldback arms revealed evidence for recent evolutionary origin of 16 MIRNA loci through inverted duplication events from protein-coding gene sequences. Interestingly, these recently evolved MIRNA genes have taken distinct paths. Whereas some non-conserved miRNAs interact with and regulate target transcripts from gene families that donated parental sequences, others have drifted to the point of non-interaction with parental gene family transcripts. Some young MIRNA loci clearly originated from one gene family but form miRNAs that target transcripts in another family. We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks.
AB - In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana. 48 non-conserved MIRNA families, nearly all of which were represented by single genes, were identified. Sequence similarity analyses of miRNA precursor foldback arms revealed evidence for recent evolutionary origin of 16 MIRNA loci through inverted duplication events from protein-coding gene sequences. Interestingly, these recently evolved MIRNA genes have taken distinct paths. Whereas some non-conserved miRNAs interact with and regulate target transcripts from gene families that donated parental sequences, others have drifted to the point of non-interaction with parental gene family transcripts. Some young MIRNA loci clearly originated from one gene family but form miRNAs that target transcripts in another family. We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks.
UR - http://www.scopus.com/inward/record.url?scp=34547115664&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0000219
DO - 10.1371/journal.pone.0000219
M3 - Article
C2 - 17299599
AN - SCOPUS:34547115664
SN - 1932-6203
VL - 2
JO - PloS one
JF - PloS one
IS - 2
M1 - e219
ER -