In plants, 24 nucleotide long heterochromatic si
- NSF-PAR ID:
- 10247547
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 89
- Issue:
- 3
- ISSN:
- 0960-7412
- Page Range / eLocation ID:
- p. 617-635
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Summary RNA s (het‐siRNA s) transcriptionally regulate gene expression byRNA ‐directedDNA methylation (RdDM ). The biogenesis of most het‐siRNA s depends on the plant‐specificRNA polymeraseIV (PolIV ), andARGONAUTE 4 (AGO 4) is a major het‐siRNA effector protein. Through genome‐wide analysis ofsRNA ‐seq data sets, we found thatAGO 4RNA s. The accumulation ofAGO 4RNA s also requires several factors known to participate in the effector portion of the RdDM pathway, includingRNA POLYMERASE V (POL V),DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM 2) andSAWADEE HOMEODOMAIN HOMOLOGUE 1 (SHH 1). Like manyAGO proteins,AGO 4 is an endonuclease that can ‘slice’RNA s. We found that a slicing‐defectiveAGO 4 was unable to fully recoverAGO 4‐RNA accumulation fromago4 mutant plants. Collectively, our data suggest thatAGO 4RNA s are secondary siRNA s dependent on the prior activity of the RdDM pathway at certain loci. -
more » « less
Prasinophytes form a paraphyletic assemblage of early diverging green algae, which have the potential to reveal the traits of the last common ancestor of the main two green lineages: (i) chlorophyte algae and (ii) streptophyte algae. Understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary processes that may have occurred in both green lineages. In this study, we sequenced the chloroplast genome of
Pyramimonas parkeae NIES 254 and compared it with that ofP. parkeae CCMP 726, the only other fully sequencedP. parkeae chloroplast genome. The results revealed thatP. parkeae chloroplast genomes are surprisingly variable. The chloroplast genome ofNIES 254 was larger than that ofCCMP 726 by 3,204 bp, theNIES 254 large single copy was 288 bp longer, the small single copy was 5,088 bp longer, and theIR was 1,086 bp shorter than that ofCCMP 726. Similarity values of the two strains were almost zero in four large hot spot regions. Finally, the strains differed in copy number for three protein‐coding genes:ycf20 ,psaC , andndhE . Phylogenetic analyses using 16S and 18SrDNA andrbcL sequences resolved a clade consisting of these twoP. parkeae strains and a clade consisting of these plus otherPyramimonas isolates. These results are consistent with past studies indicating that prasinophyte chloroplast genomes display a higher level of variation than is commonly found among land plants. Consequently, prasinophyte chloroplast genomes may be less useful for inferring the early history of Viridiplantae than has been the case for land plant diversification. -
more » « less
Summary The flowering plant
Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, includingmRNA , the various classes of non‐codingRNA , and smallRNA . TheTAIR 10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue‐specificRNA ‐Seq libraries from 113 datasets and constructed 48 359 transcript models of protein‐coding genes in eleven tissues. In addition, we annotated various classes of non‐codingRNA including microRNA , long intergenicRNA , small nucleolarRNA , natural antisense transcript, small nuclearRNA , and smallRNA using published datasets and in‐house analytic results. Altogether, we identified 635 novel protein‐coding genes, 508 novel transcribed regions, 5178 non‐codingRNA s, and 35 846 smallRNA loci that were formerly unannotated. Analysis of the splicing events andRNA ‐Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species. -
more » « less
Summary From a single transgenic line harboring five
Tnt1 transposon insertions, we generated a near‐saturated insertion population inMedicago truncatula . Using thermal asymmetric interlaced‐polymerase chain reaction followed by sequencing, we recovered 388 888 flanking sequence tags (FST s) from 21 741 insertion lines in this population.FST recovery from 14Tnt1 lines using the whole‐genome sequencing (WGS) and/orTnt1 ‐capture sequencing approaches suggests an average of 80 insertions per line, which is more than the previous estimation of 25 insertions. Analysis of the distribution pattern and preference ofTnt1 insertions showed thatTnt1 is overall randomly distributed throughout theM. truncatula genome. At the chromosomal level,Tnt1 insertions occurred on both arms of all chromosomes, with insertion frequency negatively correlated with theGC content. Based on 174 546 filteredFST s that show exact insertion locations in theM. truncatula genome version 4.0 (Mt4.0), 0.44Tnt1 insertions occurred per kb, and 19 583 genes containedTnt1 with an average of 3.43 insertions per gene. Pathway and gene ontology analyses revealed thatTnt1‐ inserted genes are significantly enriched in processes associated with ‘stress’, ‘transport’, ‘signaling’ and ‘stimulus response’. Surprisingly, gene groups with higher methylation frequency were more frequently targeted for insertion. Analysis of 19 583Tnt1 ‐inserted genes revealed that 59% (1265) of 2144 transcription factors, 63% (765) of 1216 receptor kinases and 56% (343) of 616 nucleotide‐binding site‐leucine‐rich repeat genes harbored at least oneTnt1 insertion, compared with the overall 38% ofTnt1 ‐inserted genes out of 50 894 annotated genes in the genome. -
more » « less
Abstract ARGONAUTES are the central effector proteins of
RNA silencing which bind target transcripts in a smallRNA ‐guided manner.Arabidopsis thaliana has 10ARGONAUTE AGO RNA ‐directedDNA methylation, post‐transcriptional gene silencing, and antiviral defense. To better understand specialization amongAGO AGO 1AGO 10AGO 7DNA ‐bindingTF s revealed binding of theAGO 7SPL family and the miR319‐regulatedTCP family, both of which have roles in developmental timing and leaf morphology. Possible functions forSPL andTCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern ofAGO 7AGO 7AGO 7AGO 7‐triggeredTAS 3
