Identification of novel maize miRNAs by measuring the precision of precursor processing

<p>Abstract</p> <p>Background</p> <p>miRNAs are known to play important regulatory roles throughout plant development. Until recently, nearly all the miRNAs in maize were identified by comparative analysis to miRNAs sequences of other plant species, such as rice and <it>Arabidopsis</it>.</p> <p>Results</p> <p>To find new miRNA in this important crop, small RNAs from mixed tissues were sequenced, resulting in over 15 million unique sequences. Our sequencing effort validated 23 of the 28 known maize miRNA families, including 49 unique miRNAs. Using a newly established criterion, based on the precision of miRNA processing from precursors, we identified 66 novel miRNAs in maize. These miRNAs can be grouped into 58 families, 54 of which have not been identified in any other species. Five new miRNAs were validated by northern blot. Moreover, we found targets for 23 of the 66 new miRNAs. The targets of two of these newly identified miRNAs were confirmed by 5'RACE.</p> <p>Conclusion</p> <p>We have implemented a novel method of identifying miRNA by measuring the precision of miRNA processing from precursors. Using this method, 66 novel miRNAs and 50 potential miRNAs have been identified in maize.</p

Farmers' landslide risk perceptions and willingness for restoration and conservation of world heritage site of Honghe Hani Rice Terraces, China

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Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome

<p>Abstract</p> <p>Background</p> <p>As a newly identified category of DNA transposon, <it>helitrons </it>have been found in a large number of eukaryotes genomes. <it>Helitrons </it>have contributed significantly to the intra-specific genome diversity in maize. Although many characteristics of <it>helitrons </it>in the maize genome have been well documented, the sequence of an intact autonomous <it>helitrons </it>has not been identified in maize. In addition, the process of gene fragment capturing during the transposition of <it>helitrons </it>has not been characterized.</p> <p>Results</p> <p>The whole genome sequences of maize inbred line B73 were analyzed, 1,649 <it>helitron</it>-like transposons including 1,515 helAs and 134 helBs were identified. <it>ZmhelA1</it>, <it>ZmhelB1 </it>and <it>ZmhelB2 </it>all encode an open reading frame (ORF) with intact replication initiator (Rep) motif and a DNA helicase (Hel) domain, which are similar to previously reported autonomous <it>helitrons </it>in other organisms. The putative autonomous <it>ZmhelB1 </it>and <it>ZmhelB2 </it>contain an extra replication factor-a protein1 (RPA1) transposase (RPA-TPase) including three single strand DNA-binding domains (DBD)-A/-B/-C in the ORF. Over ninety percent of maize <it>helitrons </it>identified have captured gene fragments. HelAs and helBs carry 4,645 and 249 gene fragments, which yield 2,507 and 187 different genes respectively. Many <it>helitrons </it>contain mutilple terminal sequences, but only one 3'-terminal sequence had an intact "CTAG" motif. There were no significant differences in the 5'-termini sequence between the veritas terminal sequence and the pseudo sequence. <it>Helitrons </it>not only can capture fragments, but were also shown to lose internal sequences during the course of transposing.</p> <p>Conclusions</p> <p>Three putative autonomous elements were identified, which encoded an intact Rep motif and a DNA helicase domain, suggesting that autonomous <it>helitrons </it>may exist in modern maize. The results indicate that gene fragments captured during the transposition of many <it>helitrons </it>happen in a stepwise way, with multiple gene fragments within one <it>helitron </it>resulting from several sequential transpositions. In addition, we have proposed a potential mechanism regarding how <it>helitrons </it>with multiple termini are generated.</p

Gramene 2013: comparative plant genomics resources

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology

Gramene 2016: comparative plant genomics and pathway resources

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials

Efficient Identification of Causal Mutations through Sequencing of Bulked F-2 from Two Allelic Bloomless Mutants of Sorghum bicolor

Sorghum (Sorghum bicolor Moench, L.) plant accumulates copious layers of epi-cuticular wax (EW) on its aerial surfaces, to a greater extent than most other crops. EW provides a vapor barrier that reduces water loss, and is therefore considered to be a major determinant of sorghum's drought tolerance. However, little is known about the genes responsible for wax accumulation in sorghum. We isolated two allelic mutants, bloomless40-1 (bm40-1) and bm40-2, from a mutant library constructed from ethyl methane sulfonate (EMS) treated seeds of an inbred, BTx623. Both mutants were nearly devoid of the EW layer. Each bm mutant was crossed to the un-mutated BTx623 to generated F-2 populations that segregated for the bm phenotype. Genomic DNA from 20 bm F-2 plants from each population was bulked for whole genome sequencing. A single gene, Sobic.001G228100, encoding a GDSL-like lipase/acylhydrolase, had unique homozygous mutations in each bulked F-2 population. Mutant bm40-1 harbored a missense mutation in the gene, whereas bm40-2 had a splice donor site mutation. Our findings thus provide strong evidence that mutation in this GDSL-like lipase gene causes the bm phenotype, and further demonstrate that this approach of sequencing two independent allelic mutant populations is an efficient method for identifying causal mutations. Combined with allelic mutants, MutMap provides powerful method to identify all causal genes for the large collection of bm mutants in sorghum, which will provide insight into how sorghum plants accumulate such abundant EW on their aerial surface. This knowledge may facilitate the development of tools for engineering drought-tolerant crops with reduced water loss

Crises of Biodiversity and Ecosystem Services in Satoyama Landscape of Japan: A Review on the Role of Management

Satoyama is a Japanese term used to describe the traditional rural landscape in Japan. It has changed continuously from overuse to underuse stages under the development of economy and society, which caused the loss of both biodiversity and ecosystem services. In this paper, we summarized the interactions of biodiversity and ecosystem services affected by human management in Satoyama landscape. The results indicate: (1) the concepts of Satoyama forests and Satoyama landscape varied with researchers and their objectives. The most popular one is a mosaic landscape consisting of Satoyama (secondary) forests, rice paddies, grassland, ponds, irrigating systems, and rural settlements; (2) traditional management regimes on Satoyama landscape were the disturbing mechanisms to provide multiple ecosystem services, as well as a series of semi-natural habitats for species; (3) due to significant progress in economy and technology in Japan, the aging problems of farmers, industrialized agriculture, the import of ecosystem services and goods from international markets, and global climate changes eventually caused the simplification of crop plants, the invasion of alien species, the fragmentation of habitats, and the decreasing of ecosystem services; (4) future research should pay more attention to the complex mechanisms of biodiversity crises and ecosystem services at the landscape scale, considering pattern-process relationships