Browsing by Author "Arikit, Siwaret"
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Item Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce(Nature Publishing Group, 2017-04-12) Reyes-Chin-Wo, Sebastian; Wang, Zhiwen; Yang, Xinhua; Kozik, Alexander; Arikit, Siwaret; Song, Chi; Xia, Liangfeng; Froenicke, Lutz; Lavelle, Dean O.; Truco, Marı´a-Jose´; Xia, Rui; Zhu, Shilin; Xu, Chunyan; Xu, Huaqin; Xu, Xun; Cox, Kyle; Korf, Ian; Meyers, Blake C.; Michelmore, Richard W.; Sebastian Reyes-Chin-Wo, Zhiwen Wang, Xinhua Yang, Alexander Kozik, Siwaret Arikit, Chi Song, Liangfeng Xia, Lutz Froenicke, Dean O. Lavelle, Marı´a-Jose´ Truco, Rui Xia, Shilin Zhu, Chunyan Xu, Huaqin Xu, Xun Xu, Kyle Cox, Ian Korf, Blake C. Meyers & Richard W. Michelmore; Arikit, Siwaret; Meyers, Blake CLettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.Item High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs(BioMed Central, 2016-01-28) Khatabi, Behnam; Arikit, Siwaret; Xia, Rui; Winter, Stephan; Oumar, Doungous; Mongomake, Kone; Meyers, Blake C.; Fondong, Vincent N.; Behnam Khatabi, Siwaret Arikit, Rui Xia, Stephan Winter, Doungous Oumar, Kone Mongomake, Blake C. Meyers and Vincent N. Fondong; Arikit, Siwaret; Xia, Rui; Meyers, Blake C.BACKGROUND: Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans. RESULTS: Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of secondary phased siRNAs (phasiRNAs) from 80 PHAS loci. CONCLUSIONS: Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for cassava improvement research.Item A new approach for annotation of transposable elements using small RNA mapping(Oxford University Press, 2015-03-15) El Baidouri, Moaine; Do Kim, Kyung; Abernathy, Brian; Arikit, Siwaret; Maumus, Florian; Panaud, Olivier; Meyers, Blake C.; Jackson, Scott A.; Moaine El Baidouri, Kyung Do Kim, Brian Abernathy, Siwaret Arikit, Florian Maumus, Olivier Panaud, Blake C. Meyers and Scott A. Jackson; Arikit, Siwaret; Meyers, Blake C. (orcid.org/0000-0003-3436-6097)Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants.