- transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. - Background: Juncus effusus L. - Results: In this study we carried out functional annotation and polymorphism analysis of de novo assembled RNA- Seq data from 18 genotypes using 249 million paired-end Illumina HiSeq reads and 2.8 million 454 Titanium reads.. - effusus as for the well- studied members of the Poales, Oryza sativa and Sorghum bicolor. - Juncus effusus L. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - 1 Department Environmental Biotechnology, Helmholtz Centre for Environmental Research – UFZ, Permoserstr, 15 Leipzig, Germany Full list of author information is available at the end of the article. - CH 4 oxidation in the rhizosphere [8–10]. - The pith of the stem, Junci Medulla, has been used in Chin- ese and other traditional medicines [22].. - The species is diploid (2n = 42) and has a relatively small genome with a measured DNA 1C-value of 0.3 pg [25]. - The aim of the present study was to develop a molecu- lar database of J. - The transcriptome was de novo assembled and annotated.. - Assembly of the J. - The overall process of transcriptome sequencing, assem- bly, annotation, ortholog clustering and validation of the assembly is summarized in Fig. - sequencing generated clean reads comprising a total of 47 Gb, which was considered as good transcrip- tome coverage of the estimated genome size of around 270 Mb. - The reads were de novo assembled using Trinity [29] and Mira [30, 31]. - Quality analysis of the Trinity as- sembly with the software TransRate computed an opti- mized score of 0.34, which was better than the score for about 50% of 155 sampled de novo assembled transcrip- tomes [29]. - Out of 429 single-copy ortholog genes common to the Eukaryota lineage there were 81, 82, and 78% complete single-copy BUSCOs, 42, 26, and 24% du- plicated BUSCOs and 6% fragmented BUSCOs, and 9.5, 12, and 15% missing BUSCOs respectively for J.. - A total of 42,739 sequences (38.3% of all an- notated contigs) were GO annotated out of the categories Molecular Functions, Cellular Components, and Biological Processes. - ‘binding’ (GO:0005488) and ‘ catalytic activity’ (GO:. - in the Biological Processes ontology group it were ‘cells’ (GO cellular process’ (GO:0009987), and ‘biological regulation’ (GO:0065007). - and ‘cellular parts’. - (GO:0044464) and ‘organelles’ (GO:0043226) in the. - The GO terms of the as- sembled transcriptome were compared with those of S.. - Minor contributions of ‘antioxidant activ- ity’ (GO extracellular region’ (GO:0005576),. - ‘extracellular part’ (GO:0044421), and ‘viral reproduction’. - To evaluate further the qualitative accuracy of the functional annotation, we manually checked the completeness of the fundamental pathways photosynthesis, oxidative phosphorylation, gly- colysis/gluconeogenesis, citrate cycle, pentose phosphate pathway, amino acid metabolism, and information pro- cessing. - All of those pathways were fully covered in the transcriptome.. - carrier activities in the mitochondrial matrix (e.g., GO:. - The three members of the Poaceae had more similarities to each other than to J. - effusus, which matches the topology of the phylogenetic tree based on plastome sequences [28]. - effusus with redundant KO terms likely originating from paralogous genes and orthologues in the various genotypes were combined to a total of 30,932 gene se- quences with matching hits to proteins (E <. - Ten out of the top 20 KO IDs with the highest polymorphism frequencies (ranging from 9 to 49 per KO ID) were associated with plant defense mechanisms and. - Most of the remaining KO IDs with ≥5 polymorphisms (50 IDs in total) were involved in cytoskeleton formation, repair mechanisms associated with replication, transcription and translation, as well as metabolism of the small amino acids Gly, Met, Cys, Ser and Thr.. - In order to experimentally confirm the suitable of the SNP dataset for genotyping of J. - In the past the extensive research on and the manifold biotechnological applications of the common wetland plant J. - 3 Comparisons of the core orthologous gene clusters among J. - The geographical origins of the genotypes cover a substantial portion of the European distribution range of this species. - RNA-Seq has been used for other members of the Poales, and particular of members of the family Poaceae, for various purposes such as de novo sequencing and assembly (rice, [49. - In this study we carried out both single and paired- end sequencing runs to improve the de novo assembly [57]. - The assembly was deemed successful based on a good TransRate score of 0.34 as well BUSCO results that were quite similar to those of the closer relatives S.. - In total, 70% of the contigs (111,567) were anno- tated for functional descriptions, GO terms, and con- served protein domains. - As expected from transcriptome analyses of other members of the Poa- caea the most highly represented GO terms belonged to the Molecular Functions category. - KEGG pathway analyses mirrored these similarities, and COG analysis matched the topology of the phylogenetic tree based on plastome sequences. - SNPs frequency in the transcriptome (1 in 147 bp) was similar to those of other members of the Poales. - effusus, however, the chromosomal distribution of the found SNPs cannot be assessed properly. - Plant tissues (roots and shoots) were harvested from individuals at the vegetative developmental stage that were raised from seeds collected in the field. - The geographical distribution of the sampled locations is presented in Fig. - Total RNA was extracted from roots and shoots separately using the RNeasy Plant Mini Kit according to the manufacturer’s protocol (Qiagen, Hilden, Germany).. - Standard library preparation and sequencing of total RNA using one lane of an Illumina HiSeq (2 × 100 bp PE) and two runs of Roche 454 Titanium was done at the Duke Center for Genomic and Computational Biology (Durham, USA) yielding 249 million Illumina PE reads and 2.8 million 454 reads. - sequencing adaptors, quality-controlled reads were processed using two different de novo transcriptome assemblers. - The software TransRate [65], which enables reference-free quality evaluations of de novo transcriptome assem- blies, was used for analysis of Trinity assembly. - The predicted protein sequences were submitted to the KEGG automatic annotation server (KAAS) (http://www.genome.jp/tools/. - effusus and the mem- bers of the Poaceae S. - Paired end Illumina reads were mapped using sege- mehl version 0.1.9 (Hoffmann et al., 2009) against the de novo transcriptome assembly allowing two mis- matches as well as multiple mappings to redundant sequences in the variable mapping seed. - Juncus effusus is not endangered or a protected species in Europe, and no permissions for collecting seeds in the wild were required. - MA and JAM wrote the first draft of the paper and all authors assisted with the development of the final draft.. - Juncus effusus L.(Juncus communis β effusus E. - Aerenchyma formation in the wetland plant Juncus effusus is independent of ethylene. - Sulphur transformation and deposition in the rhizosphere of Juncus effusus in a laboratory-scale constructed wetland. - Stottmeister U, Wießner A, Kuschk P, Kappelmeyer U, Kästner M, Bederski O, Müller R, et al. - Martínez-Lavanchy P, Chen Z, Lünsmann V, Marin-Cevada V, Vilchez-Vargas R, Pieper D, Reiche N, Kappelmeyer U, et al. - Removal and fate of arsenic in the rhizosphere of Juncus effusus treating artificial wastewater in laboratory-scale constructed wetlands. - The sulfur depot in the rhizosphere of a common wetland plant, Juncus effusus, can support long-term dynamics of inorganic sulfur transformations. - receptor modulators from the Chinese herbal drug Junci medulla – the pith of Juncus effusus. - Identification and characterization of microsatellite loci in the rush Juncus effusus (Juncaceae). - Goff SA, Ricke D, Lan T-H, Presting G, Wang R, Dunn M, Glazebrook J, et al.. - A draft sequence of the rice genome (Oryza sativa L. - Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, et al. - Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, Depamphilis CW, Graham SW, et al. - Assembling the tree of the monocotyledons: plastome sequence phylogeny and evolution of Poales. - Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, et al. - Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, et al. - De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. - Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, et al. - Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, et al. - Rfam 12.0: updates to the RNA families database. - Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, et al. - Elucidation of the molecular responses to waterlogging in Sesbania cannabina roots by transcriptome profiling. - Gore MA, Wright MH, Ersoz ES, Bouffard P, Szekeres ES, Jarvie TP, Hurwitz BL, et al. - Trait expression and signatures of adaptation in response to nitrogen addition in the common wetland plant Juncus effusus.. - Identification and characterization of microsatellite loci in the rush Juncus effusus (Juncaceae) 1. - X-j T, Long Y, Wang J, J-w Z, Y-y W, Li W-m, Y-f P, et al. - De novo transcriptome assembly of common wild rice (Oryza rufipogon Griff.) and discovery of drought-response genes in root tissue based on transcriptomic data. - Chu Z, Chen J, Sun J, Dong Z, Yang X, Wang Y, Xu H, et al. - De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.).. - De Carvalho JF, Poulain J, Da Silva C, Wincker P, Michon-Coudouel S, Dheilly A, Naquin D, et al. - Transcriptome de novo assembly from next- generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae).. - Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, et al. - Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). - Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, et al. - De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. - Transcriptome sequencing and de novo analysis for ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. - Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, Chiari Y, et al. - Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, et al.. - Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simao FA, Pozdnyakov IA, Ioannidis P, et al. - OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. - Kerwin R, Feusier J, Corwin J, Rubin M, Lin C, Muok A, Larson B, et al.. - reference-free quality assessment of de novo transcriptome assemblies.. - Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, et al
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