SEP2/AGL4 is required for the specification of floral organs (Wang et al. Before Plant Biotechnol J 14:284298. A total of 61.28 Gb of raw data were obtained after Illumina sequencing and deposited in the NCBI SRA database under accession In this manuscript, we highlight some de novo transcriptome assemblers that are commonly used for short-read based, reference-free or de novo based approaches and provide commented example scripts that contain mirrored README instructions (https://github.com/Jaiswal-lab/Transcriptome_Assembly_Scripts) for those specified Putative biosynthetic pathway of steroidal. RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. 2.6. CAS 10.1093/bioinformatics/btu170 De novo transcriptome assembly and analysis to identify potential gene targets for RNAi-mediated control of the tomato leafminer (Tuta absoluta). Content of steroidal sapogenins in potato, cassava, Chinese yam, D . To identify which unigenes were significantly associated with either metabolic or signal transduction pathways, we used the DEGs to query the KEGG database and compared the results to the whole-transcriptome data. The site is secure. https://doi.org/10.1007/s13353-021-00621-8. Euphorbiaceae is a family of plants with significant medical and economic relevance, containing ~ 7500 species belonging to 300 genera and 5 different subfamilies (Webster 1994). Trinity comprises three independent software modules, namely Inchworm, Chrysalis and Butterfly. -, Martin JA, Wang Z. Next-generation transcriptome assembly. Our results show that AP1/FUL, AP3/PI, AGL104, and SOC1 genes play an important role during the formation of floral organs in E. agallocha. Numerous metrics were used to assess the assemblies, including: NG50 (point at which 50% of the total genome size is reached when scaffold lengths are summed from the longest to the shortest), LG50 (number of scaffolds that are greater than, or equal to, the N50 length), genome coverage, and substitution error rate. https://doi.org/10.1016/S0378-1119(00)00243-2, Tang Y, Wang J, Bao X et al (2020) Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice. 2022). https://doi.org/10.1105/tpc.112.108688, Meng D, Cao Y, Chen T et al (2019) Evolution and functional divergence of MADS-box genes in Pyrus. 10.3390/molecules200915827 We identified a large number of sex-specific unigenes significantly associated with development and other biological processes. While in our experience, de novo transcriptome assemblies are far more fragmented than the early performance assessments would suggest, there are aspects of Our results showed differential gene expression in 14 MADS-box genes in E. agallocha (Fig. This page was last edited on 30 August 2022, at 17:31. De novo transcriptome assembly analysis suggested that AP1/FUL, AP3/PI, AGL104, and SOC1 plays potential roles in E. agallocha flower sex determination. composita . -, Chalhoub B., Denoeud F., Liu S. Y., Parkin I. 2014). 2020b). Keywords: Reads from second generation technologies (called short read technologies) like Illumina are typically short (with lengths of the order of 50-200 base pairs) and have error rates of around 0.5-2%, with the errors chiefly being substitution errors. This allowed us to identify gene functions and associated pathways (Figure S4 dataset Zhou et al. Annals of Forest Science 79, 36 (2022). -. The .gov means its official. Note: 1 Male leaf. https://doi.org/10.1093/pcp/pcf143, Kater MM, Dreni L, Colombo L (2006) Functional conservation of MADS-box factors controlling floral organ identity in rice and Arabidopsis. Viruses. Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Khnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Prez-Catalua A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Viruses. KEGG classification of the unigenes. We chose the longest transcript in each gene as the candidate unigene, and obtained a set composed by a total of 152,412 unigenes (Figure S1b dataset Zhou et al. 2014), Camellia sinensis (Pan et al. Wiley Interdiscip Rev RNA. However, de novo assembled sequences are uninformative on their own. We identified 17, 38, 61, and 11 MADS-box related DEGs in the Ea_ff vs Ea_mf, Ea_ff vs Ea_fL, Ea_mf vs Ea_mL, and Ea_fL vs Ea_mL groups, respectively (Fig. The GC content of the assembled transcriptome was 40.75 %. No tool delivered the best results for all data sets. government site. Unable to load your collection due to an error, Unable to load your delegates due to an error, Overview of the RNA-Seq data sets used (orange: eukaryote; light orange: simulated human Chr1; green: plant; pink: fungi; yellow: bacterium) and assembly tools evaluated. h Ea73650.c1.g5. Would you like email updates of new search results? Chin, Chen-Shan, David H. Alexander, Patrick Marks, Aaron A. Klammer, James Drake, Cheryl Heiner, Alicia Clum et al. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. statement and Pharmacogn Rev 10(123). All assemblers performed relatively well in this category, with all but three groups having coverage of 90% and higher, and the lowest total coverage being 78.5% (Dept. Fig 1. 7 Female flower bud (big). 2022). GO analysis revealed a large number of genes associated with various transcription factor complexes were enriched in females, membrane was significantly abundant in males, which affecting sex determination of E. agallocha. Plant Cell Online 16:6171. Ansari MA, Bano N, Kumar A, Dubey AK, Asif MH, Sanyal I, Pande V, Pandey V. Funct Integr Genomics. Fitoterapia 2006;77(3):216220. Universidade da Corua. Hempel CA, Wright N, Harvie J, Hleap JS, Adamowicz SJ, Steinke D. Nucleic Acids Res. Recently, several studies have identified and characterized MADS-domain proteins by employing genome-wide expression analyses across woody plant species, including Jatropha curcas (Tang et al. Previous studies on E. agallocha essential focused on the hereditary patterns, medicinal properties and ecological adaption of this plant to new environments (Chen and Ye 2014; Mondal et al. You need either Singularity or Docker to launch the pipeline. Jiang D, Lei J, Cao B, Wu S, Chen G, Chen C. Genes (Basel). The MADS-box proteins regulate floral organogenesis and are essential for flower development and sex determination (De Bodt et al. These include Ea49623.c0. 2021 Sep 10;12(9):1399. doi: 10.3390/genes12091399. https://doi.org/10.1007/s00497-019-00365-w, Hsu H-F (2002) An orchid (Oncidium Gower Ramsey) AP3-like MADS gene regulates floral formation and initiation. There was a problem preparing your codespace, please try again. Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. 35 enzymes, which were encoded by 79 unigenes, were related to the biosynthesis of steroidal sapogenins in this transcriptome database, covering almost all the nodes in the steroidal pathway. Figure 9. b Ea_ff vs Ea_fLgroup. l Ea78865.c1.g2. Bookshelf De novo assembly of the perennial ryegrass transcriptome The number of reads generated for the inbred genotype was 72,132,380 pairs from six different tissues. 5; Table S1 dataset Zhou et al. Clipboard, Search History, and several other advanced features are temporarily unavailable. 2015). We report the transcriptome of E. agallocha. Number of transcripts detected in. Thus We then used these short fragments as templates and synthesized double-stranded cDNA with SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) and random hexamer primers (Illumina). Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P. BMC Bioinformatics. -, Bhandari S. R., Jo J. S., Lee J. G. (2015). Centro de Investigacins Cientficas Avanzadas (CICA). PMW is funded by the Australian Research Council Federation Fellowship FF0776510. For unigenes without GO terms, the total number of bases of transcripts under and over 500 nt was 14,954,024 nt and 54,714,622 nt, respectively. South Afr J Bot 88:204218. De novo transcriptome assembly and annotation. 2021). Unable to load your collection due to an error, Unable to load your delegates due to an error. WebCoffea liberica is wildly cultivated for producing Liberian coffee which ranks only after the Arabica (Coffea arabica) and Robusta (Coffea canephora) Overall: Overall, the Baylor College of Medicine Human Genome Sequencing Center utilizing a variety of assembly methods (SeqPrep, KmerFreq, Quake, BWA, Newbler, ALLPATHS-LG, Atlas-Link, Atlas-GapFill, Phrap, CrossMatch, Velvet, BLAST, and BLASR) performed the best for the bird and fish assemblies. 2019), and is highly expressed in both male and female leaves in E. agallocha. 2022). Chinese kale, a vegetable of the cruciferous family, is a popular crop in southern China and Southeast Asia due to its high glucosinolate content and nutritional qualities. The distribution of MADS-box subfamily genes in E. agallocha is similar to those observed genes in most plants, indicating this gene family is evolutionarily conserved (Tian et al. J Exp Bot 57:34333444. Genome Biol. FOIA These transcriptome assemblies are already providing a valuable resource for studies of genes and gene family evolution in the conifers (Bagal et al. zingiberensis and, Fig 7. Bethesda, MD 20894, Web Policies doi: 10.1186/1471-2105-12-S14-S2. -. it will check the presence of Nextflow in your path, the presence of singularity and will download the BioNextflow library and information about the tools used. Accessibility Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. If nothing happens, download GitHub Desktop and try again. Federal government websites often end in .gov or .mil. HHS Vulnerability Disclosure, Help 2011 Dec 14;12 Suppl 14(Suppl 14):S2. PubMed Central Please Molecules. The integrity and purity of the RNA were measured using the 2100 Bioanalyser (Agilent Technologies, Inc., Santa Clara CA, USA). Because no MADS-box TFs had been previously identified in E. agallocha, we chose 14 EaMADS-box genes belonging to each of the MADS-box subgroups and evaluated the expression patterns of these genes (Fig. Biocontrol Potential of Endophytic Plant-Growth-Promoting Bacteria against Phytopathogenic Viruses: Molecular Interaction with the Host Plant and Comparison with Chitosan. Figure 3. CAS Aust Syst Bot 24: 6186. WebDe novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome Introduction. This work was funded collaboratively by the University of Sydney, the Commonwealth Scientific and Industrial Research Organisation, and The New Zealand Institute for Plant and Food Research. These assemblies scored an N50 of >8,000,000 bases. Bethesda, MD 20894, Web Policies 2016). Different assemblers are designed for different type of read technologies. Induction of potato steroidal glycoalkaloid biosynthetic pathway by overexpression of cDNA encoding primary metabolism HMG-CoA reductase and squalene synthase. 1999). Species distribution of the transcriptome. These algorithms typically do not work well for larger read sets, as they do not easily reach a global optimum in the assembly, and do not perform well on read sets that contain repeat regions. Gene 555:277290. Differences were considered to be significant when P < 0.05. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. Fig 3. 2018). Trinity, SPAdes, and Trans-ABySS, followed by Bridger and SOAPdenovo-Trans, generally outperformed the other tools compared. An official website of the United States government. https://doi.org/10.1007/s00239-002-2426-x, Duke NC (2006) Australias mangroves: the authoritative guide to Australias mangrove plants. https://doi.org/10.1111/pbi.12383, Liu G, Zhang Z, Wang Y, Li X (2021) Highly oxygenated ent-atisane and podocarpane diterpenoids from Excoecaria agallocha. We provide a reference transcriptome dataset for E. agallocha that can be used in future studies. and transmitted securely. Chin, Chen-Shan, Paul Peluso, Fritz J. Sedlazeck, Maria Nattestad, Gregory T. Concepcion, Alicia Clum, Christopher Dunn et al. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. (large) genomes, exomes, transcriptomes, metagenomes, ESTs, Illumina, ABI SOLiD, Roche 454, Ion Torrent, Solexa, Sanger, Protein-level assembler: assembles six-frame-translated sequencing reads into protein sequences, a suite of assemblers including de novo, metagenomic, ontology and taxonomic profiling; uses a De Bruijn graph, Illumina, Solexa, Sanger, 454, Ion Torrent, PacBio, Oxford Nanopore, Illumina and PacBio/Oxford Nanopore data, legacy 454 and Sanger data, transcriptome assemblies by de Bruijn graph, Software compared: ABySS, Phusion2, phrap, Velvet, SOAPdenovo, PRICE, ALLPATHS-LG. It would be very interesting to evaluate whether this gene may be similarly inhibited in E. agallocha, restricting leaf development. School of Life Sciences and Technology, Lingnan Normal University, Zhanjiang, China, Yan Zhou,Lulu Hao,Lexiang Huang,Xiaoming Tang,Danting Zhuo,Li Yun Wang&Ying Zhang, National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, China, You can also search for this author in Corney DC. Figshare repository V5. 2015). Front Genet 11:584817. https://doi.org/10.3389/fgene.2020.584817, Zhang Z-B, Jin Y-J, Wan H-H et al (2021) Genome-wide identification and expression analysis of the MADS-box transcription factor family in Camellia sinensis. Figure 1. Different assemblers are tailored for particular needs, such as the assembly of (small) bacterial genomes, (large) eukaryotic genomes, or transcriptomes. 2022 May;47(10):2623-2633. doi: 10.19540/j.cnki.cjcmm.20220112.102. https://doi.org/10.6084/m9.figshare.20362563.v5, Zhang Y, Chen Y, Zhou Y et al (2020b) Comparative transcriptome reveals the genes adaption to herkogamy of Lumnitzera littorea (Jack) Voigt. https://doi.org/10.1046/j.1365-313X.2002.01343.x, Article https://doi.org/10.5511/plantbiotechnology.18.0621a, Rocheta M, Sobral R et al (2014) Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber. https://doi.org/10.1080/10520290903202478, Schilling S, Kennedy A, Pan S et al (2020) Genome-wide analysis of MIKC -type MADS -box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. This allowed us to validate the identity of the different subfamilies of these genes. The nucleotide and protein sequences and conserved domains of four related genes (HMGR, CAS, SQS, and SMT1) were highly conserved between D. composita and D. zingiberensis; but expression of these four genes is greater in D. composita. The figure shows the relative abundances of RNAi genes identified in this study in terms of TPM (Transcripts Per Million) values calculated from the RSEM software. ", Koren, Sergey, Brian P. Walenz, Konstantin Berlin, Jason R. Miller, Nicholas H. Bergman, and Adam M. Phillippy. Distribution of TPM and EC residuals. 31360173), Basic and Applied Basic Research Fund of Guangdong Province (No. Gene 253:3143. 2022 Jul 9;20:3667-3675. doi: 10.1016/j.csbj.2022.07.007. 2018 May;131(3):555-562. doi: 10.1007/s10265-017-1004-7. If nothing happens, download Xcode and try again. Assessing Transcriptome Assembly Metrics Why transcriptomes? The plant Dioscorea composita has important applications in the medical and energy industries, and can be used for the extraction of steroidal sapogenins (important raw materials for the synthesis of steroidal drugs) and bioethanol production. sourceforge.net/) to perform de novo assembly on the clean data (Ea_ff1, Ea_ff2, Ea_ff3, Ea_fL1, Ea_fL2, Ea_fL3, Ea_mf1, Ea_mf2, Ea_mf3, Ea_mL1, Ea_mL2, and Ea_mL3) (Grabherr et al. 7095% of complete BUSCOs were present in the Comput Biol Chem 90:107424. https://doi.org/10.1016/j.compbiolchem.2020.107424, Xie C, Mao X, Huang J et al (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. 3 Male flower bud (big), 4 Male flower. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Identification, characterization and expression analysis of genes involved in steroidal saponin biosynthesis in Dracaena cambodiana. 2022). Federal government websites often end in .gov or .mil. 2014 Mar 10;9(3):e91776. Wu Q, Wang J, Mao S, Xu H, Wu Q, Liang M, Yuan Y, Liu M, Huang K. BMC Genomics. a Ea49623.c0.g1. . We identified a total of 73 MADS-box genes in the E. agallocha genome, which we grouped into five distinct classes (MIKCc, M, M, M, MIKC*) after phylogenetic comparisons with J. curcas homologs. Expression of four transcripts related, Fig 7. Prez-Labrada K, Brouard I, Morera C, Estvez F, Bermejo J, Rivera DG. J Mol Evol 56:573586. A total of 14 candidate genes were chosen for qRT-PCR analysis, which showed they have distinct expression profiles in different organs. m Ea79919.c2.g1. 2015; Zhang et al. Differential expression analysis for sequence count data. Moreover, a reduction in the number of subfamilies, including M, M, and MIKC*, indicates some of these families may gradually disappear during evolution. The basic idea with de novo transcriptome assembly is you feed in your reads and you get out a bunch of contigs that represent transcripts, or stretches of RNA present in the reads that dont have any BMC Genomics. Li Y, Tan C, Li Z, Guo J, Li S, Chen X, Wang C, Dai X, Yang H, Song W, Hou L, Xu J, Tong Z, Xu A, Yuan X, Wang W, Yang Q, Chen L, Sun Z, Wang K, Pan B, Chen J, Bao Y, Liu F, Qi X, Gang DR, Wen J, Li J. Hortic Res. Accessibility https://doi.org/10.1186/s13595-022-01156-6, DOI: https://doi.org/10.1186/s13595-022-01156-6. Each team was given four months to assemble their genome from Next-Generation Sequence (NGS) data, including Illumina and Roche 454 sequence data. 4a); starch and sucrose metabolism (ko00500), photosynthesis (ko00195) and phenylpropanoid biosynthesis (ko00940) in females (Ea_ff vs Ea_fL group) (Fig. 1995) that are also involved in flower organogenesis. Differential expression analysis was implemented using EdgeR (Robinson et al. In addition, several EaMADS genes were significantly upregulated in flowers compared to leaves. Preparative isolation and purification of five steroid saponins from Dioscorea zingiberensis C.H.Wright by counter-current chromatography coupled with evaporative light scattering detector. d Ea_fL vs Ea_mL group. PLoS One 12:e0181443. During the assembly of the De Bruijn graph, reads are broken into smaller fragments of a specified size, k. The k-mers are then used as nodes in the graph assembly. Boxplots of the residuals (see methods) of, Figure 4. https://doi.org/10.1111/nph.16122, Seesangboon A, Gruneck L, Pokawattana T et al (2018) Transcriptome analysis of Jatropha curcas L. flower buds responded to the paclobutrazol treatment. De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing. The main GO terms found in each of three categories cellular process (GO: 0009987) and metabolic process (GO: 0008152); cell (GO: 0005623) and cell part (GO: 0044464); and binding (GO: 0005488) and catalytic activity (GO: 0003824), respectively. Biotech Histochem:19. The length of transcripts in the final assembly ranged from 201 to 23,274 bp with an average length of 687 bp. Goodin MM, Zaitlin D, Naidu RA, Lommel SA (2008) Nicotiana benthamiana: Its History and Future as a Model for PlantPathogen Interactions. Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing. This study was funded by the National Natural Science Foundation of China (No. 2019). Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. We performed end-repair on the synthesized cDNA, followed by phosphorylation and the addition of A bases as per Illuminas library construction protocol. Proteotranscriptomics - A facilitator in omics research. 9 Fruit. The expression levels of all unigenes were analyzed in various tissues of Chinese kale. 5). https://doi.org/10.1093/bioinformatics/bti610, De Bodt S, Raes J, Florquin K et al (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. n Ea81288.c3.g1. Genomic DNA was removed using DNase I (TaKara Bio, Inc., USA). Mol Biol Evol 32:268274. Number of transcripts detected in the 9 tissues. Neighbour joining tree of AGO proteins. The former can be further grouped into M, M, and M subgroups based on the respective sequence similarities between their MADS-box regions (Pan et al. RNAi-associated pathways and their core components in plants. Gene 569:6676. https://doi.org/10.1111/j.1365-313X.2010.04148.x, Article -. The .gov means its official. De novo RNA-Seq assembly facilitates the study of transcriptomes for species without sequenced genomes, but it is challenging to select the most accurate assembly in this context. The above results highlight the highest homology obtained in our study. An ancestral MADS-box gene duplication event separates two main lineages, type I and type II (Svensson et al. While both of these methods made progress towards better assemblies, the De Bruijn graph method has become the most popular in the age of next-generation sequencing. https://doi.org/10.1371/journal.pone.0093337, Conesa A, Gotz S, Garcia-Gomez JM et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Hence, the several aspects behind the molecular evolution of this dioecious mangrove species remain unknown. The https:// ensures that you are connecting to the These observations demonstrate these samples were characterized by active cell development and differentiation. government site. Specifically, the genes FLOWERING LOCUS C (FLC), SUPRESSOR OF OVEREXPRESSION OF CONSTANTS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP) integrating signals from different flowering time regulatory pathways to regulate flowering transition (Yuan et al. Greedy algorithm assemblers are assemblers that find local optima in alignments of smaller reads. KEGG pathway analysis showed much of the identified DEGs are involved in starch and sucrose metabolism in the floral and leaf tissues of E. agallocha. 2022). Excoecaria agallocha is a dioecious species containing both male and female individuals producing unisexual flowers. 10.1016/j.jpba.2013.02.005 All Q30 values were higher than 90.45%, while the GC content in each sample was exceeded 42%. In addition, phytohormones play an essential role in sex determination, and the constitutive expression of MADS-box genes leads to precocious flower differentiation in A. thaliana (Tanurdzic 2004; Amasino 2010). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. HHS Vulnerability Disclosure, Help composita . 15:410. Key: atoB: acetyl-CoA C-acetyltransferase, HMGS: hydroxymethylglutaryl-CoA synthase, HMGR: 3-hydroxy-3-methylglutaryl-CoA reductase, MK: mevalonate kinase, PMK: phosephomevalonate kinase, MVD: diphosphomevalonate decarboxylase, DXS: 1-deoxy-D-xylulose-5-phosphate synthase, DXR: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, CMC: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, CMK: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, MCS: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, HMED: 4-Hydroxy-3-methy-2-butenyl-diphosphate synthase, HDR: 1-Hydroxy-2-methy-2-butenyl-4-diphosphate reductase, IDI: isopentenyl diphosphate isomerase, GPPS: geranyl diphosphate synthase, FPPS: farnesyl diphosphate synthase, FNTA: protein farnesyltransferase, FACE2: prenyl protein peptidase, STE24: endopeptidase, FOLK: farnesol kinase, FLDH: farnesol dehydrogenase, PCME: prenylcysteine alpha-carboxyl methylesterase, ICMT: protein-S-isoprenylcysteine O-methyltransferase, PCYOX1: prenylcysteine oxidase, SQS: squalene synthase, SQLE: squalene monooxygenase, CAS: cycloartenol synthase. https://doi.org/10.4103/0973-7847.194049, Moser M, Asquini E, Miolli GV et al (2020) The MADS-box gene MdDAM1 controls growth cessation and bud dormancy in apple. Ann Bot 113:653668. Bioinformatics 21:36743676. PubMed Jiang D, Li G, Chen G, Lei J, Cao B, Chen C. Genes (Basel). Studies focusing on overexpression assays and mutant plants suggest MADS-box genes are essential for the specification in floral organs (Krizek and Fletcher 2005; Kater et al. ", "SEQAID: a DNA sequence assembling program based on a mathematical model", "How to apply de Bruijn graphs to genome assembly", "DIMACS Workshop on Combinatorial Methods for DNA Mapping and Sequencing", "ABySS: a parallel assembler for short read sequence data", "De novo transcriptome assembly with ABySS", "Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly", "Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold", "Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies", "SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing", "Velvet: Algorithms for de novo short read assembly using de Bruijn graphs", "Full-length transcriptome assembly from RNA-Seq data without a reference genome", "Assemblathon 1: A competitive assessment of de novo short read assembly methods", "Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species", https://en.wikipedia.org/w/index.php?title=De_novo_sequence_assemblers&oldid=1107563454, Creative Commons Attribution-ShareAlike License 3.0, parallel, paired-end sequence assembler designed for large genome assembly of short reads (genomic and transcriptomic), employ a Bloom filter to De Bruijn graph, paired-end PCR-free reads (successor of ALLPATHS-LG). 2020a; Won et al. j Ea75556.c1.g1. Agrobacterium Protocols: Humana Press. 2019 Mar 8;10(3):202. doi: 10.3390/genes10030202. Fig 4. 1). -, Davidson N. M., Oshlack A. Genome-Wide Identification and Expression Profiling of 2OGD Superfamily Genes from Three, NCI CPTC Antibody Characterization Program, Anders S., Huber W. (2010). The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. 2022 Sep 19;2022:4955209. doi: 10.1155/2022/4955209. Nat Rev Genet. Only high-quality RNA samples (OD260/280 = 1.8 ~ 2.2, OD260/230 2.0, RIN 8.0, 28S:18S 1.0, > 1 g) were used to construct the sequencing library. String graph and De Bruijn graph method assemblers were introduced at a DIMACS[5] workshop in 1994 by Waterman[6] and Gene Myers. See this image and copyright information in PMC. For all assemblies, SGA, BCM, Meraculous, and Ray submitted competitive assemblies and evaluations. Plant J 31:161169. of Comp. 6 Female flower bud (small). California Privacy Statement, Huang YP, Chen IH, Kao YS, Hsu YH, Tsai CH. ZL2032). We identified specific DEGs in female and male E. agallocha plants based on the sexuality-specific unigenes present in leaf and flower samples (p value < 0.05 and |log2(fold change)| > 5). 2022 Sep 9;50(16):9279-9293. doi: 10.1093/nar/gkac689. In particular, for non-model organisms and in the absence of an appropriate reference genome, RNA-Seq is used to reconstruct the transcriptome de novo. Regulation of Growth and Main Health-Promoting Compounds of Chinese Kale Baby-Leaf by UV-A and FR Light. The remaining 50 MADS-box proteins belonged to the MIKCc subgroup (Fig. The E-value distribution of the top-scoring BLASTX hits against the NR database showed that 25.5% of the mapped sequences exhibited high homology (< 1e45). An official website of the United States government. PubMed Central Zhu JH, Li HL, Guo D, Wang Y, Dai HF, Mei WL, Peng SQ. Furthermore, the NR BLASTX matches showed that the top two species were J. curcas (26.90%) and R. communis (21.60%) (Figure S4d dataset Zhou et al. However, there is no expression of these key enzymes in potato and no steroidal sapogenins are synthesized. eCollection 2022. Proportion of unigenes with and. GO functional enrichment map of differentially gene expression between female and male of E.agallocha in different comparison groups. De novo transcriptome assembly is often the preferred method to studying non-model organisms, since it is cheaper and easier than building a genome, and reference-based methods are not possible without an existing genome. eCollection 2016. 2019 May 14;20(1):377. doi: 10.1186/s12864-019-5758-2. Nat Rev Genet 6:688698. Cite this article. https://doi.org/10.1080/14786419.2021.1900177, Ma J, Yang Y, Luo W et al (2017) Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.). 2005) program was used to obtain GO annotations of uniquely assembled transcripts to describe the associated biological processes, molecular functions and cellular components. Figure 2. 2022). The basic idea with de novo transcriptome assembly is you feed in your reads and you get out a bunch of contigs that represent transcripts, or stretches of doi: 10.1093/hr/uhac165. "HINGE: long-read assembly achieves optimal repeat resolution. Assemblathon 2[22] improved on Assemblathon 1 by incorporating the genomes of multiples vertebrates (a bird (Melopsittacus undulatus), a fish (Maylandia zebra), and a snake (Boa constrictor constrictor)) with genomes estimated to be 1.2, 1.0, and 1.6Gbp in length) and assessment by over 100 metrics. The figure shows the relative abundances of RNAi, MeSH We isolated total RNA from male leaf (mL), male flower (mf), female leaf (fL), and female flower (ff) to build the transcriptome of E. agallocha. https://doi.org/10.1104/pp.109.135806, Article https://doi.org/10.1016/j.sajb.2013.07.021, Article https://doi.org/10.1016/j.gene.2015.05.018, Won SY, Jung J-A, Kim JS (2021) Genome-wide analysis of the MADS-box gene family in chrysanthemum. sharing sensitive information, make sure youre on a federal As reported in the Norway spruce, B-type MADS-box genes are active in male organ primordia (Sundstrom and Engstrom 2002). Please enable it to take advantage of the complete set of features! 2020), Populus trichocarpa (Leseberg et al. 10.1186/gb-2010-11-10-r106 doi: 10.1371/journal.pone.0153104. Graph method assemblers[4] come in two varieties: string and De Bruijn. We found a higher number of DEGs involved in the ribosome and plant hormone signal transduction pathway affecting male flowers. https://doi.org/10.1093/bioinformatics/btp616, Rounsley SD, Ditta GS, Yanofsky MF (1995) Diverse roles for MADS box genes in Arabidopsis development. Figure 8. RNAi-associated pathways and their core. Metabolic pathway analysis was performed using KEGG (http://www.genome.jp/kegg/) (Ogata et al. Nodes that overlap by some amount (generally, k-1) are then connect by an edge. 4b); starch and sucrose metabolism (ko00500) , plant hormone signal transduction (ko04075) and phenylpropanoid biosynthesis (ko00940) in males (Ea_mf vs Ea_mL group) (Fig. 2015; Schilling et al. Front Plant Sci. Springer Nature. 2020). Ka/Ks) 3 Whole-genome HHS Vulnerability Disclosure, Help To further characterize the biological functions and interaction between unigenes, these groups were then classified into different metabolic pathways with KEGG (Table S5 dataset Zhou et al. 2022; Table 1). Trends Plant Sci 7:2231. The figure shows the percentage of unigenes larger (green) and smaller (yellow) than 500 nt that could be annotated with (right) or without (left) GO terms. Trinotate was used to carry out functional annotation of Also, expression in the shoots was low. 2011). Taken together, these results suggest the transcriptome data agreed with the observed expression patterns of most E. agallocha genes. Note: The actin gene as the internal control for gene expression analysis. We extracted total RNA from leaf and flower tissues using the TRIzol Reagent (Plant RNA Purification Reagent) following manufacturers instructions (Invitrogen, Carlsbad, CA, USA). 2022). Privacy Bookshelf The N50 value of 1011 bp and L50 sequence ", Kamath, Govinda M., Ilan Shomorony, Fei Xia, Thomas A. Courtade, and N. Tse David. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers. KEGG classification of the unigenes from RNA-Seq experiments on D . To identify the MADS-box from E. agallocha transcriptomes, we searched all significant MADS-box-related genes against a database composed of plant TFs (PlantTFDB 4.0; http://planttfdb.gao-lab.org/). https://doi.org/10.1016/j.gene.2006.05.022, Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. After quantification by TBS380, we sequenced 12 RNAseq libraries on an Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA) using one lane and 2 150 bp paired-end reads. k Ea78824.c3.g2. Competing Interests: The authors have declared that no competing interests exist. 2018 Feb 18;23(2):454. doi: 10.3390/molecules23020454. Finally, we found 3 genes with M, 1 with M,1 with M, 6 with the MIKCc subgroup in leaves (Ea_fL vs Ea_mL group). https://doi.org/10.1093/jxb/erl097, Krizek BA, Fletcher JC (2005) Molecular mechanisms of flower development: an armchair guide. Nucleic Acids Res 39:316322. GO and KEGG enrichment analyzes were performed on DEGs to identify relevant pathways and functions using Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do), respectively (Xie et al. The plant materials were immersed in liquid nitrogen and stored at 80 C before downstream analyses were performed. In apples, SUPRESSOR OF CONSTANS 1 (SOC1) regulates the induction of the flower bud (Xing et al. Zhang X, Ito Y, Liang J, Su Q, Zhang Y, Liu J, et al. A further 9396 DEGs existed between female and male leaves, of which 4846 were upregulated and 4550 were downregulated in the Ea_fL vs Ea_mL group. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. We propose AP1/FUL, AP3/PI, AGL104, and SOC1 should be considered candidate regulators of sex determination in E. agallocha. Plant Cell 7:12591269. For the right panel, only EC values greater than 0 were used. -, Palazn J, Moyano E, Bonfill M, Osuna LT, Cusid RM, Piol MT. See this image and copyright information in PMC. Google Scholar, Bai G, Yang DH, Cao PJ et al (2019) Genome-wide identification, gene structure and expression analysis of the MADS-box gene family indicate their function in the development of tobacco (Nicotiana tabacum L.). Background: eCollection 2014. Overview of the RNA-Seq data sets used (orange: eukaryote; light orange: simulated human, Heat map showing for each data set (column) and each assembler (row) the, Selected BUSCO (benchmarked universal single-copy, Selected BUSCO (benchmarked universal single-copy orthologs) [43,42] assessment results for E. coli (A), MeSH 2019), while others are seemingly involved in regulatory networks that control flowering time and initiation. In fact, both J. curcas and E. agallocha belong to Euphorbiaceae (Satyan et al. J Plant Res. Front Plant Sci 5. https://doi.org/10.3389/fpls.2014.00599, Robinson MD, McCarthy DJ, Smyth GK (2010) EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. 2021). Here, we present a large-scale comparative study in which 10 de novo assembly tools are applied to 9 RNA-Seq data sets spanning different kingdoms of life. Sequences from N. benthamiana (Nbenth), A. thaliana, The figure shows the domains of the RNAi proteins, Figure 8. (2014). sharing sensitive information, make sure youre on a federal 2016;17(1):13. Sci Rep 9:1266. https://doi.org/10.1038/s41598-018-37897-6, Mondal S, Ghosh D, Ramakrishna K (2016) A complete profile on blind-your-eye mangrove Excoecaria agallocha L. (Euphorbiaceae): Ethnobotany, phytochemistry, and pharmacological aspects. WebCentro de Investigacins Cientficas Avanzadas (CICA). 2022 Jul 12;14(7):1522. doi: 10.3390/v14071522. i Ea73657.c0.g3. 2020), Quercus suber (Rocheta et al. Unable to load your collection due to an error, Unable to load your delegates due to an error, A BLASTx using a cutoff value of E-value <1e. 2022 Jul 25;9:uhac165. Journal of Pharmaceutical and Biomedical Analysis 2013;84:117123. sh INSTALL.sh it will check the presence of Nextflow While some assemblers excelled in one category, they did not in others, suggesting that there is still much room for improvement in assembler software quality. 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