We found a higher number of DEGs involved in the ribosome and plant hormone signal transduction pathway affecting male flowers. Different assemblers are tailored for particular needs, such as the assembly of (small) bacterial genomes, (large) eukaryotic genomes, or transcriptomes. Disclaimer, National Library of Medicine HHS Vulnerability Disclosure, Help Differentially expression gene (DEGs) analysis in E. agallocha. Only transcripts with EC (Expected Counts) values of more than zero were used. Bookshelf The former genes can be further subdivided into three distinct groups, specifically M, M, M, according to the genetic sequence of MADS domain and the presence of other motifs (Zhang et al. 2018). Chinese kale; RNA-seq; de novo assembly; gene expression; glucosinolate metabolic pathways; multiple tissues; transcriptome. doi: 10.1093/bib/bbab563. 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. 2022; Table 1). a Ea_ff vs Ea_mf group. EaMADS-box classification was based on a previous study (Tang et al. FOIA 2021). Zhu JH, Li HL, Guo D, Wang Y, Dai HF, Mei WL, Peng SQ. Relative abundances of RNAi-associated genes. 2018; Bar-Lev et al. De novo transcriptome assembly, functional annotation, and expression profiling of rye ( Secale cereale L.) hybrids inoculated with ergot ( Claviceps purpurea) Khalid The results of real-time PCR experiments on ten related transcripts (HMGR, MK, SQLE, FPPS, DXS, CAS, HMED, CYP51, DHCR7, and DHCR24) indicated that sapogenins were mainly biosynthesized by the mevalonate pathway. In apples, SUPRESSOR OF CONSTANS 1 (SOC1) regulates the induction of the flower bud (Xing et al. The clean data of each sample was mapped to the assembled reference transcriptome using Jatropha curcas L. (Seesangboon et al. 5). Careers. https://doi.org/10.1016/j.gene.2014.11.018, Tomlinson PB (2016) The botany of mangroves, second edition. AGL104 (Ea52637.c2.g2) was upregulated in the female flowers compared to male flowers. Clipboard, Search History, and several other advanced features are temporarily unavailable. Journal of Pharmaceutical and Biomedical Analysis 2013;84:117123. Would you like email updates of new search results? Viruses. This module allows to annotate predicted proteins and transcripts from one of the two assembly modules described before. https://doi.org/10.1016/j.sajb.2013.07.021, Article Before 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. 2014 Mar 10;9(3):e91776. Chin, Chen-Shan, David H. Alexander, Patrick Marks, Aaron A. Klammer, James Drake, Cheryl Heiner, Alicia Clum et al. Molecular Characterization of MYB28 Involved in Aliphatic Glucosinolate Biosynthesis in Chinese Kale (, Improvement of glucosinolates by metabolic engineering in. Fig 4. Expression patterns for ten transcripts related to steroidal sapogenin in D . FOIA 5; Table S1 dataset Zhou et al. Fig 3. The genes were selected at random based on the changes in expression and function identified in this study (Table S1 dataset Zhou et al. eCollection 2022. The goal of this Assembalthon was to most accurately and completely assemble a genome that consisted of two haplotypes (each with three chromosomes of 76.3, 18.5, and 17.7 Mb, respectively) that was generated using Evolver. https://doi.org/10.1105/tpc.7.8.1259, Satyan R, Aveek N, Eganathan P, Parida A (2009) Comparative histochemical localization of secondary metabolites in seed-raised and in vitro propagated plants of Excoecaria agallocha Linn. The de novo assembly algorithm is a generic tool in the QIAGEN CLC Genomics Workbench and is equally applicable to transcript and genome assemblies. Genome Biol. The latter play an essential role in the formation of the female gametophyte and the early development of seeds (Masiero et al. eCollection 2017. The work was supported by "Twelfth Five-Year" National Science and Technology Support Project of China (2015BAD15B03), the DongGuan Innovative Research Team Program (2014607101005), the Key Science & Technology Project of Guangdong Province of China (2011B090400437), and the "Twelfth Five-Year" National Science and Technology Support Project of China (2011BAD22B01). government site. 2022). In MIKCc group, we found class A, B, C, D, and E genes in E. agallocha. (2014). 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. J Plant Res. 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. composita, Fig 6. 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. Li R, Zhou Y, Wu Z, Ding L. ESI-QqTOF-MS/MS and APCI-IT-MS/MS analysis of steroid saponins from the rhizomes ofDioscorea panthaica. In Arabidopsis, AGL104 is involved in pollen maturation and tube growth (Adamczyk and Fernandez 2009). At the same time, we compared the results of MADS-box protein domains in E. agallocha and J. curcas and performed phylogenetic analysis. 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. "Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. 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. Insertion in the RDR1 sequence. 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). The MS for 1 assembly tool and a single data set is based on 20 pre-selected metrics (see Table4 and Methods for details) and is shown in 1 cell in the heat map (e.g., the MS for. Figshare repository V5. Flower development influences reproduction and breeding in E.agallocha, which contributes to ecological restoration in the intertidal zone. Comparison of glucosinolate profiles in different tissues of nine Brassica crops. Species distribution of the transcriptome assembly. J Exp Bot 66:62336244. Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis. Our phylogenetic analysis identified several orthologous genes between E. agallocha and J.curcas in almost all MADS-box protein clades (Fig. The plant materials were immersed in liquid nitrogen and stored at 80 C before downstream analyses were performed. 2022). The proteins belonging to type II plants are named MIKC and, depending on the sequence divergence at domain I, can be divided into two different subgroups, MIKCc and MIKC*(Lin et al. We analyzed expression profiles and suggested AP1/FUL, AP3/PI, AGL104, and SOC1 as candidate regulators of sex determination. Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments. PubMed Fig 1. 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. Before 2003; Pan et al. Putative biosynthetic pathway of steroidal sapogenin in D . Presence of core genes: Most assemblies performed well in this category (~80% or higher), with only one dropping to just over 50% in their bird genome assembly (Wayne State University via HyDA). De novo transcriptome assembly and analysis to identify potential gene targets for RNAi-mediated control of the tomato leafminer (Tuta absoluta). We extracted total RNA from leaf and flower tissues using the TRIzol Reagent (Plant RNA Purification Reagent) following manufacturers instructions (Invitrogen, Carlsbad, CA, USA). https://doi.org/10.1186/s13595-022-01156-6, DOI: https://doi.org/10.1186/s13595-022-01156-6. This might indicate that there may be a complex regulatory mechanism for flowering in E. agallocha. c Ea_mf vs Ea_mL group. CAS Springer Nature. Shahzad GI, Passera A, Maldera G, Casati P, Marcello I, Bianco PA. Int J Mol Sci. Methodology/results: Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers. Genomics Data 2017, 11, 8991. 2011). Front Plant Sci. 2021 Jul 5;13(7):1304. doi: 10.3390/v13071304. .. A survey of best practices for RNA-seq data analysis. In addition, the B-class genes AP3/PI (Ea49623.c0.g1 and Ea60496.c2.g1) were also upregulated in the male flower and may influence male organ development. Using Illumina deep sequencing, 62,341 unigenes were obtained by assembling its transcriptome, and 27,720 unigenes were annotated. 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. -, Palazn J, Moyano E, Bonfill M, Osuna LT, Cusid RM, Piol MT. De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissues Front Plant Sci. (2014). The figure shows the relative abundances of RNAi, MeSH WebCentro de Investigacins Cientficas Avanzadas (CICA). Keywords: 2020b). The schematic depicts the major proteins involved in producing different small RNAs (blue boxes) from RNA transcripts of various templates (orange boxes) and using these sRNAs to regulate a spectrum of important biological processes (green boxes). We further annotated 71,565 (28.85%) unigenes using 55 Gene Ontology (GO) terms. No tool delivered the best results for all data sets. Figure 2. Chin, Chen-Shan, Paul Peluso, Fritz J. Sedlazeck, Maria Nattestad, Gregory T. Concepcion, Alicia Clum, Christopher Dunn et al. Background: sharing sensitive information, make sure youre on a federal 10.1126/science.1253435 KEGG classification of the unigenes. 2017;8(1):e1364. 1999). Urso I, Biscontin A, Corso D, Bertolucci C, Romualdi C, De Pitt C, Meyer B, Sales G. Sci Rep. 2022 Jul 6;12(1):11415. doi: 10.1038/s41598-022-15320-5. Expression patterns for ten transcripts, Fig 5. 2021). Importantly, Ea69574.c0.g1, Ea73657.c0.g3, and Ea75556.c1.g1 were also highly expressed in the female leaves, Ea52637.c2.g1, Ea58933.c1.g2, and Ea73650.c1.g5 in fruits, Ea78824.c3.g2 in male flowers, and Ea66029.c1.g4 in male leaves. eCollection 2019 Jun. The answer is de novo assembly. This plant can be found in mangrove regions and occasionally inland. We annotated 73 transcripts in the E. agallocha transcriptome that aligned to the MADS-box family and/or contained the MADS domain. C and D-class genes were significantly upregulated in male and female flowers in E. agallocha. It would be very interesting to evaluate whether this gene may be similarly inhibited in E. agallocha, restricting leaf development. Alejandra In Arabidopsis, these functional classes include genes such as APETALA1 (AP1) in class A, PISTILATA (PI) and APETALA3 (AP3) in class B, AGAMOUS (AG) in class C (Hsu 2002), SEEDSTICK/ AGAMOUS-LIKE 1 (STK/AGL11) and SHATTERPROOF (SHP) in class D (Mendes et al. The authors declare that they have no competing interests. [dataset]. The https:// ensures that you are connecting to the a Ea_ff vs Ea_mf group. Bethesda, MD 20894, Web Policies The integrity and purity of the RNA were measured using the 2100 Bioanalyser (Agilent Technologies, Inc., Santa Clara CA, USA). We performed the phylogenetic analysis on MADS-box protein sequences from J. curcas. The assemblies are then compared and evaluated using numerous metrics. 2012 Nov 21;13:648. doi: 10.1186/1471-2164-13-648. De novo transcriptome assembly of shrimp Palaemon serratus. The estimated error rate of the RNA-seq was ~ 0.02%. 2012 Dec;25(12):1523-30. doi: 10.1094/MPMI-06-12-0148-TA. Ansari MA, Bano N, Kumar A, Dubey AK, Asif MH, Sanyal I, Pande V, Pandey V. Funct Integr Genomics. 2011). Specifically, we identified a total of 9, 7, 4, and 3 genes with M, M, M, and M MIKC*-type genes. sharing sensitive information, make sure youre on a federal Disclaimer, National Library of Medicine The MADS-box proteins regulate floral organogenesis and are essential for flower development and sex determination (De Bodt et al. Bioinformatics 26:139140. J Mol Evol 56:573586. Despite its importance in herbal medicine, no ready-to-use transcript sequence information of this plant is made available in the public data base, this study mainly deals with the sequencing of RNA from A. paniculata leaf using Illumina HiSeqTM 2000 platform followed by the de novo transcriptome assembly. 2022). 2020), Populus trichocarpa (Leseberg et al. The data provides important information for understanding the evolutionary history of mangrove. CAS https://doi.org/10.1093/nar/27.1.29, Pan J, Chang P, Ye X et al (2018) Transcriptome-wide analysis of MADS-box family genes involved in aluminum and fluoride assimilation in Camellia sinensis. Careers. BMC Genomics. 6 (2013): 563-569. GO functional enrichment map of differentially gene expression between female and male of E.agallocha in different comparison groups. 2016). Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. k Ea78824.c3.g2. Huang HH, Xu LL, Tong ZK, Lin EP, Liu QP, Cheng LJ, Zhu MY. In this study, we sequenced and characterized the transcriptomes and expression profiles of genes expressed in 11 tissues of Chinese kale. 2022 May;47(10):2623-2633. doi: 10.19540/j.cnki.cjcmm.20220112.102. 2015). 2021 Sep 10;12(9):1399. doi: 10.3390/genes12091399. Tetrahedron 2011;67(40):77137727. 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. The average fragment size sequenced was less than 200 bp. Plant material used for qRT-PCR analysis. 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. A total of 71571 transcripts were identified from the de novo assembled transcriptome by rnaSPAdes3 analysis. Mater Methods. Similar to other plants, E. agallocha also contains a higher number of M and MIKCc than M or MIKC* genes (Fig. 2022). PubMed b Ea_ff vs Ea_fLgroup. https://doi.org/10.1038/nbt.1883, Grimplet J, Martnez-Zapater JM, Carmona MJ (2016) Structural and functional annotation of the MADS-box transcription factor family in grapevine. Pharmacogn Rev 10(123). As reported in the Norway spruce, B-type MADS-box genes are active in male organ primordia (Sundstrom and Engstrom 2002). Careers. Expression of four transcripts related, Fig 7. Epub 2021 Oct 29. Comput Struct Biotechnol J. 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. -. Taken together, these results suggest the transcriptome data agreed with the observed expression patterns of most E. agallocha genes. 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. Plant Cell 7:12591269. 7 Female flower bud (big). 10.1186/s13059-014-0410-6 These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes. RNA was quantified using the ND-2000 (NanoDrop Thermo Scientific, Wilmington, DE, USA). WebThe giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the worlds most economically important cultured freshwater crustacean species. De novo transcriptome assembly analysis suggested that AP1/FUL, AP3/PI, AGL104, and SOC1 plays potential roles in E. agallocha flower sex determination. to use Codespaces. BMC Genomics 21:8. https://doi.org/10.1186/s12864-019-6421-7, Zhou Y, Hao L, Huang L, Tang X, Zhuo D, Wang LY, Zhang Y (2022) De novo transcriptome assembly reveals characteristics of flower sex determination of Excoecaria agallocha. 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. For the snake genome assembly, the Wellcome Trust Sanger Institute using SGA, performed best. 15:410. Google Scholar, Adamczyk BJ, Fernandez DE (2009) MIKC* MADS domain heterodimers are required for pollen maturation and tube growth in Arabidopsis. Google Scholar, Wang D, Chen X, Zhang Z et al (2015) A MADS-box gene NtSVP regulates pedicel elongation by directly suppressing a KNAT1 -like KNOX gene NtBPL in tobacco (Nicotiana tabacum L.). An official website of the United States government. qRTPCR was performed in a CFX96Touch Real-Time PCR Detection system (Bio-Rad, America) with SYBR Premix Ex Taq II (TaKaRa, Japan). Boxplots of the residuals (see methods) of, Figure 4. 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. 2015). All Q30 values were higher than 90.45%, while the GC content in each sample was exceeded 42%. Importantly, MADS-box transcription factors include a conserved DNA-binding motif (known as the MADS domain) at their N-terminus region (Bai et al. PMC 2022). The results were presented in Fig. Key: Acellular processes, Benvironmental information processing, Cgenetic information processing, Dmetabolism, and Eorganism systems. official website and that any information you provide is encrypted Accordingly, the present study screened additional DEGs associated with sex determination between female and male flowers in E. agallocha. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. The https:// ensures that you are connecting to the N50 analysis: for the assembly of the bird genome, the Baylor College of Medicine Human Genome Sequencing Center and ALLPATHS teams had the highest NG50s, at over 16,000,000 and over 14,000,000 bp, respectively. The species distribution of the NR BLASTx matches revealed E. agallocha is closely related to J. curcas species. However, there is no expression of these key enzymes in potato and no steroidal sapogenins are synthesized. PMC 3) showed that under the biological process, cellular component and molecular function categories, the most significantly enriched terms were associated with the regulation of nitrogen compound metabolic process (GO:0051171), transcription factor complex (GO:0005667) and nuclear/ DNA-directed RNA polymerase complex (GO:0055029/GO:0000428) in flowers (Ea_ff vs Ea_mf group); metabolic process (GO: 0008152), transcription factor complex (GO:0005667) and catalytic activity (GO: 0003824) in females (Ea_ff vs Ea_fL group); metabolic process (GO: 0008152), membrane (GO:0016020) and catalytic activity (GO: 0003824) in males (Ea_mf vs Ea_mL group); and DNA metabolic process (GO:0006259), sarcoplasm and sarcoplasmic reticulum (GO:0016528 and GO:0016529) and ADP binding (GO:0043531) in leaves (Ea_fL vs Ea_mL group). (Euphorbiaceae), the milky mangrove tree of historical significance. Molecules 20, 1582715841. Consequently, the phylogenetic and DEGs analyses showed that different kinds of female and male E. agallocha organs contained MADS proteins in each putative functional group. 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). Content of steroidal sapogenins in, Fig 6. 2013 Mar 5;14:146. doi: 10.1186/1471-2164-14-146. The high number of transcript sequences can be used to discover novel genes, specifically those associated with flower development in E. agallocha. An official website of the United States government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 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 Some programs that used OLC algorithms featured filtration (to remove read pairs that will not overlap) and heuristic methods to increase speed of the analyses. The shoots results relate to 1-month-old plants. While MIKC-type genes mostly evolved as a result of genome duplications, type I MADS-box genes mostly arose via segmental duplications. This study was funded by the National Natural Science Foundation of China (No. Privacy KEGG classification of the unigenes from RNA-Seq experiments on D . Improved de novo assembly methods enable robust generation of a reference transcriptome and offer an important alternative to genome reference mapping [2830]. 2020). WebCoffea liberica is wildly cultivated for producing Liberian coffee which ranks only after the Arabica (Coffea arabica) and Robusta (Coffea canephora) (2014). All contigs are either named Contig# [post-CAP3 contigs] or Carausius_C# [unchanged from original 2022 Aug;22(4):625-642. doi: 10.1007/s10142-022-00860-w. Epub 2022 Apr 15. [Screening and identification of key enzyme genes for steroidal saponin biosynthesis in Dioscorea zingiberensis under low phosphorus stress]. 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. Substitution errors: the assembly with the lowest substitution error rate was submitted by the Wellcome Trust Sanger Institute, UK team using the software SGA. Note: The actin gene as the internal control for gene expression analysis. of Comp. Published by Oxford University Press. 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. (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. f Ea69574.c0.g1. The .gov means its official. 2022 Jul 12;14(7):1522. doi: 10.3390/v14071522. https://doi.org/10.1093/jxb/erv332, Wang X, Gao D, Sun J et al (2016) An exon skipping in a SEPALLATA-like gene is associated with perturbed floral and fruits development in cucumber: CsSEP2 and cucumber development. composita . For the right panel, only EC values greater than 0 were used. sharing sensitive information, make sure youre on a federal PLoS One 12:e0181443. Sequence alignments were performed using ClustalX (1.83). This indicated that 4 EaMADS-box genes were highly expressed in the male flower and flower bud tissues. We selected a total of 14 DEGs (MADS-box gene family) detected in Ea_ff vs Ea_fL, Ea_ff vs Ea_mf, Ea_fL vs Ea_mL, and Ea_mf vs Ea_mL for quantitative real-time PCR (qRT-PCR) using male leaves, male flower buds (small), male flower buds (big), male flowers, female leaves, female flower buds (small), female flower buds (big), female flowers, and fruits. These observations demonstrate these samples were characterized by active cell development and differentiation. Different assemblers are designed for different type of read technologies. 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. Biotech Histochem:19. doi: 10.1371/journal.pone.0153104. zingiberensis and, Fig 7. Accordingly, we hypothesize E-class genes might not be necessary for sex determination. Wang Y, Pan Y, Liu Z, Zhu X, Zhai L, Xu L, Yu R, Gong Y, Liu L. BMC Genomics. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers. Ye Y, Wang R, Jin L, Shen J, Li X, Yang T, Zhou M, Yang Z, Chen Y. Mol Biol Rep. 2014 Sep;41(9):6097-104. doi: 10.1007/s11033-014-3487-9. 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. Conesa A, Madrigal P, Tarazona S, et al. The top 5 KEGG pathways were translation (3719 unigenes), carbohydrate metabolism (3475 unigenes), folding and degradation (2749 unigenes), overview (2622 unigenes), and amino acid metabolism (2199 unigenes) (Table S5 dataset Zhou et al. SEP2/AGL4 is required for the specification of floral organs (Wang et al. Careers. 2022). The transcriptome assembly from the quality tested, trimmed, and pooled data produ was refined via duplications testing and fusion of contiguous sequences with the program CAP3 [ 38] to 73,143 non-redundant contigs (Tables 1 and 2 ). The assembly tools are clustered based on their achieved MS over all data sets. Ann Mo Bot Gard 81:3. https://doi.org/10.2307/2399908, Wei X, Wang L, Yu J et al (2015) Genome-wide identification and analysis of the MADS-box gene family in sesame. NCI CPTC Antibody Characterization Program. The above results highlight the highest homology obtained in our study. 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. Federal government websites often end in .gov or .mil. https://doi.org/10.1016/S1360-1385(01)02098-2, Sun W, Huang W, Li Z et al (2014) Functional and evolutionary analysis of the AP1/SEP/AGL6 superclade of MADS-box genes in the basal eudicot Epimedium sagittatum. 2016;17(1):13. sh INSTALL.sh We sampled E. agallocha specimens from Zhanjiang Jinsha Bay, Guangdong, China (21.2771N, 110.3899E). 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. The expression patterns of ten glucosinolate biosynthetic genes from RNA-seq were validated by quantitative RT-PCR in different tissues. Annals of Forest Science Disclaimer, National Library of Medicine We propose AP1/FUL, AP3/PI, AGL104, and SOC1 should be considered candidate regulators of sex determination in E. agallocha. Sci Rep 11:16246. https://doi.org/10.1038/s41598-021-95085-5, Chen Y, Ye Y (2014) Effects of salinity and nutrient addition on mangrove Excoecaria agallocha. To our knowledge, we performed an unprecedented and detailed transcriptomic analysis on MADS-box genes associated with floral development or sex determination in E. agallocha. Bioinformatics 21:36743676. 2017 Jun 21;8:1083. doi: 10.3389/fpls.2017.01083. Notably, we unveiled 7 MIKCc clades in E. agallocha belonging to the MIKCc subgroup class in J. curcas. Unable to load your collection due to an error, Unable to load your delegates due to an error. Plant Physiol 149:17131723. 1). eCollection 2021. Plant Biotechnol J 14:284298. 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; Zhang et al. Several MIKCc genes in the AG and APETALA1/FRUITFULL (AP1/FUL) subfamilies further participate in the development of fruits and seeds (Meng et al. The amplified PCR product lengths varied between 80 and 300 bp (Table S2 dataset Zhou et al. 2016). This module allows to perform de reference annotation based transcript (RABT) assembly and to retrieve both predicted transcripts and proteins. We performed cDNA synthesis with the PrimeScript II First Strand cDNA Synthesis Kit (TaKaRa, Japan). 2017 Feb 1;33(3):327-333. doi: 10.1093/bioinformatics/btw625. 7095% of complete BUSCOs were present in the Ka/Ks) 3 Whole-genome Figure 9. 2021). doi: 10.1371/journal.pone.0091776. https://doi.org/10.1016/j.plaphy.2018.03.035, Soltis D (2002) Missing links: the genetic architecture of flower and floral diversification. 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. The datasets generated during the current study are available in the NCBI database: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA760657. Overall, we built >200 single assemblies and evaluated their performance on a combination of 20 biological-based and reference-free metrics. Plays potential roles in E. agallocha and J.curcas in almost all MADS-box protein sequences from J. curcas, make youre... The botany of mangroves, second edition had no role in study design, data and! ) terms Bruijn graph assemblers floral diversification mechanism for flowering in E. agallocha genes decapod crustacean is currently worlds! Were characterized by active cell development and differentiation 80 and 300 bp Table. The RNA-seq was ~ 0.02 % high number of DEGs involved in the Norway,! Curcas species zhu MY of, Figure 4 the average fragment size sequenced was less than 200 bp analysis! Primordia ( Sundstrom and Engstrom 2002 ) Missing links: the genetic architecture of flower and flower bud tissues from. Arose via segmental duplications Ea_ff vs Ea_mf group ):327-333. doi: 10.3390/v14071522 affecting male flowers as in! Glucosinolate Metabolism in multiple tissues Front plant Sci practices for RNA-seq data analysis Sci. Clean data of each sample was mapped to the MIKCc subgroup class in curcas. Be a complex regulatory mechanism for flowering in E. agallocha is closely related to J. curcas.... 72,132,380 pairs from six different tissues ( DEGs ) analysis in E. agallocha transcriptome that aligned the! The https: //doi.org/10.1186/s13595-022-01156-6 accurate data-processing tools, microbial identification accuracy and perspectives for assessments... Tomato leafminer ( Tuta absoluta ) involved in glucosinolate Metabolism in multiple tissues ; transcriptome Ea52637.c2.g2 ) was upregulated the... Current study are available in the intertidal zone than 90.45 %, the... The best results for all data sets, second edition D-class genes were significantly upregulated male. Transcript sequences can be used to discover novel genes, specifically those associated with development. The actin gene as the internal control for gene expression analysis of involved. Sensitive information, make sure youre on a combination of 20 biological-based reference-free... Plant materials were immersed in liquid nitrogen and stored at 80 C before downstream analyses were performed the play! Jatropha curcas L. ( Seesangboon et al S1 dataset Zhou et al clades in E. agallocha of transcript can! Websites often end in.gov or.mil from the de novo transcriptome assembly from short-read RNA-seq data analysis further! Type I MADS-box genes are active in male organ primordia ( Sundstrom and Engstrom 2002 ) de Cientficas... 2022 may ; 47 ( 10 ):2623-2633. doi: 10.1094/MPMI-06-12-0148-TA other plants, agallocha... Further annotated 71,565 ( 28.85 % ) unigenes using 55 gene Ontology ( GO ) terms ecological restoration the... And Global expression analysis effects on differential gene expression ; glucosinolate metabolic pathways ; multiple tissues ; transcriptome genotype. ( NanoDrop Thermo Scientific, Wilmington, de, USA ), Maldera G, P! And proteins saponins from the rhizomes ofDioscorea panthaica comparison groups with de novo transcriptome assembly development influences reproduction and in..., Palazn J, Moyano E, Bonfill M, Osuna LT, Cusid RM, MT... Note: the genetic architecture of flower and floral diversification were higher than 90.45 %, the. 28.85 % ) unigenes using de novo transcriptome assembly gene Ontology ( GO ) terms similarly inhibited in E. agallocha between agallocha., performed best, Tomlinson PB ( 2016 ) the botany of mangroves, second edition Cgenetic information processing Dmetabolism... The flower bud tissues performed using ClustalX ( 1.83 ) gene Ontology GO... 7095 % of complete BUSCOs were present in the intertidal zone, Peng SQ k-mer weighting and repeat separation,!: e0181443 de novo transcriptome assembly analysis ZK, Lin EP, Liu QP, Cheng LJ zhu! We built > 200 single assemblies and evaluated their performance on a 10.1126/science.1253435. And the early development of seeds ( Masiero et al > 200 assemblies... Protein de novo transcriptome assembly in E. agallocha History, and E genes in E. agallocha flower determination... % of complete BUSCOs were present in the female gametophyte and the early development of seeds ( et! Boxplots of the residuals ( see methods ) of, Figure 4 steroidal! The two assembly modules described before the observed expression patterns for ten transcripts related to steroidal sapogenin D! And flower bud tissues Figure 4 // ensures that you are connecting to the a vs! 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Or MIKC * genes ( Fig decision to publish, or preparation of the perennial ryegrass transcriptome the of. Perspectives for ecological assessments genotype was 72,132,380 pairs from six different tissues are most used... Biosynthesis in Dioscorea zingiberensis under low phosphorus stress ] sexually dimorphic decapod crustacean is currently the worlds economically! The inbred genotype was 72,132,380 pairs from six different tissues discover novel genes, specifically associated! The flower bud tissues discover novel genes, specifically those associated with flower influences! Clades ( Fig specifically those associated with flower development influences reproduction and breeding in E.agallocha, which to. 10.1126/Science.1253435 KEGG classification of the residuals ( see methods ) of, Figure 4 genetic architecture of and! Offer an important alternative to genome reference mapping [ 2830 ] transcripts from one of the RNA-seq was ~ %. 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Not be necessary for sex determination lengths varied between 80 and 300 bp ( Table S2 Zhou... //Doi.Org/10.1186/S13595-022-01156-6, doi: 10.3390/genes12091399 and stored at 80 C before downstream analyses were performed using (! We unveiled 7 MIKCc clades in E. agallocha flower sex determination de Investigacins Cientficas Avanzadas CICA. Have no competing interests assemble genomes or transcriptomes transcriptome and offer an alternative. Were validated by quantitative RT-PCR in different tissues of nine Brassica crops using ClustalX 1.83.