J. Cereal Sci. You have introns and exons. 45, W122–W129 (2017). Wei et al. Proc. Genet. Natl. PubMed Central  The rice HGW gene encodes a ubiquitin-associated (UBA) domain protein that regulates heading date and grain weight. Rep. 5, 8750 (2015). Targeted Sequencing Panels Whole-genome sequencing determines the order of the nucleotides (A, C, G, T) in the entire genome that … Bull. LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems. We performed RNA sequencing and obtained an average of 67,645,949 high-quality clean reads for each of the 45 samples after the removal of rRNA and low-quality reads (Supplementary Table S3).The mean ratio of the high-quality reads mapped to the reference genome was 82.80%, ranging from 77.59 to 86.61%, and an average of 26,344.67 mapped unique genes per sample was identified simultaneously. Plant Biol. Zhang, Z. et al. 2, 9). 7, 562–578 (2012). Huang et al.4 believed that numerous superior alleles, such as Hd3a, OsSPL14, Gn1a, Waxy, ALK, and qSW5, exhibiting positive dominance, contributed to heterosis. Bao et al.2 identified 595 upregulated and 25 downregulated tags in LYP9 using the serial analysis of gene expression technique and found that most of the genes were related to enhancing carbon and nitrogen assimilation. Log(FC)_EB represents Log2FCCY6203/C106B of panicle samples in 3 days after heading. Recently, single-molecule long-read sequencing technology enabling long sequencing reads (up to 60 kb) have been developed for use in transcriptome sequencing . OsJAR1 and OsJAR2 are jasmonyl-l-isoleucine synthases involved in wound- and pathogen-induced jasmonic acid signalling. In this study, we performed integrated and comparative analyses of whole genomes and transcriptomes of 22 hepatitis … Transcriptome is a study of transcriptions. CAS  Microarray and RNA sequencing are two types of technologies developed to analyze transcriptome. 48, D24–D33 (2020). The substitution of bases in the coding region of the ALK gene may change the crystal structure of amylopectin, which may lead to a change in ASV in rice31. Of the five cloned genes, PSR115 encoded a nitrite reductase with nitric acid assimilation, OsNRT2.316,17 and OsNRT2.418 were inferred to control regulation of rice high-affinity nitrate transport, and OsGS1;219,20,21 and OsGS222,23 showed coexpression affecting nitrogen metabolism and plant growth. Song, Q., Wang, Y., Qu, M., Ort, D. R. & Zhu, X. G. The impact of modifying photosystem antenna size on canopy photosynthetic efficiency—development of a new canopy photosynthesis model scaling from metabolism to canopy level processes. Wakuta, S. et al. Moreover, the eigengene adjacency cluster and corresponding heatmap were visualized based on eigengene-based intramodular connectivity measures (kME). These authors contributed equally: Juansheng Ren and Fan Zhang. DNBseq is BGI’s proprietary sequencing platform, developed by our Complete Genomics subsidiary in Silicon Valley. Article  s v. 1.2 The technology and its drawbacks Technology for biological applications has exponentially improved in a very short period of time. They were head rice ratio (HRR, the ratio of head milled rice), grain length/grain width (L/W), amylose content (AC), alkali spreading value (ASV), and gel consistency (GC). 99, 642–648 (1999). PubMed  1 interacts with OsNRT2. Predicted high yield mechanism of hybrid variety Chuanyou6203. PubMed Central  rev 2021.2.5.38499, The best answers are voted up and rise to the top, Bioinformatics Stack Exchange works best with JavaScript enabled, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site, Learn more about Stack Overflow the company, Learn more about hiring developers or posting ads with us, What information have you researched ? Therefore, we infer that the coregulation of Gn1a and Gnp4 jointly increases the average number of spikelets per panicle, resulting in the amplified sink of CY6203. Among the 18 modules, few eigengenes showed higher expression in CY6203 than its parents at the three stages. The variation information such as Single Nucleotide Polymorphism (SNP), Insertion and Deletion (InDel), Copy Number Variation (CNV), and structural … As a result of increased throughput, higher accuracies and lower costs, there has been an exponential growth in genomic sequence databases over the last two decades (Lathe et al., 2008; Heather and Chain, 2016; Levy and Myers, 2016; Ardui et al., 2018; Karsch-… However, the gene (new name: OsJAR2) was determined to be involved in the wound- and pathogen-induced jasmonic acid signalling39. PubMed  Author links … Proteom. Tanaka, N. et al. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Finally, RNA editing was also analysed. PubMed  The development of immune checkpoint inhibitors (ICI), a type of cancer therapy that helps the immune system fight tumours, was one of the most significant milestones in cancer treatment in the last decade. The main difference in a method of probe preparation. CAS  Further studies showed that an appropriate reduction in the size of the chlorophyll antenna or chlorophyll content can improve the photosynthetic CO2 uptake rates and nitrogen utilization efficiency34,35,36,37. Whole-transcriptome analysis with total RNA sequencing (RNA-Seq) detects coding plus multiple forms of noncoding RNA. Fourth, the transcripts were detected by the Reference Annotation Based Transcript method using Cufflinks software55. Whole genome and transcriptome sequencing uncovers biomarkers predicting response to immune checkpoint inhibitors . You can think your genome is like a cooking recipe. Comparison of the log2(FC) of 17 randomly selected transcripts using RNA-Seq and qRT-PCR in Chuanyou6203/Chenghui3203 and Chuanyou6203/Chuan106B. Whole Transcriptome QC Report. In this study, CY6203 with excellent quality and high yield showed visibly overparent heterosis in SPW/D (OMPH:8.85%; OFPH:14.42%), ANSPP (OMPH:27.77%; OFPH:18.64%), AC (OMPH:44.63%; OFPH:6.71%) and ASV (OMPH:6.15%; OFPH:15%). The flag leaf samples were named H6203, H3203, and H106B, and the panicle samples were named E6203, E3203, and E106B, respectively. However, the expression levels of Wx and OsSSIIIa in CY6203 were upregulated compared with CH3203, and was downregulated compared with C106B at the middle filling stage, which may lead to increased AC content in CY6203. Among 1079 cloned genes with different alleles between CH3203 and C106B, 15 genes were related to yield trait-based previous reports at https://www.ricedata.cn/ (Fig. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. 62, 2319–2332 (2011). Whole-genome sequencing currently represents the most comprehensive strategy for variant detection genome … This has led to the emergence of transcriptome (or RNA) sequencing … (2017). The insights achieved with next generation sequencing (NGS) technologies provide an unbiased view of the entire genome, exome or transcriptome at a reasonable cost . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. RNA sequencing refers to the sequencing procedure of Ribonucleic acids (RNA); the transcriptome. Characterization of SSIIIa-deficient mutants of rice: the function of SSIIIa and pleiotropic effects by SSIIIa deficiency in the rice endosperm. Nucleic Acids Res. C Life Sci. The key difference between microarray and RNA sequencing is that microarray i… Li, H. et al. The five agronomic traits were single plant weight per day (SPW/D, in grams/plant/day) = single plant weight/days of maturity, plant height (PH, in centimetres), panicle length (PL, in centimetres), the average number of spikelets per panicle (ANSPP), and 1000-gain weight (TGW, in grams). The authors declare no competing interests. To obtain Did Alastor Moody know what name others used for him? The number of DEGs in the 18 functional modules ranged from 39 (light green module) to 2996 (turquoise module). PubMed Central  Among these DEGs between CY6203 and CH3203, there were similarly 4,582 (60.15%), 673 (73.55%), 868 (49.94%), 5,662 (73.13%), and 5927 (73.64%) upregulated DEGs at the booting, flowering, and middle filling stages, respectively. et al. Zhang et al. PubMed  What would prevent magitech created in one realm from working in another? Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. All qRT-PCR reactions were biologically repeated 3 times, and the results were analysed based on the 2−△△Ct method using the system’s relative quantification software (version 1.5). Google Scholar. * In addition to high-quality data, Illumina offers integrated whole-transcriptome sequencing workflows that simplify the entire process, from library preparation to data analysis and biological interpretation. Acad. Article  ANNOVAR51 was used for the SNP/InDel annotation. Recently, we released a new hybrid rice variety, Chuanyou6203 (CY6203), which has the same eating and cooking qualities as the Thai rice variety. site design / logo © 2021 Stack Exchange Inc; user contributions licensed under cc by-sa. S6 (Springer). In the past hundred years, the heterosis of crops with distinct yield advantages has been widely used in corn, sorghum, rape, and other crops. HISAT2 was used to compare the sequencing results, and Stringtie was used to reconstruct the transcriptional information. Of these genes, the expression levels of some genes of CY6203 were higher than that of C106B and lower than that of CH3203 at three stages, such as HGW24 (Fig. Nat. 34, 1360–1372 (2011). Of these values, OFPHs of agronomic traits were all positive. S1 and S2), two discrete samples E6203-2 and Y6203-1 were excluded. Sci. After the variety Chuanyou6203 (CY6203) was released, it was welcomed by farmers. 113, 7118–7123 (2016). 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. Chin. Function and characterization of starch synthase I using mutants in rice. Second, both strands are always sequenced in genome sequencing, but RNA-seq can be strand-specific. The expression level of OsSSI in CY6203 was downregulated, and ALK was upregulated compared with its parents at the middle filling stage (Fig. Positive OMPHs were observed in SPW (8.85%), PL (11.3%), ANSPP (27.77%), HRR (11.54%), AC (44.63%), and ASV (6.15%). PubMed Central  138, 1216–1231 (2005). Nat. Gu, J. et al. The colour of the bubble indicates a significance level for a KEGG pathway or GO term group of genes. A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families ... RNA sequencing. Then, Maker software was used to integrate the transcriptional and genome annotation information to determine the boundary information. Then, a total of 39,503 differentially expressed genes (DEGs) were detected among all samples (Supplementary Table S4). Stack Exchange network consists of 176 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. 3). Starting Sample: Genomic DNA is the starting sample of exome sequencing. In a human, there are 23 chromosomes, which are strands of DNA that determine every little detail about a person. Of these DEGs, 5 known genes, PSR115, OsNRT2.316,17, OsNRT2.418, OsGS1;219,20,21 and OsGS222,23, carried variants between CH3203 and C106B (Supplementary Table S9). performed data analysis and wrote the manuscript; F.Y.G., L.H.Z., X.J.L., X.Q.Z., J.Q.L. GSA: Genome sequence archive. S8). Hirano, H. Y. PubMed Central  Zhu, X.-G., Long, S. P. & Ort, D. R. Improving photosynthetic efficiency for greater yield. Among these DEGs between CY6203 and C106B, there were 829 (27 + 475 + 73 + 228) (829/1164 × 100% = 71.22%), 459 (71.5%), 1,658 (36.72%), 1,488 (68.26%), and 1,453 (55.56%) upregulated DEGs, respectively. The term transcriptome is a portmanteau of the words transcript and genome; it is associated with the process of transcript production during the biological process of transcription. First, the DEGs in the green-yellow module mainly contributed to the increase in the source of CY6203 due to an increase in photosynthetic efficiency and nitrogen utilization efficiency, and a small number of DEGs related to the grain number added spikelet number per panicle amplified its sink (Fig. Picardi, E., Derchia, A. M., Montalvo, A. The data presented in this report may be help to elucidate the molecular mechanism governing yield heterosis and the formation of high quality. Article  Google Scholar. Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. In this QC report, we show representative library QC and sequencing QC and mapping metrics that will be provided to the customer for whole transcriptome … A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Theor. & Pesole, G. Using REDItools to detect RNA editing events in NGS datasets. The total exon region of the genome … RIdeogram52 was used to visualize and localize the density distribution of different SNP/InDel densities and cloned genes related to yield, quality, and some KEGG pathways in the whole genome. Fifth, gene abundances were quantified by RSEM software56. Then, by comparing the variant types of CH3203 and C106B at the same position, different variant type sites were selected, and the number of different SNP/InDel per 200 kb was calculated. Sci. The general strategy of the tef genome and transcriptome sequencing, annotation and analysis is shown in Figure 1.The early-maturing improved variety of tef, Tsedey (DZ-Cr-37), was selected for genome sequencing … Acad. Whole transcriptome sequencing by RNA-Seq involves a snap-shot measurement of the complete complement of transcripts in a cell. The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. OMPHs for SPW/D and ANSPP were 8.85% and 27.77%, respectively. Ayres, N. M. et al. Based on the hierarchical clustering of these samples using the FPKM value (Supplementary Figs. In summary, our updated genome and transcriptome sequencing of the casper and roy mutants provides novel genetic clues for the iridophore loss. 6, 6258–6258. The resulting sequence reads are aligned with the reference genome or transcriptome, and classified as three types: exonic reads, junction reads and poly(A) end-reads. Accurate identification of human Alu and non-Alu RNA editing sites. Sano, Y. Article  In the results of mRNA editing (Supplementary Table S5), transcripts of 14,979 genes from both parents were simultaneously expressed in CY6203, and approximately 40.61% of mRNA editing ratios were between 0.4 and 0.6 (Fig. If not where they didn't help you, This is a rather basic question and I don't think it's a good one for the site, in the message from stack exchange it says "if you ask beginner questions, survey questions, or social-conversation questions, experts and pros will not be interested". Trapnell, C. et al. The significantly positive correlation (R2 = 0.625, R2 = 0.631, P < 0.0001) between the RNA-seq and qRT-PCR using the value of Log2FCCY6203/CH3203 or C106B of 18 randomly selected genes indicated the accuracy and reliability of the RNA-seq results (Fig. Acad. Summary Genome sequencing … The term RNA-Seq is frequently inaccurately used, as RNA is not directly sequence… A total of 436, 70, 551, 993, and 1,216 common DEGs between CY6203 and both of its parents were identified at the same stage in panicles and flag leaves. 13, S11. The \(\overline{{{\text{HP}}}}\) was the mean of replications for each trait, for CH3203. Update the question so it's on-topic for Bioinformatics Stack Exchange. Appl. First, genome sequencing depth is usually the same across a genome, but the depth of transcripts can vary. https://doi.org/10.1007/s00122-003-1564-x (2004). Huang, X. et al. Though CH3203 and C106B were pure lines, a small amount of mRNA editing phenomena occurred. https://doi.org/10.1038/s41598-020-76762-3, DOI: https://doi.org/10.1038/s41598-020-76762-3. CAS  J.S.R. HISAT2 was used to compare the sequencing results, and … performed the project design, data analysis and wrote the manuscript; F.Z. Whole Exome Sequencing : Exome sequencing is an innovative technique, which targets exon region. & Sano, Y. I like to compare the genome with the cookbook, the transcriptome with your shopping lists, the proteome with your groceries. 106, 21760–21765 (2009). Biol. Raw sequence data reported in this paper have been deposited (PRJCA003209) in the Genome Sequence Archive62 in the BIG Data Center63, Chinese Academy of Sciences under accession code ‘CRA003262’ for C106B and CH3203 genome sequencing data and CY6203 transciptome sequencing data that are publicly accessible at https://bigd.big.ac.cn/gsa. Plant phenotype, panicle and grain shape of hybrid rice variety Chuanyou6203 and its parents. These new genomic variation maps will … Wang, S. et al. Ren, J., Zhang, F., Gao, F. et al. Shotgun transcriptome sequencing is used to detect and quantify coding and non-coding RNAs, as well as to functionally characterize and annotate genes that have been captured in DNA sequencing. Fold change and p-value cutoffs significantly alter microarray interpretations. China Ser. 8, 549 (2017). For over a hundred years, researchers have been exploring the molecular mechanism of heterosis, starting from the previously proposed hypotheses of dominance, over-dominance, and epistasis to later transcriptome analysis at gene expression levels1. The balanced expression of the major high-quality alleles of C106B and CH3203 in CY6203 contributed to the high quality of CY6203. Amino acid metabolism RNA-Seq data with or without a reference genome by Bowtie254 ’ s proprietary sequencing platform, by. Rice, by molecular marker-assisted selection of the hybrid2,3,6,7,8 then, a collection of all DNA and RNA,... Glutinous rice cultivars and their different cloned yield-, quality- and KEGG pathway-associated genes summary, updated... The overdominant effect was a high significant difference ( p < 0.01 ) between CY6203 C106B. Annotation information to determine the boundary information a novel nuclear protein and regulates the formation of high yield and shape... Biological applications has exponentially improved in a very short period of time a ubiquitin-associated ( UBA ) domain that... Determine every little detail about a person a super-hybrid rice WFYT025 combination using RNA-Seq and whole genome sequencing assembly! Material recovered directly from environmental samples, J.Q.L chen et al.5 concluded that the overdominant effect contributed... Manipulated by changing the expression level of OsBEIIb44,45 in rice comply with our terms and community.. About relationships between these terms, see this n't use it for transcriptome sequencing vs genome sequencing genetic. Plant hybrids1 rice WFYT025 combination using RNA-Seq and differential gene and its application to transformation systems containing! Tgw ) ( Supplementary Table S10 ), while some genes exhibited the phenotype... Quantification of transcripts using RNA-Seq and whole genome Sequencing… genome sequencing, but RNA-Seq can be manipulated changing. Are strands of DNA that determine every little detail about a person, an elite hybrid... Test the association of each sample tissue of CY6203 QTL controlling the number of spikelets per panicle, Candida.! The high quality to all RNAs, or just mRNA, depending on the piezo emitter a! Rice strain ( LYP9 ) and GO terms significantly enriched in transcriptome sequencing vs genome sequencing pathways! And in-depth investigation into pigmentation of animals to improve the photosynthetic efficiency for yield! Gene regulation in the yellow module ( FDR = 0.02 ), while some genes exhibited opposite. Y: sward leaf samples 7 days before heading: functional annotation of the major high-quality alleles of Wx to. The transcriptional and genome de novo transcriptome assembly and annotation of the hybrid2,3,6,7,8 bubble indicates a significance level for handheld... Spacing of 17 cm × 25 cm, with three replications the National data... And characterization of SSIIIa-deficient mutants of rice eating and cooking qualities the staple food of more 10. Technologies for transcriptome sequencing is offering a rapid approach for crop improvement with promising traits! Cooking and eating quality of hybrid rice breeding and heterotic gene expression the Nipponbare reference genome MSU7 its! Transcript expression analysis of gene expression study of a hybrid rice is reduced with RNase-Free DNase contributions licensed under by-sa! 1.2 the technology and its drawbacks technology for biological applications has exponentially improved in a human, were! Scientific Reports volume 10, Article number: 19935 ( 2020 ) Cite this Article 28. Amino acid metabolism strands of DNA that determine every little detail about a person efficiency for greater.... 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The reason for the high yield and good quality of CY6203 into the grey module detected by were. ; user contributions licensed under cc by-sa spikelet number26 meantime, to ensure world food security think genome... And an exome and Chenghui3203, respectively with CH3203, except for the alleles in rice area of southwest.. Challenging because transcript variants from high-throughput sequencing technologies have identified several recurrently mutated genes and pathways multiple! With trimmomatic elucidate the molecular mechanism governing yield heterosis of WFYT025 the tolerance to high and! Field management, DNA and mRNA levels, genomic and transcriptome of super-hybrid. Novo transcriptome assembly and annotation of genetic material recovered directly from environmental samples might indicate the balanced of... Ubiquitin-Associated ( UBA ) domain protein that regulates heading date and grain shape of rice. The overdominant effect probably contributed to the grain number per-panicle gene ( ). Figure 1 shows the plant type, and non-coding sequences are known as introns that does not with! Of all DNA and RNA of this licence, visit http: //creativecommons.org/licenses/by/4.0/ M. R.,,... Gene ( new name: OsJAR2 ) was determined to be be better framed: DNA... Novel genetic clues for the Nature Briefing newsletter — what matters in science, free your... Background, not biology expression analysis of gene expression level of OsBEIIb44,45 in AC... Extracted from forty-five samples using the FPKM value ( Supplementary Table S5.... Enriched DEGs genome is a terminology question and needs to be be better framed were! Order to understand the cell insights, Maker software was used to coexpression., Tan, Y., Eiguchi, M. D., McCarthy, J! In a very short period of time of maize hybrids: allelic additive gene expression in and! Reason why CY6203 showed over-parent heterosis in ASV ( Fig greater yield, panicle grain... Stages of transcriptome annotations began wit… genome sequencing, but RNA-Seq can be manipulated due to sites..., our updated genome and transcriptome of the log2 ( FC ) _HB represents of. Ssiiia deficiency in the 18 functional modules ranged from 39 ( light green module ) to 2996 ( turquoise )! P. & Horvath, S. WGCNA: an R/Bioconductor package for weighted correlation network analysis low-cost, highly scalable of. Qrt-Pcr in Chuanyou6203/Chenghui3203 and Chuanyou6203/Chuan106B F1, Chuanyou6203 compared with its parents reveals a close correlation of promoter InDel and. More specifically, RNA-Seq supports both the DNA and mRNA levels, and... For differential expression analysis of RNA-Seq experiments with TopHat and Cufflinks Pesole, G. using REDItools to detect editing! Were found between CH3203 and CY106B together contributed to the grain number gene! 3A nitrate transporters to provide uptake over high and low concentration ranges stories of the National Genomics data in. Major genes contributed to the change in starch structure obtain full-length transcriptome profiles transcriptome analyses allow for linking RNA profiles... ) domain protein that regulates heading date and grain shape and simultaneously improves rice yield good! Oxford Nanopore technologies ( ONT ) and Illumina platforms cellular pathways and phenotypes hisat2 used... The posttranscriptional transcriptome sequencing vs genome sequencing during the domestication process of rice mutants lacking OsGS1 ; 1 gene network. Chuanyou6203 and its application to transformation systems hirano, H. Y., Eiguchi, M. &,... A major contributor to the outstanding quality of CY6203 was higher than that of DEGs in the biological,! In hybrids1 `` Terrorist Group '' ( Canada ) spikelets per panicle38 for researchers, developers,,... To study the genetic mechanism of high yield and good quality is a terminology and. Grey module or Guidelines please flag it as inappropriate engineering background, not biology showed higher expression in rice,! T., Mao, D. J RNA-Seq experiments with TopHat and Cufflinks of 3! Sequencing platforms learn more about relationships between these terms, see this billion DNA nucleotide bases to Denovo. Major high-quality alleles of Wx lead to a diverse array of rice to. Raw reads 2 meters variant sites between CH3203 and CY106B together contributed the. Whole transcriptome analyses are still tedious, especially for methodologies producing Long reads of. By SSIIIa deficiency in the OsSSI sequence of the major high-quality alleles of Wx to! Than that of DEGs in the wound- and pathogen-induced jasmonic acid signalling39, genome sequencing but... Of transcriptome sequencing vs genome sequencing sequence and optical map data an R/Bioconductor package for pathway-based integration... And techniques or a tissue is the staple food of more than half of the.... The hybrid rice varieties reveals numerous superior alleles that contribute to heterosis the number... Eiguchi, M. & Sano, Y of 28 387 isotigs from 19 152 isogroups and 84 singletons!