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Xu H, Li M, Ma D, Gao J, Tao J, Meng J. Identification of key genes for triacylglycerol biosynthesis and storage in herbaceous peony (Paeonia lactifolra Pall.) seeds based on full-length transcriptome. BMC Genomics 2024; 25:601. [PMID: 38877407 PMCID: PMC11179206 DOI: 10.1186/s12864-024-10513-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND The herbaceous peony (Paeonia lactiflora Pall.) is extensively cultivated in China due to its root being used as a traditional Chinese medicine known as 'Radix Paeoniae Alba'. In recent years, it has been discovered that its seeds incorporate abundant unsaturated fatty acids, thereby presenting a potential new oilseed plant. Surprisingly, little is known about the full-length transcriptome sequencing of Paeonia lactiflora, limiting research into its gene function and molecular mechanisms. RESULTS A total of 484,931 Reads of Inserts (ROI) sequences and 1,455,771 full-Length non-chimeric reads (FLNC) sequences were obtained for CDS prediction, TF analysis, SSR analysis and lncRNA identification. In addition, gene function annotation and gene structure analysis were performed. A total of 4905 transcripts were related to lipid metabolism biosynthesis pathway, belonging to 28 enzymes. We use these data to identify 10 oleosin (OLE) and 5 diacylglycerol acyltransferase (DGAT) gene members after de-redundancy. The analysis of physicochemical properties and secondary structure showed them similarity in gene family respectively. The phylogenetic analysis showed that the distribution of OLE and DGAT family members was roughly the same as that of Arabidopsis. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses revealed expression changes in different seed development stages, and showed a trend of increasing and then decreasing. CONCLUSION In summary, these results provide new insights into the molecular mechanism of triacylglycerol (TAG) biosynthesis and storage during the seedling stage in Paeonia lactiflora. It provides theoretical references for selecting and breeding oil varieties and understanding the functions of oil storage as well as lipid synthesis related genes in Paeonia lactiflora.
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Affiliation(s)
- Huajie Xu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Miao Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Di Ma
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jiajun Gao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jun Tao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Jiasong Meng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Liang Y, Hao J, Wang J, Zhang G, Su Y, Liu ZJ, Wang T. Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304848. [PMID: 38647414 DOI: 10.1002/advs.202304848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/26/2024] [Indexed: 04/25/2024]
Abstract
Simple sequence repeats (SSRs) are found in nonrandom distributions in genomes and are thought to impact gene expression. The distribution patterns of 48 295 SSRs of Paphiopedilum malipoense are mined and characterized based on the first full-length transcriptome and comprehensive transcriptome dataset from 12 organs. Statistical genomics analyses are used to investigate how SSRs in transcripts affect gene expression. The results demonstrate the correlations between SSR distributions, characteristics, and expression level. Nine expression-modulating motifs (expMotifs) are identified and a model is proposed to explain the effect of their key features, potency, and gene function on an intra-transcribed region scale. The expMotif-transcribed region combination is the most predominant contributor to the expression-modulating effect of SSRs, and some intra-transcribed regions are critical for this effect. Genes containing the same type of expMotif-SSR elements in the same transcribed region are likely linked in function, regulation, or evolution aspects. This study offers novel evidence to understand how SSRs regulate gene expression and provides potential regulatory elements for plant genetic engineering.
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Affiliation(s)
- Yingyi Liang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jieyu Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Guoqiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518107, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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Zhu F, Lu J, Sun K, Deng C, Xu Y. Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing. BMC Genom Data 2024; 25:23. [PMID: 38408920 PMCID: PMC10895795 DOI: 10.1186/s12863-024-01208-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Indotyphlops braminus, the only known triploid parthenogenetic snake, is a compelling species for revealing the mechanism of polyploid emergence in vertebrates. METHODS In this study, we applied PacBio isoform sequencing technology to generate the first full-length transcriptome of I. braminus, aiming to improve the understanding of the molecular characteristics of this species. RESULTS A total of 51,849 nonredundant full-length transcript assemblies (with an N50 length of 2980 bp) from I. braminus were generated and fully annotated using various gene function databases. Our analysis provides preliminary evidence supporting a recent genome duplication event in I. braminus. Phylogenetic analysis indicated that the divergence of I. braminus subgenomes occurred approximately 11.5 ~ 15 million years ago (Mya). The full-length transcript resource generated as part of this research will facilitate transcriptome analysis and genomic evolution studies in the future.
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Affiliation(s)
- Fei Zhu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China.
| | - Jing Lu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Ke Sun
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Cao Deng
- Department of Bioinformatics, DNA Stories Bioinformatics Center, 610000, Chengdu, China
| | - Yu Xu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
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Ma J, Zhao X, Qi E, Han R, Yu T, Li G. Highly efficient clustering of long-read transcriptomic data with GeLuster. Bioinformatics 2024; 40:btae059. [PMID: 38310330 PMCID: PMC10881092 DOI: 10.1093/bioinformatics/btae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/08/2024] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
MOTIVATION The advancement of long-read RNA sequencing technologies leads to a bright future for transcriptome analysis, in which clustering long reads according to their gene family of origin is of great importance. However, existing de novo clustering algorithms require plenty of computing resources. RESULTS We developed a new algorithm GeLuster for clustering long RNA-seq reads. Based on our tests on one simulated dataset and nine real datasets, GeLuster exhibited superior performance. On the tested Nanopore datasets it ran 2.9-17.5 times as fast as the second-fastest method with less than one-seventh of memory consumption, while achieving higher clustering accuracy. And on the PacBio data, GeLuster also had a similar performance. It sets the stage for large-scale transcriptome study in future. AVAILABILITY AND IMPLEMENTATION GeLuster is freely available at https://github.com/yutingsdu/GeLuster.
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Affiliation(s)
- Junchi Ma
- Research Center for Mathematics and Interdisciplinary Sciences (Frontiers Science Center for Nonlinear Expectations), Shandong University, Qingdao 266237, China
- School of Mathematics, Shandong University, Jinan, Shandong 250100, China
| | - Xiaoyu Zhao
- School of Mathematics, Shandong University, Jinan, Shandong 250100, China
| | - Enfeng Qi
- School of Mathematics and Statistics, Guangxi Normal University, Guilin 541000, China
| | - Renmin Han
- Research Center for Mathematics and Interdisciplinary Sciences (Frontiers Science Center for Nonlinear Expectations), Shandong University, Qingdao 266237, China
| | - Ting Yu
- Research Center for Mathematics and Interdisciplinary Sciences (Frontiers Science Center for Nonlinear Expectations), Shandong University, Qingdao 266237, China
| | - Guojun Li
- Research Center for Mathematics and Interdisciplinary Sciences (Frontiers Science Center for Nonlinear Expectations), Shandong University, Qingdao 266237, China
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Liao T, Zhang L, Wang Y, Guo L, Cao J, Liu G. Full-length transcriptome characterization of Platycladus orientalis based on the PacBio platform. Front Genet 2024; 15:1345039. [PMID: 38304337 PMCID: PMC10830785 DOI: 10.3389/fgene.2024.1345039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
As a unique and native conifer in China, Platycladus orientalis is widely used in soil erosion control, garden landscapes, timber, and traditional Chinese medicine. However, due to the lack of reference genome and transcriptome, it is limited to the further molecular mechanism research and gene function mining. To develop a full-length reference transcriptome, tissues from five different parts of P. orientalis and four cone developmental stages were sequenced and analyzed by single-molecule real-time (SMRT) sequencing through the PacBio platform in this study. Overall, 37,111 isoforms were detected by PacBio with an N50 length of 2,317 nt, an average length of 1,999 bp, and the GC content of 41.81%. Meanwhile, 36,120 coding sequences, 5,645 simple sequence repeats (SSRs), 1,201 non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events with five types were identified using the results obtained from the PacBio transcript isoforms. Furthermore, 1,659 transcription factors (TFs) were detected and belonged to 51 TF families. A total of 35,689 transcripts (96.17%) were annotated through the NCBI nr, KOG, Swiss-Prot and KEGG databases, and 385 transcript isoforms related to 8 types of hormones were identified incorporated into plant hormone signal transduction pathways. The assembly and revelation of the full-length transcriptome of P. orientalis offer a pioneering insight for future investigations into gene function and genetic breeding within Platycladus species.
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Affiliation(s)
| | | | | | | | | | - Guobin Liu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Zhao J, Li S, Xu Y, Ahmad N, Kuang B, Feng M, Wei N, Yang X. The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis. J Adv Res 2023; 54:1-13. [PMID: 36781019 DOI: 10.1016/j.jare.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
INTRODUCTION Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum, with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear. OBJECTIVE To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation. METHODS PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation. RESULTS A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed, reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids. CONCLUSION Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation.
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Affiliation(s)
- Jihan Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuzhi Xu
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Nazir Ahmad
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China
| | - Bowen Kuang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Mengfan Feng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ni Wei
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China.
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Al-Dossary O, Furtado A, KharabianMasouleh A, Alsubaie B, Al-Mssallem I, Henry RJ. Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows. PLANT METHODS 2023; 19:112. [PMID: 37865785 PMCID: PMC10589961 DOI: 10.1186/s13007-023-01091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Long read sequencing allows the analysis of full-length transcripts in plants without the challenges of reliable transcriptome assembly. Long read sequencing of transcripts from plant genomes has often utilized sized transcript libraries. However, the value of including libraries of differing sizes has not been established. METHODS A comprehensive transcriptome of the leaves of Jojoba (Simmondsia chinensis) was generated from two different PacBio library preparations: standard workflow (SW) and long workflow (LW). RESULTS The importance of using both transcript groups in the analysis was demonstrated by the high proportion of unique sequences (74.6%) that were not shared between the groups. A total of 37.8% longer transcripts were only detected in the long dataset. The completeness of the combined transcriptome was indicated by the presence of 98.7% of genes predicted in the jojoba male reference genome. The high coverage of the transcriptome was further confirmed by BUSCO analysis showing the presence of 96.9% of the genes from the core viridiplantae_odb10 lineage. The high-quality isoforms post Cd-Hit merged dataset of the two workflows had a total of 167,866 isoforms. Most of the transcript isoforms were protein-coding sequences (71.7%) containing open reading frames (ORFs) ≥ 100 amino acids (aa). Alternative splicing and intron retention were the basis of most transcript diversity when analysed at the whole genome level and by specific analysis of the apetala2 gene families. CONCLUSION This suggests the need to specifically target the capture of longer transcripts to provide more comprehensive genome coverage in plant transcriptome analysis and reveal the high level of alternative splicing.
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Affiliation(s)
- Othman Al-Dossary
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Ardashir KharabianMasouleh
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Bader Alsubaie
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Ibrahim Al-Mssallem
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia.
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Thirugnanasambandam PP, Singode A, Thalambedu LP, Athiappan S, Krishnasamy M, Purakkal SV, Govind H, Furtado A, Henry R. Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum. FRONTIERS IN PLANT SCIENCE 2023; 14:1199748. [PMID: 37662143 PMCID: PMC10469502 DOI: 10.3389/fpls.2023.1199748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023]
Abstract
Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.
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Affiliation(s)
| | - Avinash Singode
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Millets Research, Hyderabad, Telangana, India
| | | | - Selvi Athiappan
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Mohanraj Krishnasamy
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | | | - Hemaprabha Govind
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
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Petri AJ, Sahlin K. isONform: reference-free transcriptome reconstruction from Oxford Nanopore data. Bioinformatics 2023; 39:i222-i231. [PMID: 37387174 PMCID: PMC10311309 DOI: 10.1093/bioinformatics/btad264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION With advances in long-read transcriptome sequencing, we can now fully sequence transcripts, which greatly improves our ability to study transcription processes. A popular long-read transcriptome sequencing technique is Oxford Nanopore Technologies (ONT), which through its cost-effective sequencing and high throughput, has the potential to characterize the transcriptome in a cell. However, due to transcript variability and sequencing errors, long cDNA reads need substantial bioinformatic processing to produce a set of isoform predictions from the reads. Several genome and annotation-based methods exist to produce transcript predictions. However, such methods require high-quality genomes and annotations and are limited by the accuracy of long-read splice aligners. In addition, gene families with high heterogeneity may not be well represented by a reference genome and would benefit from reference-free analysis. Reference-free methods to predict transcripts from ONT, such as RATTLE, exist, but their sensitivity is not comparable to reference-based approaches. RESULTS We present isONform, a high-sensitivity algorithm to construct isoforms from ONT cDNA sequencing data. The algorithm is based on iterative bubble popping on gene graphs built from fuzzy seeds from the reads. Using simulated, synthetic, and biological ONT cDNA data, we show that isONform has substantially higher sensitivity than RATTLE albeit with some loss in precision. On biological data, we show that isONform's predictions have substantially higher consistency with the annotation-based method StringTie2 compared with RATTLE. We believe isONform can be used both for isoform construction for organisms without well-annotated genomes and as an orthogonal method to verify predictions of reference-based methods. AVAILABILITY AND IMPLEMENTATION https://github.com/aljpetri/isONform.
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Affiliation(s)
- Alexander J Petri
- Department of Mathematics, Science for Life Laboratory, Stockholm University, Stockholm 106 91, Sweden
| | - Kristoffer Sahlin
- Department of Mathematics, Science for Life Laboratory, Stockholm University, Stockholm 106 91, Sweden
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Full-Length RNA Sequencing Provides Insights into Goldfish Evolution under Artificial Selection. Int J Mol Sci 2023; 24:ijms24032735. [PMID: 36769054 PMCID: PMC9916754 DOI: 10.3390/ijms24032735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/14/2023] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Goldfish Carassius auratus is an ideal model for exploring fish morphology evolution. Although genes underlying several ornamental traits have been identified, little is known about the effects of artificial selection on embryo gene expression. In the present study, hybrid transcriptome sequencing was conducted to reveal gene expression profiles of Celestial-Eye (CE) and Ryukin (RK) goldfish embryos. Full-length transcriptome sequencing on the PacBio platform identified 54,218 and 54,106 transcript isoforms in CE and RK goldfish, respectively. Of particular note was that thousands of alternative splicing (AS) and alternative polyadenylation (APA) events were identified in both goldfish breeds, and most of them were inter-breed specific. RT-PCR and Sanger sequencing showed that most of the predicted AS and APA were correct. Moreover, abundant long non-coding RNA and fusion genes were detected, and again most of them were inter-breed specific. Through RNA-seq, we detected thousands of differentially expressed genes (DEGs) in each embryonic stage between the two goldfish breeds. KEGG enrichment analysis on DEGs showed extensive differences between CE and RK goldfish in gene expression. Taken together, our results demonstrated that artificial selection has led to far-reaching influences on goldfish gene expression, which probably laid the genetic basis for hundreds of goldfish variations.
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Mason PJ, Hoang NV, Botha FC, Furtado A, Marquardt A, Henry RJ. Organ-specific expression of genes associated with the UDP-glucose metabolism in sugarcane (Saccharum spp. hybrids). BMC Genomics 2023; 24:18. [PMID: 36639618 PMCID: PMC9840354 DOI: 10.1186/s12864-023-09124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The importance of uridine 5'-diphosphate glucose (UDP-G) synthesis and degradation on carbon (C) partitioning has been indicated in several studies of plant systems, whereby the kinetic properties and abundance of involved enzymes had a significant effect upon the volume of C moving into the hemicellulose, cellulose and sucrose pools. In this study, the expression of 136 genes belonging to 32 gene families related to UDP-G metabolism was studied in 3 major sugarcane organs (including leaf, internode and root) at 6 different developmental stages in 2 commercial genotypes. RESULTS Analysis of the genes associated with UDP-G metabolism in leaves indicated low expression of sucrose synthase, but relatively high expression of invertase genes, specifically cell-wall invertase 4 and neutral acid invertase 1-1 and 3 genes. Further, organs that are primarily responsible for sucrose synthesis or bioaccumulation, i.e., in source organs (mature leaves) and storage sink organs (mature internodes), had very low expression of sucrose, cellulose and hemicellulose synthesis genes, specifically sucrose synthase 1 and 2, UDP-G dehydrogenase 5 and several cellulose synthase subunit genes. Gene expression was mostly very low in both leaf and mature internode samples; however, leaves did have a comparatively heightened invertase and sucrose phosphate synthase expression. Major differences were observed in the transcription of several genes between immature sink organs (roots and immature internodes). Gene transcription favoured utilisation of UDP-G toward insoluble and respiratory pools in roots. Whereas, there was comparatively higher expression of sucrose synthetic genes, sucrose phosphate synthase 1 and 4, and comparatively lower expression of many genes associated with C flow to insoluble and respiratory pools including myo-Inositol oxygenase, UDP-G dehydrogenase 4, vacuolar invertase 1, and several cell-wall invertases in immature internodes. CONCLUSION This study represents the first effort to quantify the expression of gene families associated with UDP-G metabolism in sugarcane. Transcriptional analysis displayed the likelihood that C partitioning in sugarcane is closely related to the transcription of genes associated with the UDP-G metabolism. The data presented may provide an accurate genetic reference for future efforts in altering UDP-G metabolism and in turn C partitioning in sugarcane.
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Affiliation(s)
- Patrick J. Mason
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Nam V. Hoang
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia ,grid.4818.50000 0001 0791 5666Wageningen University and Research (WUR), PO Box 9101, Wageningen, 6700 HB The Netherlands
| | - Frederik C. Botha
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Agnelo Furtado
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Annelie Marquardt
- grid.1003.20000 0000 9320 7537Commonwealth Scientific and Industrial Research Organisation (CSIRO), Level 3, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
| | - Robert J. Henry
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation (QAAFI), Level 2, Queensland Biosciences Precinct [#80], The University of Queensland, St Lucia, QLD 4072 Australia
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12
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Li Y, Li H, Wang S, Li J, Bacha SAS, Xu G, Li J. Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry ( Vaccinium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1082245. [PMID: 37152168 PMCID: PMC10157174 DOI: 10.3389/fpls.2023.1082245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.
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Affiliation(s)
- Yinping Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Haifei Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Shiyao Wang
- Department of Applied Biosciences, Toyo University, Ora-gun, Japan
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Syed Asim Shah Bacha
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Guofeng Xu
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
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13
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Kishi-Kaboshi M, Tanaka T, Sasaki K, Noda N, Aida R. Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization. Sci Rep 2022; 12:17874. [PMID: 36284128 PMCID: PMC9596691 DOI: 10.1038/s41598-022-22589-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/17/2022] [Indexed: 01/20/2023] Open
Abstract
Chrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editing, in C. morifolium. In this study, we used single-molecule real-time (SMRT) sequencing and RNA-seq technologies, combined them with an error-correcting process, and obtained high-coverage ray-floret transcriptome. The SMRT-seq data increased the ratio of long mRNAs containing complete open-reading frames, and the combined dataset provided a more complete transcriptomic data than those produced from either SMRT-seq or RNA-seq-derived transcripts. We finally obtained 'Sei Arabella' transcripts containing 928,645 non-redundant mRNA, which showed 96.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) score. We also validated the reliability of the dataset by analyzing a mapping rate, annotation and transcript expression. Using the dataset, we searched anthocyanin biosynthesis gene orthologs and performed a qRT-PCR experiment to assess the usability of the dataset. The assessment of the dataset and the following analysis indicated that our dataset is reliable and useful for molecular biology. The combination of sequencing methods provided genetic information and a way to analyze the complicated C. morifolium transcriptome.
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Affiliation(s)
- Mitsuko Kishi-Kaboshi
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan ,grid.416835.d0000 0001 2222 0432Present Address: Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Tsuyoshi Tanaka
- grid.416835.d0000 0001 2222 0432Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Katsutomo Sasaki
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
| | - Naonobu Noda
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
| | - Ryutaro Aida
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
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14
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Chen T, Liu Y, Song S, Bai J, Li C. Full-length transcriptome analysis of the bloom-forming dinoflagellate Akashiwo sanguinea by single-molecule real-time sequencing. Front Microbiol 2022; 13:993914. [PMID: 36325025 PMCID: PMC9618608 DOI: 10.3389/fmicb.2022.993914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The dinoflagellate Akashiwo sanguinea is a harmful algal species and commonly observed in estuarine and coastal waters around the world. Harmful algal blooms (HABs) caused by this species lead to serious environmental impacts in the coastal waters of China since 1998 followed by huge economic losses. However, the full-length transcriptome information of A. sanguinea is still not fully explored, which hampers basic genetic and functional studies. Herein, single-molecule real-time (SMRT) sequencing technology was performed to characterize the full-length transcript in A. sanguinea. Totally, 83.03 Gb SMRT sequencing clean reads were generated, 983,960 circular consensus sequences (CCS) with average lengths of 3,061 bp were obtained, and 81.71% (804,016) of CCS were full-length non-chimeric reads (FLNC). Furthermore, 26,461 contigs were obtained after being corrected with Illumina library sequencing, with 20,037 (75.72%) successfully annotated in the five public databases. A total of 13,441 long non-coding RNA (lncRNA) transcripts, 3,137 alternative splicing (AS) events, 514 putative transcription factors (TFs) members from 23 TF families, and 4,397 simple sequence repeats (SSRs) were predicted, respectively. Our findings provided a sizable insights into gene sequence characteristics of A. sanguinea, which can be used as a reference sequence resource for A. sanguinea draft genome annotation, and will contribute to further molecular biology research on this harmful bloom algae.
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Affiliation(s)
- Tiantian Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Qingdao, China
| | - Yun Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shuqun Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Qingdao, China
| | - Caiwen Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Caiwen Li,
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15
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Hou L, Li G, Chen Q, Zhao J, Pan J, Lin R, Zhu X, Wang P, Wang X. De novo full length transcriptome analysis and gene expression profiling to identify genes involved in phenylethanol glycosides biosynthesis in Cistanche tubulosa. BMC Genomics 2022; 23:698. [PMID: 36209069 PMCID: PMC9548140 DOI: 10.1186/s12864-022-08921-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background The dried stem of Cistanche, is a famous Chinese traditional medicine. The main active pharmacodynamic components are phenylethanol glycosides (PhGs). Cistanche tubulosa produces higher level of PhGs in its stems than that of Cistanche deserticola. However, the key genes in the PhGs biosynthesis pathway is not clear in C. tubulosa. Results In this study, we performed the full-length transcriptome sequencing and gene expression profiling of C. tubulosa using PacBio combined with BGISEQ-500 RNA-seq technology. Totally, 237,772 unique transcripts were obtained, ranging from 199 bp to 31,857 bp. Among the unique transcripts, 188,135 (79.12%) transcripts were annotated. Interestingly, 1080 transcripts were annotated as 22 enzymes related to PhGs biosynthesis. We measured the content of echinacoside, acteoside and total PhGs at two development stages, and found that the content of PhGs was 46.74% of dry matter in young fleshy stem (YS1) and then decreased to 31.22% at the harvest stage (HS2). To compare with YS1, 13,631 genes were up-regulated, and 15,521 genes were down regulated in HS2. Many differentially expressed genes (DEGs) were identified to be involved in phenylpropanoid biosynthesis pathway, phenylalanine metabolism pathway, and tyrosine metabolism pathway. Conclusions This is the first report of transcriptome study of C. tubulosa which provided the foundation for understanding of PhGs biosynthesis. Based on these results, we proposed a potential model for PhGs biosynthesis in C. tubulosa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08921-x.
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Affiliation(s)
- Lei Hou
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Guanghui Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Qingliang Chen
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - JinJin Zhao
- Shandong Academy of Grape, Shandong Engineering Research Center for Grape Cultivation and Deep-Processing, Jinan, 250100, China
| | - Jiaowen Pan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Ruxia Lin
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Xiujin Zhu
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Pengfei Wang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China.
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China.
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16
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Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system. Mol Genet Genomics 2022; 297:1403-1421. [PMID: 35879567 DOI: 10.1007/s00438-022-01929-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/09/2022] [Indexed: 10/16/2022]
Abstract
KEY MESSAGE Nitrate uptake in sugarcane roots is regulated at the transcriptional and posttranscriptional levels based on the physiological status of the plant and is likely a determinant mechanism for discrimination against nitrate. Sugarcane (Saccharum spp.) is one of the most suitable energy crops for biofuel feedstock, but the reduced recovery of nitrogen (N) fertilizer by sugarcane roots increases the crop carbon footprint. The low nitrogen use efficiency (NUE) of sugarcane has been associated with the significantly low nitrate uptake, which limits the utilization of the large amount of nitrate available in agricultural soils. To understand the regulation of nitrate uptake in sugarcane roots, we identified the major canonical nitrate transporter genes (NRTs-NITRATE TRANSPORTERS) and then determined their expression profiles in roots under contrasting N conditions. Correlation of gene expression with 15N-nitrate uptake revealed that under N deprivation or inorganic N (ammonium or nitrate) supply in N-sufficient roots, the regulation of ScNRT2.1 and ScNRT3.1 expression is the predominant mechanism for the modulation of the activity of the nitrate high-affinity transport system. Conversely, in N-deficient roots, the induction of ScNRT2.1 and ScNRT3.1 transcription is not correlated with the marked repression of nitrate uptake in response to nitrate resupply or high N provision, which suggested the existence of a posttranscriptional regulatory mechanism. Our findings suggested that high-affinity nitrate uptake is regulated at the transcriptional and presumably at the posttranscriptional levels based on the physiological N status and that the regulation of NRT2.1 and NRT3.1 activity is likely a determinant mechanism for the discrimination against nitrate uptake observed in sugarcane roots, which contributes to the low NUE in this crop species.
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17
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Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol 2022; 23:149. [PMID: 35799267 PMCID: PMC9264592 DOI: 10.1186/s13059-022-02711-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/15/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. RESULTS We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. CONCLUSIONS AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.
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Affiliation(s)
- Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Max Coulter
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Present address: Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Yamile Marquez
- Centre for Genomic Regulation, C/ Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Linda Milne
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Stefan Riegler
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
- Present address: Institute of Science and Technology Austria, Am Campus 1, 3400, Klosterneuburg, Austria
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Sarah Harvey
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York Wentworth Way, York, YO10 5DD, UK
| | - Yubang Gao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Theresa Wießner-Kroh
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Martin Crespi
- French National Centre for Scientific Research | CNRS INRAE-Universities of Paris Saclay and Paris, Institute of Plant Sciences Paris Saclay IPS2, Rue de Noetzlin, 91192, Gif sur Yvette, France
| | - Katherine Denby
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York Wentworth Way, York, YO10 5DD, UK
| | - Asa Ben Hur
- Department of Computer Science, Colorado State University, 1873 Campus Delivery, Fort Collins, CO, 80523-1873, USA
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, 100 East 24th St., Austin, TX, 78712-1095, USA
| | - Michael Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17 A-1090, Vienna, Austria
| | - Artur Jarmolowski
- Department of Gene Expression, Adam Mickiewicz University, Poznań, Poland
| | - Tino Koester
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Sascha Laubinger
- Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Qingshun Quinn Li
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lianfeng Gu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Andreas Wachter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Present address: Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Liming Xiong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiao-Ning Zhang
- Biology Department, School of Arts and Sciences, St. Bonaventure University, 3261 West State Road, St. Bonaventure, NY, 14778, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Center of Medical Biochemistry, Dr.-Bohr-Gasse 9/3, A-1030, Vienna, Austria
| | - Maria Kalyna
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
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18
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Cardoso-Silva CB, Aono AH, Mancini MC, Sforça DA, da Silva CC, Pinto LR, Adams KL, de Souza AP. Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2022; 13:923069. [PMID: 35845637 PMCID: PMC9280035 DOI: 10.3389/fpls.2022.923069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological functions difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements and whole-genome duplication occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis revealed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs are involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes.
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Affiliation(s)
- Cláudio Benício Cardoso-Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre Hild Aono
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Melina Cristina Mancini
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Cristina da Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Agronomy Department, Federal University of Viçosa (UFV), Viçosa, Brazil
| | - Luciana Rossini Pinto
- Sugarcane Research Advanced Centre, Agronomic Institute of Campinas (IAC/APTA), Ribeirão Preto, Brazil
| | - Keith L. Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Anete Pereira de Souza
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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19
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Co-Expression Analysis Reveals Differential Expression of Homologous Genes Associated with Specific Terpenoid Biosynthesis in Rehmannia glutinosa. Genes (Basel) 2022; 13:genes13061092. [PMID: 35741854 PMCID: PMC9222246 DOI: 10.3390/genes13061092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/29/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Terpenoids are naturally occurring compounds involved in respiration, photosynthesis, membrane fluidity, and pathogen interactions and are classified according to the structure of their carbon skeleton. Although most terpenoids possess pharmacological activity, knowledge about terpenoid metabolism in medicinal plants is insufficient. Rehmannia glutinosa (R. glutinosa) is a traditional herb that is widely used in East Asia and has been reported to contain various terpenoids. In this study, we performed a comprehensive transcriptome analysis of terpenoid metabolism in R. glutinosa using two RNA sequencing platforms: Illumina and PacBio. The results show that the sterol, saponin, iridoid, and carotenoid pathways are active in R. glutinosa. Sterol and saponin biosynthesis were mevalonate pathway dependent, whereas iridoid and carotenoid biosynthesis were methylerythritol 4-phosphate pathway dependent. In addition, we found that the homologous genes of key enzymes involved in terpenoid metabolism were expressed differentially and that the differential expression of these genes was associated with specific terpenoid biosynthesis. The different expression of homologous genes encoding acetyl-CoA acetyltransferase, 3-hydroxy-3-methylglutaryl-CoA reductase, mevalonate kinase, mevalonate diphosphate decarboxylase, farnesyl pyrophosphate synthase, squalene synthase, and squalene epoxidase was associated with sterol and saponin biosynthesis. Homologous genes encoding 1-deoxy-D-xylulose 5-phosphate synthase were also differentially expressed and were associated with carotenoid and iridoid biosynthesis. These results suggest that the biosynthesis of specific terpenoids can be regulated by the homologous of key enzymes involved in plant terpenoid metabolism.
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de Oliveira LP, Navarro BV, de Jesus Pereira JP, Lopes AR, Martins MCM, Riaño-Pachón DM, Buckeridge MS. Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane. Sci Rep 2022; 12:7516. [PMID: 35525890 PMCID: PMC9079074 DOI: 10.1038/s41598-022-11508-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.
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Affiliation(s)
- Lauana Pereira de Oliveira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Bruno Viana Navarro
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - João Pedro de Jesus Pereira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | | | - Marina C M Martins
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia Computacional, Centro de Energia Nuclear na Agricultura, Evolutiva e de Sistemas, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
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21
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Zeng Q, Hu B, Blanco AH, Zhang W, Zhao D, Martínez P, Hong Y. Full-Length Transcriptome Sequences Provide Insight Into Hermaphroditism of Freshwater Pearl Mussel Hyriopsis schlegelii. Front Genet 2022; 13:868742. [PMID: 35401664 PMCID: PMC8987123 DOI: 10.3389/fgene.2022.868742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
The freshwater mussel Hyriopsis schlegelii is a cultured bivalve in China, and the quality of the pearls produced is affected by the type of gonads. However, because of the lack of a published genome and the complexity of sex determination, research on sex reversal and development of this species is limited. In this study, Illumina RNA-seq and PacBio Isoform Sequencing (Iso-Seq) were combined to analyze the gonads of H. schlegelii. A total of 201,481 high-quality transcripts were generated. The study identified 7,922 differentially expressed genes in three comparison group (females versus males, hermaphrodites versus females, and hermaphrodites versus males). Twenty-four genes were identified as potential sex-related genes, including sox9 and wnt4 involved in sex determination, and vtg, cyp17a1 and 17β-hsd2 involved in gonadal development. We also speculated a possible pathways for the formation of hermaphroditism in H. schlegelii. The data provide a clear view of the transcriptome for H. schlegelii gonads and will be valuable in elucidating the mechanisms of gonad development.
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Affiliation(s)
- Qi Zeng
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Beijuan Hu
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
| | - Andres Hortas Blanco
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Wanchang Zhang
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Daxian Zhao
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Paulino Martínez
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Yijiang Hong
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
- *Correspondence: Yijiang Hong,
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22
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Xu L, Deng ZN, Wu KC, Malviya MK, Solanki MK, Verma KK, Pang T, Li YJ, Liu XY, Kashyap BK, Dessoky ES, Wang WZ, Huang HR. Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid. FRONTIERS IN PLANT SCIENCE 2022; 13:852886. [PMID: 35371161 PMCID: PMC8969426 DOI: 10.3389/fpls.2022.852886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/14/2022] [Indexed: 05/30/2023]
Abstract
Sugarcane is a cash crop that plays an integral part in the sugar industry. The Sustainable Sugarcane Initiative (SSI) has been adopted globally, ensuring enough and aiming for more yield, helping increase disease-free sugarcane cultivation. Single-bud seeds could be the best approach for sugarcane cultivation. Indole-3-butyric acid (IBA) is a rooting agent utilized significantly in seedling propagation. Greenhouse experiment results discovered the significant growth promotion in sugarcane seedlings and accumulation of plant hormones at 100 ppm IBA. Next, we performed transcriptomic analysis of sugarcane buds using RNA sequencing and compared their gene expression during root development due to affect of IBA (100 ppm). A total of 113,475 unigenes were annotated with an average length of 836 bp (N50 = 1,536). The comparative RNA-seq study between the control (CK) and IBA-treated (T) buds showed significant differentially expressed unigenes (494 upregulated and 2086 downregulated). The IBA influenced major biological processes including metabolic process, the cellular process, and single-organism process. For cellular component category, cell, cell part, organelle, membrane, and organelle part were mainly affected. In addition, catalytic activity and binding were primarily affected in the molecular function categories. Furthermore, the expression of genes related to plant hormones and signaling pathways was analyzed by qRT-PCR, which was consistent with the RNA-seq expression profile. This study provides new insights into the IBA response to the bud sprouting in sugarcane based on RNA sequencing, and generated information could help further research on breeding improvement of sugarcane.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zhi-Nian Deng
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kai-Chao Wu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Tian Pang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yi-Jie Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiao-Yan Liu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, India
| | - Eldessoky S. Dessoky
- Department of Plant Genetic Transformation, Agriculture Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Wei-Zan Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hai-Rong Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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23
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Comparison of the root, leaf and internode transcriptomes in Sugarcane (Saccharum spp. hybrids). CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Kasirajan L, Valiyaparambth R, Kamaraj K, Sebastiar S, Hoang NV, Athiappan S, Srinivasavedantham V, Subramanian K. Deep sequencing of suppression subtractive library identifies differentially expressed transcripts of Saccharum spontaneum exposed to salinity stress. PHYSIOLOGIA PLANTARUM 2022; 174:e13645. [PMID: 35112353 DOI: 10.1111/ppl.13645] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Saccharum spontaneum, a wild relative of sugarcane, is highly tolerant to drought and salinity. The exploitation of germplasm resources for salinity tolerance is a major thrust area in India. In this study, we utilized suppression subtractive hybridization (SSH) followed by sequencing for the identification of upregulated transcripts during salinity stress in S. spontaneum clones coming from different geographical regions of India. Our sequencing of the SSH library revealed that 95% of the transformants contained inserts of size 200-1500 bp. We have identified 314 differentially expressed transcripts in the salinity-treated samples after subtraction, which were subsequently validated by quantitative real-time polymerase chain reaction. Functional annotation and pathway analysis revealed that the upregulated transcripts were a result of protein modifications, stress, and hormone signaling along with cell wall development and lignification. The prominently upregulated transcripts included UDP glucose dehydrogenase, cellulose synthase, ribulose, cellulose synthase COBRA, leucine-rich protein, NAC domain protein, pectin esterase, ABA-responsive element binding factor 1, and heat stress protein. Our results is a step forward the understanding of the molecular response of S. spontaneum under salinity stress, which will lead to the identification of genes and transcription factors as novel targets for salinity tolerance in sugarcane.
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Affiliation(s)
- Lakshmi Kasirajan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Rabisha Valiyaparambth
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Keerthana Kamaraj
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Sheelamary Sebastiar
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Nam V Hoang
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Selvi Athiappan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | | | - Karthigeyan Subramanian
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
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Mohan C, Easterling M, Yau YY. Gene Editing Technologies for Sugarcane Improvement: Opportunities and Limitations. SUGAR TECH : AN INTERNATIONAL JOURNAL OF SUGAR CROPS & RELATED INDUSTRIES 2022; 24:369-385. [PMID: 34667393 PMCID: PMC8517945 DOI: 10.1007/s12355-021-01045-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/07/2021] [Indexed: 05/05/2023]
Abstract
Plant-based biofuels present a promising alternative to depleting non-renewable fuel resources. One of the benefits of biofuel is reduced environmental impact, including reduction in greenhouse gas emission which causes climate change. Sugarcane is one of the most important bioenergy crops. Sugarcane juice is used to produce table sugar and first-generation biofuel (e.g., bioethanol). Sugarcane bagasse is also a potential material for second-generation cellulosic biofuel production. Researchers worldwide are striving to improve sugarcane biomass yield and quality by a variety of means including biotechnological tools. This paper reviews the use of sugarcane as a feedstock for biofuel production, and gene manipulation tools and approaches, including RNAi and genome-editing tools, such as TALENs and CRISPR-Cas9, for improving its quality. The specific focus here is on CRISPR system because it is low cost, simple in design and versatile compared to other genome-editing tools. The advance of CRISPR-Cas9 technology has transformed plant research with its ability to precisely delete, insert or replace genes in recent years. Lignin is the primary material responsible for biomass recalcitrance in biofuel production. The use of genome editing technology to modify lignin composition and distribution in sugarcane cell wall has been realized. The current and potential applications of genome editing technology for sugarcane improvement are discussed. The advantages and limitations of utilizing RNAi and TALEN techniques in sugarcane improvement are discussed as well.
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Affiliation(s)
- Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mona Easterling
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
- Northeast Campus, Tulsa Community College, 3727 East Apache St, Tulsa, OK 74115 USA
| | - Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
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26
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Yan M, Jin X, Liu Y, Chen H, Ye T, Hou Z, Su Z, Chen Y, Aslam M, Qin Y, Niu X. Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane. PeerJ 2021; 9:e12298. [PMID: 34721982 PMCID: PMC8532975 DOI: 10.7717/peerj.12298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.
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Affiliation(s)
- Maokai Yan
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xingyue Jin
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Yanhui Liu
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Huihuang Chen
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Tao Ye
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Zhimin Hou
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Zhenxia Su
- Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Yingzhi Chen
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Mohammad Aslam
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yuan Qin
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China.,Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuzhou, China
| | - Xiaoping Niu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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Liu Y, Aslam M, Yao LA, Zhang M, Wang L, Chen H, Huang Y, Qin Y, Niu X. Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development. BMC Genomics 2021; 22:767. [PMID: 34706643 PMCID: PMC8549313 DOI: 10.1186/s12864-021-08090-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane. Results In the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues. Conclusions The sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08090-3.
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Affiliation(s)
- Yanhui Liu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.,College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mohammad Aslam
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Li-Ang Yao
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Man Zhang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lulu Wang
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Huihuang Chen
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youmei Huang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Qin
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China. .,College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xiaoping Niu
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
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28
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Trujillo-Montenegro JH, Rodríguez Cubillos MJ, Loaiza CD, Quintero M, Espitia-Navarro HF, Salazar Villareal FA, Viveros Valens CA, González Barrios AF, De Vega J, Duitama J, Riascos JJ. Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid. FRONTIERS IN PLANT SCIENCE 2021; 12:694859. [PMID: 34484261 PMCID: PMC8414525 DOI: 10.3389/fpls.2021.694859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 05/04/2023]
Abstract
Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. Synteny analysis between CC 01-1940 and the S. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. Analysis of RNA-Seq data from leaf and root tissue of contrasting sugarcane genotypes subjected to water stress treatments revealed 17,490 differentially expressed genes, from which 3,633 correspond to genes expressed exclusively in tolerant genotypes. We expect the resources presented here to serve as a source of information to improve the selection processes of new varieties of the breeding programs of sugarcane.
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Affiliation(s)
- Jhon Henry Trujillo-Montenegro
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
- Research Group in Bioinformatics, Department of Computer Science, Faculty of Engineering, Universidad Del Valle,Cali, Colombia
| | - María Juliana Rodríguez Cubillos
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Faculty of Engineering, Universidad de los Andes, Bogotá, Colombia
| | | | - Manuel Quintero
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
| | | | | | | | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Faculty of Engineering, Universidad de los Andes, Bogotá, Colombia
| | - José De Vega
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - John J. Riascos
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
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Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance. Sci Rep 2021; 11:15730. [PMID: 34344928 PMCID: PMC8333424 DOI: 10.1038/s41598-021-95116-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/19/2021] [Indexed: 11/10/2022] Open
Abstract
Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.
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Full-length transcriptome assembly of Andrias davidianus (Amphibia: Caudata) skin via hybrid sequencing. Biosci Rep 2021; 41:229267. [PMID: 34282833 PMCID: PMC8329649 DOI: 10.1042/bsr20210511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The Chinese giant salamander, Andrias davidianus, is the largest amphibian species in the world; it is thus an economically and ecologically important species. The skin of A. davidianus exhibits complex adaptive structural and functional adaptations to facilitate survival in aquatic and terrestrial ecosystems. Here, we report the first full-length amphibian transcriptome from the dorsal skin of A. davidianus, which was assembled using hybrid sequencing and the PacBio and Illumina platforms. A total of 153,038 transcripts were hybrid assembled (mean length of 2039 bp and N50 of 2172 bp), and 133,794 were annotated in at least one database (nr, Swiss-Prot, KEGG, KOGs, GO, and nt). A total of 58,732, 68,742, and 115,876 transcripts were classified into 24 KOG categories, 1903 GO term categories, and 46 KEGG pathways (level 2), respectively. A total of 207,627 protein-coding regions, 785 transcription factors, 27,237 potential long non-coding RNAs, and 8299 simple sequence repeats were also identified. The hybrid-assembled transcriptome recovered more full-length transcripts, had a higher N50 contig length, and a higher annotation rate of unique genes compared with that assembled in previous studies using next-generation sequencing. The high-quality full-length reference gene set generated in this study will help elucidate the genetic characteristics of A. davidianus skin and aid the identification of functional skin proteins.
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Sun J, Chen T, Tao J. Single molecule, full-length transcript sequencing provides insight into the TPS gene family in Paeonia ostii. PeerJ 2021; 9:e11808. [PMID: 34316413 PMCID: PMC8286706 DOI: 10.7717/peerj.11808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/27/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The tree peony (Paeonia section Moutan DC), one of the traditional famous flowers with both ornamental and medicinal value, was widely used in China. Surprisingly little is known about the full-length transcriptome sequencing in tree peony, limiting the research on its gene function and molecular mechanism. The trehalose phosphate phosphatase (TPS) family genes has been found to affect plant growth and development and the function of TPS genes in Paeonia ostii is unknown. METHODS In our study, we performed single molecule, full-length transcript sequencing in P. ostii. 10 TPS family members were identified from PacBio sequencing for bioinformatics analysis and transcriptional expression analysis. RESULTS A total of 230,736 reads of insert (ROI) sequences and 114,215 full-Length non-chimeric reads (FLNC) were obtained for further ORFs and transcription factors prediction, SSR analysis and lncRNA identification. NR, Swissprot, GO, COG, KOG, Pfam and KEGG databases were used to obtain annotation information of transcripts. 10 TPS family members were identified with molecular weights between 48.0 to 108.5 kD and isoelectric point between 5.61 to 6.37. Furthermore, we found that TPS family members contain conserved TPP or TPS domain. Based on phylogenetic tree analysis, PoTPS1 protein was highly similar to AtTPS1 protein in Arabidopsis. Finally, we analyzed the expression levels of all TPS genes in P. ostii and found PoTPS5 expressed at the highest level. In conclusion, this study combined the results of the transcriptome to systematically analyze the 10 TPS family members, and sets a framework for further research of this important gene family in development of tree peony.
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Affiliation(s)
- Jing Sun
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Tian Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Jun Tao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
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Li X, Wu J, Xiao X, Rong Y, Yang H, Li J, Zhou Q, Zhou W, Shi J, Qi H, Du H. Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq. DNA Res 2021; 28:6275749. [PMID: 33989386 PMCID: PMC8320875 DOI: 10.1093/dnares/dsab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/11/2021] [Indexed: 11/30/2022] Open
Abstract
The Tibetan Schizothoracinae fish Gymnocypris przewalskii has the ability to adapt to the extreme plateau environment, making it an ideal biological material for evolutionary biology research. However, the lack of well-annotated reference genomes has limited the study of the molecular genetics of G. przewalskii. To characterize its transcriptome features, we first used long-read sequencing technology in combination with RNA-seq for transcriptomic analysis. A total of 159,053 full-length (FL) transcripts were captured by Iso-Seq, having a mean length of 3,445 bp with N50 value of 4,348. Of all FL transcripts, 145,169 were well-annotated in the public database and 134,537 contained complete open reading frames. There were 4,149 pairs of alternative splicing events, of which three randomly selected were defined by RT–PCR and sequencing, and 13,293 long non-coding RNAs detected, based on all-vs.-all BLAST. A total of 118,185 perfect simple sequence repeats were identified from FL transcripts. The FL transcriptome might provide basis for further research of G. przewalskii.
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Affiliation(s)
- Xindan Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Jinming Wu
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Xinping Xiao
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Yifeng Rong
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Haile Yang
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Junyi Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Qiong Zhou
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Weiguo Zhou
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Jianquan Shi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hongfang Qi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hao Du
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China.,The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
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Mei M, Wei J, Ai W, Zhang L, Lu XJ. Integrated RNA and miRNA sequencing analysis reveals a complex regulatory network of Magnolia sieboldii seed germination. Sci Rep 2021; 11:10842. [PMID: 34035372 PMCID: PMC8149418 DOI: 10.1038/s41598-021-90270-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 04/20/2021] [Indexed: 02/04/2023] Open
Abstract
Magnolia sieboldii K. Koch (M. sieboldii) is a deciduous Chinese tree species of the Magnoliaceae family with high ornamental, medicinal, and economic benefits. The germination of M. sieboldii seeds under natural conditions is extremely difficult, thereby hindering the cultivation and breeding of this important species. The molecular mechanisms underlying M. sieboldii seed germination remain unclear due to the lack of genomic and transcriptomic resources. Here, we integrated both mRNA and miRNA sequencing to identify the genes and pathways related to M. sieboldii germination. A comprehensive full-length transcriptome containing 158,083 high-quality unigenes was obtained by single-molecule real-time (SMRT) sequencing technology. We identified a total of 13,877 genes that were differentially expressed between non-germinated and germinated seeds. These genes were mainly involved in plant hormone signal transduction and diverse metabolic pathways such as those involving lipids, sugars, and amino acids. Our results also identified a complex regulatory network between miRNAs and their target genes. Taken together, we present the first transcriptome of M. sieboldii and provide key genes and pathways associated with seed germination for further characterization. Future studies of the molecular basis of seed germination will facilitate the genetic improvement M. sieboldii.
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Affiliation(s)
- Mei Mei
- grid.412557.00000 0000 9886 8131Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jun Wei
- grid.9227.e0000000119573309Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wanfeng Ai
- grid.412557.00000 0000 9886 8131Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Lijie Zhang
- grid.412557.00000 0000 9886 8131Department of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Xiu-jun Lu
- grid.412557.00000 0000 9886 8131Department of Forestry, Shenyang Agricultural University, Shenyang, China
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Yan H, Zhou H, Luo H, Fan Y, Zhou Z, Chen R, Luo T, Li X, Liu X, Li Y, Qiu L, Wu J. Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development. BMC PLANT BIOLOGY 2021; 21:228. [PMID: 34022806 PMCID: PMC8140441 DOI: 10.1186/s12870-021-02989-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/27/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. RESULTS Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. CONCLUSIONS Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.
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Affiliation(s)
- Haifeng Yan
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Huiwen Zhou
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Hanmin Luo
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Yegeng Fan
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Zhongfeng Zhou
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Rongfa Chen
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Ting Luo
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Xujuan Li
- Sugarcane Research Institute of Yunnan Academy of Agricultural Sciences, East Lingquan Road 172, Kaiyun, 661600, Yunnan, China
| | - Xinlong Liu
- Sugarcane Research Institute of Yunnan Academy of Agricultural Sciences, East Lingquan Road 172, Kaiyun, 661600, Yunnan, China
| | - Yangrui Li
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China
| | - Lihang Qiu
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China.
| | - Jianming Wu
- Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, and Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, East Daxue Road 172, Nanning, 530004, Guangxi, China.
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Hodgson-Kratky K, Perlo V, Furtado A, Choudhary H, Gladden JM, Simmons BA, Botha F, Henry RJ. Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. PLANT MOLECULAR BIOLOGY 2021; 106:173-192. [PMID: 33738678 DOI: 10.1007/s11103-021-01136-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/02/2021] [Indexed: 05/11/2023]
Abstract
A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition. Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.
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Affiliation(s)
- K Hodgson-Kratky
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - V Perlo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - H Choudhary
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - J M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - F Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.
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Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia. Sci Rep 2021; 11:8734. [PMID: 33888729 PMCID: PMC8062547 DOI: 10.1038/s41598-021-87538-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/22/2021] [Indexed: 01/22/2023] Open
Abstract
Paulownia catalpifolia is an important, fast-growing timber species known for its high density, color and texture. However, few transcriptomic and genetic studies have been conducted in P. catalpifolia. In this study, single-molecule real-time sequencing technology was applied to obtain the full-length transcriptome of P. catalpifolia leaves treated with varying degrees of drought stress. The sequencing data were then used to search for microsatellites, or simple sequence repeats (SSRs). A total of 28.83 Gb data were generated, 25,969 high-quality (HQ) transcripts with an average length of 1624 bp were acquired after removing the redundant reads, and 25,602 HQ transcripts (98.59%) were annotated using public databases. Among the HQ transcripts, 16,722 intact coding sequences, 149 long non-coding RNAs and 179 alternative splicing events were predicted, respectively. A total of 7367 SSR loci were distributed throughout 6293 HQ transcripts, of which 763 complex SSRs and 6604 complete SSRs. The SSR appearance frequency was 28.37%, and the average distribution distance was 5.59 kb. Among the 6604 complete SSR loci, 1-3 nucleotide repeats were dominant, occupying 97.85% of the total SSR loci, of which mono-, di- and tri-nucleotide repeats were 44.68%, 33.86% and 19.31%, respectively. We detected 112 repeat motifs, of which A/T (42.64%), AG/CT (12.22%), GA/TC (9.63%), GAA/TTC (1.57%) and CCA/TGG (1.54%) were most common in mono-, di- and tri-nucleotide repeats, respectively. The length of the repeat SSR motifs was 10-88 bp, and 4997 (75.67%) were ≤ 20 bp. This study provides a novel full-length transcriptome reference for P. catalpifolia and will facilitate the identification of germplasm resources and breeding of new drought-resistant P. catalpifolia varieties.
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Zhao C, He L, Xia H, Zhou X, Geng Y, Hou L, Li P, Li G, Zhao S, Ma C, Tang R, Pandey MK, Varshney RK, Wang X. De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses. Genomics 2021; 113:1579-1588. [PMID: 33819563 DOI: 10.1016/j.ygeno.2021.03.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/21/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
The perennial ornamental peanut Arachis glabrata represents one of the most adaptable wild Arachis species. This study used PacBio combined with BGISEQ-500 RNA-seq technology to study the transcriptome and gene expression dynamics of A. glabrata. Of the total 109,747 unique transcripts obtained, >90,566 transcripts showed significant homology to known proteins and contained the complete coding sequence (CDS). RNA-seq revealed that 1229, 1039, 1671, 3923, 1521 and 1799 transcripts expressed specifically in the root, stem, leaf, flower, peg and pod, respectively. We also identified thousands of differentially expressed transcripts in response to drought, salt, cold and leaf spot disease. Furthermore, we identified 30 polyphenol oxidase encoding genes associated with the quality of forage, making A. glabrata suitable as a forage crop. Our findings presented the first transcriptome study of A. glabrata which will facilitate genetic and genomics studies and lays the groundwork for a deeper understanding of the A. glabrata genome.
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Affiliation(s)
- Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China.
| | - Liangqiong He
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, People's Republic of China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Ximeng Zhou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yun Geng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guanghui Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Ronghua Tang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, People's Republic of China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China.
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Wang L, Zhu P, Mo Q, Luo W, Du Z, Jiang J, Yang S, Zhao L, Gong Q, Wang Y. Comprehensive analysis of full-length transcriptomes of Schizothorax prenanti by single-molecule long-read sequencing. Genomics 2021; 114:456-464. [PMID: 33516848 DOI: 10.1016/j.ygeno.2021.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Schizothorax prenanti (S. prenanti) is one of the most important aquaculture species in the southwest of China. However, information of the full-length transcripts in S. prenanti remains unknown. In this study, single-molecule real-time (SMRT) sequencing was performed to generate full-length transcriptomes of S.prenanti. In total, 23.26 Gb of clean reads were generated. A total of 312,587 circular consensus sequences (CCS) were obtained with average lengths of 2634 bp and 84.16% (270,662) of CCS were full-length non-chimeric reads. After being corrected with Illumina library sequencing, 18,005 contigs were obtained, with 17,797 (98.81%) successfully annotated in eight public databases, including 15,839 complete open reading frames (ORFs) with an average length of 1330 bp. Furthermore, a total of 4152 alternative splicing (AS) events and 250 long non-coding RNA (lncRNA) transcripts were detected. Additionally, a total of 1129 putative transcription factors (TFs) members from 56 TF families and 11,660 simple sequence repeats (SSRs) were identified. This study provided a valuable resource of full-length transcripts for further research on S. prenanti.
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Affiliation(s)
- Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Peng Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Qilang Mo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Zongjun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Liulan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Quan Gong
- Fisheries institute, Sichuan Academy of Agricultural Sciences, Chengdu 611713, Sichuan, PR China
| | - Yan Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China.
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Tu Z, Shen Y, Wen S, Liu H, Wei L, Li H. A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2021; 12:705321. [PMID: 34367224 PMCID: PMC8343429 DOI: 10.3389/fpls.2021.705321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/28/2021] [Indexed: 05/08/2023]
Abstract
Liriodendron chinense is an economically and ecologically important deciduous tree species. Although the reference genome has been revealed, alternative polyadenylation (APA), transcription factors (TFs), long non-coding RNAs (lncRNAs), and co-expression networks of tissue-specific genes remain incompletely annotated. In this study, we used the bracts, petals, sepals, stamens, pistils, leaves, and shoot apex of L. chinense as materials for hybrid sequencing. On the one hand, we improved the annotation of the genome. We detected 13,139 novel genes, 7,527 lncRNAs, 1,791 TFs, and 6,721 genes with APA sites. On the other hand, we found that tissue-specific genes play a significant role in maintaining tissue characteristics. In total, 2,040 tissue-specific genes were identified, among which 9.2% of tissue-specific genes were affected by APA, and 1,809 tissue-specific genes were represented in seven specific co-expression modules. We also found that bract-specific hub genes were associated plant defense, leaf-specific hub genes were involved in energy metabolism. Moreover, we also found that a stamen-specific hub TF Lchi25777 may be involved in the determination of stamen identity, and a shoot-apex-specific hub TF Lchi05072 may participate in maintaining meristem characteristic. Our study provides a landscape of APA, lncRNAs, TFs, and tissue-specific gene co-expression networks in L. chinense that will improve genome annotation, strengthen our understanding of transcriptome complexity, and drive further research into the regulatory mechanisms of tissue-specific genes.
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Affiliation(s)
- Zhonghua Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yufang Shen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoying Wen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huanhuan Liu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lingmin Wei
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Huogen Li,
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Modern Approaches for Transcriptome Analyses in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:11-50. [DOI: 10.1007/978-3-030-80352-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Marquardt A, Henry RJ, Botha FC. Effect of sugar feedback regulation on major genes and proteins of photosynthesis in sugarcane leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:321-333. [PMID: 33250321 DOI: 10.1016/j.plaphy.2020.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
Productivity of sugarcane (Saccharum spp.) relies upon sucrose production in leaves and movement to sinks. The feedback regulatory effect of sugar upon photosynthesis balances this process involving Phosphoenolpyruvate carboxylase (PEPCase) and Rubisco where greater understanding in this area may allow manipulation to achieve higher yields. Accumulation of sucrose in leaves and decreased photosynthesis are early symptoms of the condition called yellow canopy syndrome (YCS) in sugarcane, which presents as a system in which to study sucrose feedback regulation. This work investigates changes in gene expression and protein abundance which coincide with the sugar accumulation in the leaves of YCS symptomatic sugarcane. During the early-stage of sugar accumulation, the levels of the Photosystem II core protein D1, and PsbQ of the oxygen-evolving complex decreased significantly. Transcript levels of these proteins also decreased, suggesting both nuclear and chloroplast gene expression were affected early in sugar build-up of YCS development. Transcript level of primary carbon fixation reactions enzyme NADP malate dehydrogenase was especially downregulated. However, PEPCase, decarboxylation and re-fixation (Rubisco) enzymes were not negatively regulated at the transcript or protein abundance level. Phosphoenolpyruvate carboxykinase was upregulated in both gene expression and protein abundance. The Calvin cycle in the bundle sheath was sensitive through the CP12 protein. Two isoforms of CP12 were found, one of which showed downregulation which coincided with a decrease in CP12 protein. This suggests transcript and protein decrease of PEPCase and Rubisco may be secondary regulation points of the sugar feedback regulation process upon photosynthesis in sugarcane leaves.
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Affiliation(s)
- Annelie Marquardt
- Sugar Research Australia, PO Box 68, Indooroopilly, Qld, 4068, Australia; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, 4067, Australia.
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, 4067, Australia
| | - Frederik C Botha
- Sugar Research Australia, PO Box 68, Indooroopilly, Qld, 4068, Australia; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, 4067, Australia
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Khanbo S, Tangphatsornruang S, Piriyapongsa J, Wirojsirasak W, Punpee P, Klomsa-Ard P, Ukoskit K. Candidate gene association of gene expression data in sugarcane contrasting for sucrose content. Genomics 2020; 113:229-237. [PMID: 33321201 DOI: 10.1016/j.ygeno.2020.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022]
Abstract
Association mapping of gene expression data, generated from transcriptome and proteome studies, provides a means of understanding the functional significance and trait association potential of candidate genes. In this study, we applied candidate gene association mapping to validate sugarcane genes, using data from the starch and sucrose metabolism pathway, transcriptome, and proteome. We performed multiplex PCR targeted amplicon sequencing of 109 candidate genes, using NGS technology. A range of statistical models, both single-locus and multi-locus, were compared for minimization of false positives in association mapping of four sugar-related traits with different heritability. The Fixed and random model Circulating Probability Unification model effectively suppressed false positives for both low- and high-heritability traits. We identified favorable alleles of the candidate genes involved in signalling and transcriptional regulation. The results will support genetic improvement of sugarcane and may help clarify the genetic architecture of sugar-related traits.
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Affiliation(s)
- Supaporn Khanbo
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jittima Piriyapongsa
- National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Warodom Wirojsirasak
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Prapat Punpee
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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Shi K, Li J, Lv J, Liu P, Li J, Li S. Full-length transcriptome sequences of ridgetail white prawn Exopalaemon carinicauda provide insight into gene expression dynamics during thermal stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141238. [PMID: 32799022 DOI: 10.1016/j.scitotenv.2020.141238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/10/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Marine heat waves and extreme high temperature become more frequent and intense in these years, which affected the survival of aquaculture animals. The ridgetail white prawn Exopalaemon carinicauda is an important economic species in eastern China, which has remarkable thermal tolerance. However, there has been little study of its thermal-adaptation mechanisms due to the complex genetic structure and unknown genome. To better understand the molecular mechanisms of E. carinicauda to adapt to the changing temperature, a combination of Illumina-based short reads RNA-seq and single molecule real-time-based full-length transcriptome sequencing was used in this study. In total, 17,212 unigenes from high-quality transcripts of E. carinicauda were generated and 14,663 complete ORFs were detected with an average length of 1980 bp. In addition, the transcriptome profiles of E. carinicauda treated with 34 °C heat stress for 6 and 24 h were analyzed. These differentially expressed genes were primarily enriched in oxidation-reduction process (Gene Ontology enrichment, GO) and the pathways of starch and sucrose metabolism (Kyoto Encyclopedia of Genes and Genomes enrichment, KEGG) after 6 h thermal stress, which indicated that E. carinicauda was suffering the attack by reactive oxygen species. After 24 h thermal stress, these differentially expressed genes were enriched in the pathway of lysosome, glycine, serine and threonine metabolism, fatty acid metabolism (KEGG), which indicated the oxidative stress was decreased. Interestingly, 40 genes for hemocyanin were found to be downregulated after 6 h heat stress, which indicated that the immunocompetence of E. carinicauda decreased after short term thermal stress (6 h). After 24 h thermal stress, E. carinicauda showed transcriptional adaptation to high temperature by upregulating of 11 genes encoding molecular chaperones, including HSP40 and HSP90 which were firstly reported to be related to thermal stress in E. carinicauda. These results promote a better understanding of the thermal-adaptation mechanism of E. carinicauda.
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Affiliation(s)
- Kunpeng Shi
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jitao Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jianjian Lv
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.
| | - Sedong Li
- Guangdong Evergreen Ltd. Corporation, Zhanjiang, PR China
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Aono AH, Costa EA, Rody HVS, Nagai JS, Pimenta RJG, Mancini MC, Dos Santos FRC, Pinto LR, Landell MGDA, de Souza AP, Kuroshu RM. Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance. Sci Rep 2020; 10:20057. [PMID: 33208862 PMCID: PMC7676261 DOI: 10.1038/s41598-020-77063-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
Sugarcane is an economically important crop, but its genomic complexity has hindered advances in molecular approaches for genetic breeding. New cultivars are released based on the identification of interesting traits, and for sugarcane, brown rust resistance is a desirable characteristic due to the large economic impact of the disease. Although marker-assisted selection for rust resistance has been successful, the genes involved are still unknown, and the associated regions vary among cultivars, thus restricting methodological generalization. We used genotyping by sequencing of full-sib progeny to relate genomic regions with brown rust phenotypes. We established a pipeline to identify reliable SNPs in complex polyploid data, which were used for phenotypic prediction via machine learning. We identified 14,540 SNPs, which led to a mean prediction accuracy of 50% when using different models. We also tested feature selection algorithms to increase predictive accuracy, resulting in a reduced dataset with more explanatory power for rust phenotypes. As a result of this approach, we achieved an accuracy of up to 95% with a dataset of 131 SNPs related to brown rust QTL regions and auxiliary genes. Therefore, our novel strategy has the potential to assist studies of the genomic organization of brown rust resistance in sugarcane.
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Affiliation(s)
- Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Estela Araujo Costa
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Hugo Vianna Silva Rody
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - James Shiniti Nagai
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Ricardo José Gonzaga Pimenta
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Melina Cristina Mancini
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Luciana Rossini Pinto
- Advanced Center of Sugarcane Agrobusiness Technological Research, Agronomic Institute of Campinas (IAC), Ribeirão Preto, SP, Brazil
| | | | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Department of Plant Biology, Institute of Biology (IB), University of Campinas (UNICAMP), Campinas, SP, Brazil.
| | - Reginaldo Massanobu Kuroshu
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil.
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Liu J, Wang J, Xiao X, Lai X, Dai D, Zhang X, Zhu X, Zhao Z, Wang J, Li Z. A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model. BMC Genomics 2020; 21:753. [PMID: 33208104 PMCID: PMC7677778 DOI: 10.1186/s12864-020-07008-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background The emergence of the third generation sequencing technology, featuring longer read lengths, has demonstrated great advancement compared to the next generation sequencing technology and greatly promoted the biological research. However, the third generation sequencing data has a high level of the sequencing error rates, which inevitably affects the downstream analysis. Although the issue of sequencing error has been improving these years, large amounts of data were produced at high sequencing errors, and huge waste will be caused if they are discarded. Thus, the error correction for the third generation sequencing data is especially important. The existing error correction methods have poor performances at heterozygous sites, which are ubiquitous in diploid and polyploidy organisms. Therefore, it is a lack of error correction algorithms for the heterozygous loci, especially at low coverages. Results In this article, we propose a error correction method, named QIHC. QIHC is a hybrid correction method, which needs both the next generation and third generation sequencing data. QIHC greatly enhances the sensitivity of identifying the heterozygous sites from sequencing errors, which leads to a high accuracy on error correction. To achieve this, QIHC established a set of probabilistic models based on Bayesian classifier, to estimate the heterozygosity of a site and makes a judgment by calculating the posterior probabilities. The proposed method is consisted of three modules, which respectively generates a pseudo reference sequence, obtains the read alignments, estimates the heterozygosity the sites and corrects the read harboring them. The last module is the core module of QIHC, which is designed to fit for the calculations of multiple cases at a heterozygous site. The other two modules enable the reads mapping to the pseudo reference sequence which somehow overcomes the inefficiency of multiple mappings that adopt by the existing error correction methods. Conclusions To verify the performance of our method, we selected Canu and Jabba to compare with QIHC in several aspects. As a hybrid correction method, we first conducted a groups of experiments under different coverages of the next-generation sequencing data. QIHC is far ahead of Jabba on accuracy. Meanwhile, we varied the coverages of the third generation sequencing data and compared performances again among Canu, Jabba and QIHC. QIHC outperforms the other two methods on accuracy of both correcting the sequencing errors and identifying the heterozygous sites, especially at low coverage. We carried out a comparison analysis between Canu and QIHC on the different error rates of the third generation sequencing data. QIHC still performs better. Therefore, QIHC is superior to the existing error correction methods when heterozygous sites exist.
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Affiliation(s)
- Jiaqi Liu
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China. .,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.
| | - Xiao Xiao
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Xin Lai
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Daocheng Dai
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Xuanping Zhang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Xiaoyan Zhu
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Zhongmeng Zhao
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Shaanxi Engineering Research Center of Medical and Health Big Data, School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China
| | - Juan Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China.,Annoroad Gene Institute, Beijing, 100176, China
| | - Zhimin Li
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710048, China. .,Annoroad Gene Institute, Beijing, 100176, China.
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Schaarschmidt S, Fischer A, Lawas LMF, Alam R, Septiningsih EM, Bailey-Serres J, Jagadish SVK, Huettel B, Hincha DK, Zuther E. Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. Int J Mol Sci 2020; 21:ijms21218148. [PMID: 33142722 PMCID: PMC7663775 DOI: 10.3390/ijms21218148] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 01/05/2023] Open
Abstract
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.
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Affiliation(s)
- Stephanie Schaarschmidt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Lovely Mae F. Lawas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - S. V. Krishna Jagadish
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;
| | - Dirk K. Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
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47
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Kuo RI, Cheng Y, Zhang R, Brown JWS, Smith J, Archibald AL, Burt DW. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics 2020; 21:751. [PMID: 33126848 PMCID: PMC7596999 DOI: 10.1186/s12864-020-07123-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Background The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide additional evidence for rare transcripts and genes such as mono-exonic and non-coding genes that were previously either undetectable or impossible to differentiate from sequencing noise. Results We developed the Transcriptome Annotation by Modular Algorithms (TAMA) software to leverage the power of long read transcript sequencing and address the issues with current data processing pipelines. TAMA achieved high sensitivity and precision for gene and transcript model predictions in both reference guided and unguided approaches in our benchmark tests using simulated Pacific Biosciences (PacBio) and Nanopore sequencing data and real PacBio datasets. By analyzing PacBio Sequel II Iso-Seq sequencing data of the Universal Human Reference RNA (UHRR) using TAMA and other commonly used tools, we found that the convention of using alignment identity to measure error correction performance does not reflect actual gain in accuracy of predicted transcript models. In addition, inter-read error correction can cause major changes to read mapping, resulting in potentially over 6 K erroneous gene model predictions in the Iso-Seq based human genome annotation. Using TAMA’s genome assembly based error correction and gene feature evidence, we predicted 2566 putative novel non-coding genes and 1557 putative novel protein coding gene models. Conclusions Long read transcript sequencing data has the power to identify novel genes within the highly annotated human genome. The use of parameter tuning and extensive output information of the TAMA software package allows for in depth exploration of eukaryotic transcriptomes. We have found long read data based evidence for thousands of unannotated genes within the human genome. More development in sequencing library preparation and data processing are required for differentiating sequencing noise from real genes in long read RNA sequencing data.
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Affiliation(s)
- Richard I Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.
| | - Yuanyuan Cheng
- The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee, Scotland, UK.,Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
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48
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Chen MX, Zhang KL, Zhang M, Das D, Fang YM, Dai L, Zhang J, Zhu FY. Alternative splicing and its regulatory role in woody plants. TREE PHYSIOLOGY 2020; 40:1475-1486. [PMID: 32589747 DOI: 10.1093/treephys/tpaa076] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 05/22/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional process to enhance proteome diversity in eukaryotic organisms. In plants, numerous reports have primarily focused on AS analysis in model plant species or herbaceous plants, leading to a notable lack of research on AS in woody plants. More importantly, emerging evidence indicates that many important traits, including wood formation and stress resistance, in woody plants are controlled by AS. In this review article, we summarize the current progress of all kinds of AS studies in different tree species at various stages of development and in response to various stresses, revealing the significant role played by AS in woody plants, as well as the similar properties and differential regulation within their herbaceous counterparts. Furthermore, we propose several potential strategies to facilitate the functional characterization of splicing factors in woody plants and evaluate a general pipeline for the systematic characterization of splicing isoforms in a complex AS regulatory network. The utilization of genetic studies and high-throughput omics integration approaches to analyze AS genes and splicing factors is likely to further advance our understanding of AS modulation in woody plants.
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Affiliation(s)
- Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Debatosh Das
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Yan-Ming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lei Dai
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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49
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de Mello US, Vidigal PMP, Vital CE, Tomaz AC, de Figueiredo M, Peternelli LA, Barbosa MHP. An overview of the transcriptional responses of two tolerant and susceptible sugarcane cultivars to borer (Diatraea saccharalis) infestation. Funct Integr Genomics 2020; 20:839-855. [PMID: 33068201 DOI: 10.1007/s10142-020-00755-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023]
Abstract
Diatraea saccharalis constitutes a threat to the sugarcane productivity, and obtaining borer tolerant cultivars is an alternative method of control. Although there are studies about the relationship between the interaction of D. saccharalis with sugarcane, little is known about the molecular and genomic basis of defense mechanisms that confer tolerance to sugarcane cultivars. Here, we analyzed the transcriptional profile of two sugarcane cultivars in response to borer attack, RB867515 and SP80-3280, which are considered tolerant and sensitive to the borer attack, respectively. A sugarcane genome and transcriptome were used for read mapping. Differentially expressed transcripts and genes were identified and termed to as DETs and DEGs, according to the sugarcane database adopted. A total of 745 DETs and 416 DEGs were identified (log2|ratio| > 0.81; FDR corrected P value ≤ 0.01) after borer infestation. Following annotation of up- and down-regulated DETs and DEGs by similarity searches, the sugarcane cultivars demonstrated an up-regulation of jasmonic acid (JA), ethylene (ET), and defense protein genes, as well as a down-regulation of pathways involved in photosynthesis and energy metabolism. The expression analysis also highlighted that RB867515 cultivar is possibly more transcriptionally activated after 12 h from infestation than SP80-3280, which could imply in quicker responses by probably triggering more defense-related genes and mediating metabolic pathways to cope with borer attack.
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Affiliation(s)
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa (UFV), Viçosa, Minas Gerais, Brazil.
| | - Camilo Elber Vital
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa (UFV), Viçosa, Minas Gerais, Brazil
| | - Adriano Cirino Tomaz
- Department of Agronomy, Universidade Federal de Viçosa (UFV), Viçosa, Minas Gerais, Brazil
| | - Milene de Figueiredo
- Department of Agronomy, Universidade Federal de Viçosa (UFV), Viçosa, Minas Gerais, Brazil
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50
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Li L, Liu H, Wen W, Huang C, Li X, Xiao S, Wu M, Shi J, Xu D. Full Transcriptome Analysis of Callus Suspension Culture System of Bletilla striata. Front Genet 2020; 11:995. [PMID: 33193583 PMCID: PMC7593603 DOI: 10.3389/fgene.2020.00995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Background Bletilla striata has been widely used in the pharmacology industry. To effectively produce the secondary metabolites through suspension cultured cells of B. striata, it is important to exploring the full-length transcriptome data and the genes related to cell growth and chemical producing of all culture stages. We applied a combination of Real-Time Sequencing of Single Molecule (SMRT) and second-generation sequencing (SGS) to generate the complete and full-length transcriptome of B. striata suspension cultured cells. Methods The B. striata transcriptome was formed in de novo way by using PacBio isoform sequencing (Iso-Seq) on a pooled RNA sample derived from 23 samples of 10 culture stages, to explore the potential for capturing full-length transcript isoforms. All unigenes were obtained after splicing, assembling, and clustering, and corrected by the SGS results. The obtained unigenes were compared with the databases, and the functions were annotated and classified. Results and conclusions A total of 100,276 high-quality full-length transcripts were obtained, with an average length of 2530 bp and an N50 of 3302 bp. About 52% of total sequences were annotated against the Gene Ontology, 53,316 unigenes were hit by KOG annotations and divided into 26 functional categories, 80,020 unigenes were mapped by KEGG annotations and clustered into 363 pathways. Furthermore, 15,133 long-chain non-coding RNAs (lncRNAs) were detected. And 68,996 coding sequences were identified based on SSR analysis, among which 31 pairs of primers selected at random were amplified and obtained stable bands. In conclusion, our results provide new full-length transcriptome data and genetic resources for identifying growth and metabolism-related genes, which provide a solid foundation for further research on its growth regulation mechanisms and genetic engineering breeding mechanisms of B. striata.
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Affiliation(s)
- Lin Li
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Houbo Liu
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Weie Wen
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Ceyin Huang
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Xiaomei Li
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Shiji Xiao
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Mingkai Wu
- Institute of Modern Chinese Herbal of Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junhua Shi
- The Department of Imaging, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Delin Xu
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
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