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Hu H, Dong B, Fan X, Wang M, Wang T, Liu Q. Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2023; 16:11. [PMID: 36849744 PMCID: PMC9971424 DOI: 10.1186/s12284-023-00627-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit for further understanding their underlying evolutionary mechanism in plants. Using internal correspondence analysis (ICA), we reveal a significant difference in synonymous codon usage between SEGs and multiple-exon genes (MEGs) in rice. But the effect is weak, accounting for only 2.61% of the total codon usage variability. SEGs and MEGs contain remarkably different base compositions, and are under clearly differential selective constraints, with the former having higher GC content, and evolving relatively faster during evolution. In the group of SEGs, the variability in synonymous codon usage among genes is partially due to the variations in GC content, gene function, and gene expression level, which accounts for 22.03%, 5.99%, and 3.32% of the total codon usage variability, respectively. Therefore, mutational bias and natural selection should work on affecting the synonymous codon usage of SEGs in rice. These findings may deepen our knowledge for the mechanisms of origination, differentiation and regulation of SEGs in plants.
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Affiliation(s)
- Huan Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Boran Dong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Xiaoji Fan
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China
| | - Meixia Wang
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China
| | - Tingzhang Wang
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China.
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China.
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2
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Liu Y, Wang Z, Wu X, Zhu J, Luo H, Tian D, Li C, Luo J, Zhao W, Hao H, Jing HC. SorGSD: updating and expanding the sorghum genome science database with new contents and tools. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:165. [PMID: 34344425 PMCID: PMC8336335 DOI: 10.1186/s13068-021-02016-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/24/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C4 model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has been accumulated for sorghum. Integrating this information may accelerate genetic research and improve molecular breeding for sorghum agronomic traits. RESULTS We updated the Sorghum Genome SNP Database (SorGSD) by adding new data, new features and renamed it to Sorghum Genome Science Database (SorGSD). In comparison with the original version SorGSD, which contains SNPs from 48 sorghum accessions mapped to the reference genome BTx623 (v2.1), the new version was expanded to 289 sorghum lines with both single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs), which were aligned to the newly assembled and annotated sorghum genome BTx623 (v3.1). Moreover, phenotypic data and panicle pictures of critical accessions were provided in the new version. We implemented new tools including ID Conversion, Homologue Search and Genome Browser for analysis and updated the general information related to sorghum research, such as online sorghum resources and literature references. In addition, we deployed a new database infrastructure and redesigned a new user interface as one of the Genome Variation Map databases. The new version SorGSD is freely accessible online at http://ngdc.cncb.ac.cn/sorgsd/ . CONCLUSIONS SorGSD is a comprehensive integration with large-scale genomic variation, phenotypic information and incorporates online data analysis tools for data mining, genome navigation and analysis. We hope that SorGSD could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis.
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Affiliation(s)
- Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhonghuang Wang
- University of Chinese Academy of Sciences, Beijing, 100049 China
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Junwei Zhu
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Dongmei Tian
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Cuiping Li
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jingchu Luo
- College of Life Sciences and Center for Bioinformatics, Peking University, Beijing, 100871 China
| | - Wenming Zhao
- University of Chinese Academy of Sciences, Beijing, 100049 China
- China National Center for Bioinformation, Beijing, 100101 China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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3
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Chen T, Meng D, Liu X, Cheng X, Wang H, Jin Q, Xu X, Cao Y, Cai Y. RIGD: A Database for Intronless Genes in the Rosaceae. Front Genet 2020; 11:868. [PMID: 32849839 PMCID: PMC7426402 DOI: 10.3389/fgene.2020.00868] [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: 01/23/2020] [Accepted: 07/16/2020] [Indexed: 11/13/2022] Open
Abstract
Most eukaryotic genes are interrupted by one or more introns, and only prokaryotic genomes are composed of mainly single-exon genes without introns. Due to the absence of introns, intronless genes in eukaryotes have become important materials for comparative genomics and evolutionary biology. There is currently no cohesive database that collects intronless genes in plants into a single database, although many databases on exons and introns exist. In this study, we constructed the Rosaceae Intronless Genes Database (RIGD), a user-friendly web interface to explore and collect information on intronless genes from different plants. Six Rosaceae species, Pyrus bretschneideri, Pyrus communis, Malus domestica, Prunus persica, Prunus mume, and Fragaria vesca, are included in the current release of the RIGD. Sequence data and gene annotation were collected from different databases and integrated. The main purpose of this study is to provide gene sequence data. In addition, attribute analysis, functional annotations, subcellular localization prediction, and GO analysis are reported. The RIGD allows users to browse, search, and download data with ease. Blast and comparative analyses are also provided through this online database, which is available at http://www.rigdb.cn/.
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Affiliation(s)
- Tianzhe Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Dandan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Xin Liu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China.,Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, Hefei, China
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Begum Y, Mondal SK. Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species. J Biomol Struct Dyn 2020; 39:2387-2414. [PMID: 32292132 DOI: 10.1080/07391102.2020.1748717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chlorophyll (Chl) biosynthesis is one of the most important cellular processes essential for plant photosynthesis. Chl degradation pathway is also important catabolic process occurs during leaf senescence, fruit ripening and under biotic or abiotic stress conditions. Here we have systematically investigated the molecular evolution, gene structure, compositional analysis along with ENc plot, correspondence analysis and codon usage bias of the proteins and encoded genes involved in Chl metabolism from monocots and dicots. The gene and species specific phylogenetic trees using amino acid sequences showed clear clustering formation of the selected species based on monocots and dicots but not supported by 18S rRNA. Nucleotide composition of the encoding genes showed that average GC%, GC1%, GC2% and GC3% were higher in monocots. RSCU analysis depicts that genes from monocots for both pathways and genes for synthesis pathway from dicots only biased to G/C-ending synonymous codons but in degradation pathway most optimal codons (except UUG) in dicots biased to A/U-ending synonymous codons. We found strong evidence of episodic diversifying selection at several amino acid sites in all genes investigated. Conserved domain and gene structures were observed for the genes with varying lengths of introns and exons, involved in Chl metabolism along with some intronless genes within synthesis pathway. ENc and correspondence analyses suggested the mutational or selection constraint on the genes to shape the codon usage. These comprehensive studies may be helpful in further research in molecular phylogenetics and genomics and to better understand the evolutionary dynamics of Chl metabolic pathway.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-II), University of Calcutta, Kolkata, West Bengal, India
| | - Sunil Kanti Mondal
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
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5
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Rahman F, Hassan M, Hanano A, Fitzpatrick DA, McCarthy CGP, Murphy DJ. Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi. BMC Genomics 2018; 19:976. [PMID: 30593269 PMCID: PMC6309107 DOI: 10.1186/s12864-018-5334-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/29/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Caleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim of this study was to investigate the evolution and functions of the CLO/PXGs in the Fungi and other non-plant clades and to elucidate the overall origin of this gene family. RESULTS CLO/PXG-like genes are distributed across the full range of fungal groups from the basal clades, Cryptomycota and Microsporidia, to the largest and most complex Dikarya species. However, the genes were only present in 243 out of 844 analysed fungal genomes. CLO/PXG-like genes have been retained in many pathogenic or parasitic fungi that have undergone considerable genomic and structural simplification, indicating that they have important functions in these species. Structural and functional analyses demonstrate that CLO/PXGs are multifunctional proteins closely related to similar proteins found in all major taxa of the Chlorophyte Division of the Viridiplantae. Transcriptome and physiological data show that fungal CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression and are upregulated in response to a range of biotic and abiotic stresses as well as participating in key metabolic and developmental processes such as lipid metabolism, signalling, reproduction and pathogenesis. Biochemical data also reveal that the Aspergillus flavus CLO/PXG has specific functions in sporulation and aflatoxin production as well as playing roles in lipid droplet function. CONCLUSIONS In contrast to plants, CLO/PXGs only occur in about 30% of sequenced fungal genomes but are present in all major taxa. Fungal CLO/PXGs have similar but not identical roles to those in plants, including stress-related oxylipin signalling, lipid metabolism, reproduction and pathogenesis. While the presence of CLO/PXG orthologs in all plant genomes sequenced to date would suggest that they have core housekeeping functions in plants, the selective loss of CLO/PXGs in many fungal genomes suggests more restricted functions in fungi as accessory genes useful in particular environments or niches. We suggest an ancient origin of CLO/PXG-like genes in the 'last eukaryotic common ancestor' (LECA) and their subsequent loss in ancestors of the Metazoa, after the latter had diverged from the ancestral fungal lineage.
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Affiliation(s)
- Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
| | - Mehedi Hassan
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
| | - Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | | | | | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL UK
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6
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Kumar A, Pandeya A, Malik G, Sharma M, P. HK, S. AK, Gahlaut V, Gajula MP, Singh KP, Suravajhala P, Balyan HS, Gupta PK. ---A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants. F1000Res 2018; 7:ISCB Comm J-673. [PMID: 30135718 PMCID: PMC6073097 DOI: 10.12688/f1000research.14561.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Cereals are key contributors to global food security. Genes involved in the uptake (transport), assimilation and utilization of macro- and micronutrients are responsible for the presence of these nutrients in grain and straw. Although many genomic databases for cereals are available, there is currently no cohesive web resource of manually curated nutrient use efficiency (NtUE)-related genes and quantitative trait loci (QTLs). In this study, we present a web-resource containing information on NtUE-related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops (wheat ( Triticum aestivum), rice ( Oryza sativa), maize ( Zea mays), barley ( Hordeum vulgare)), two alien species related to wheat ( Triticum urartu and Aegilops tauschii), and two model species ( Brachypodium distachyon and Arabidopsis thaliana). Gene annotations integrated in the current web resource were manually curated from the existing databases and the available literature. The primary goal of developing this web resource is to provide descriptions of the NtUE-related genes and their functional annotation. MicroRNAs targeting some of the NtUE related genes and the QTLs for NtUE-related traits are also included. The genomic information embedded in the web resource should help users to search for the desired information.
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Affiliation(s)
- Anuj Kumar
- Advanced Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, Uttarakhand, 248007, India
| | - Ajay Pandeya
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, 248002, India
| | - Girik Malik
- Bioclues.org, Hyderabad, 500072, India
- Labrynthe, New Delhi, India
| | - Mansi Sharma
- Bioinformatics Laboratory, Institute of Cytology and Preventative Oncology, Noida, 201301, India
| | - Hima Kumari P.
- Department of Genetics, Osmania University, Hyderabad, Telengana, 500007, India
| | - Anil Kumar S.
- Department of Genetics, Osmania University, Hyderabad, Telengana, 500007, India
| | - Vijay Gahlaut
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India
| | - M.N.V. Prasad Gajula
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar , Telangana, 500030, India
| | - Krishna Pal Singh
- Advanced Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, Uttarakhand, 248007, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, 500072, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Technology & Science, Jaipur, Rajasthan, 302001, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India
| | - Pushpendra K. Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India
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7
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Hawkins LK, Warburton ML, Tang J, Tomashek J, Alves Oliveira D, Ogunola OF, Smith JS, Williams WP. Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination. Toxins (Basel) 2018; 10:E61. [PMID: 29385107 PMCID: PMC5848162 DOI: 10.3390/toxins10020061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/21/2022] Open
Abstract
Many projects have identified candidate genes for resistance to aflatoxin accumulation or Aspergillus flavus infection and growth in maize using genetic mapping, genomics, transcriptomics and/or proteomics studies. However, only a small percentage of these candidates have been validated in field conditions, and their relative contribution to resistance, if any, is unknown. This study presents a consolidated list of candidate genes identified in past studies or in-house studies, with descriptive data including genetic location, gene annotation, known protein identifiers, and associated pathway information, if known. A candidate gene pipeline to test the phenotypic effect of any maize DNA sequence on aflatoxin accumulation resistance was used in this study to determine any measurable effect on polymorphisms within or linked to the candidate gene sequences, and the results are published here.
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Affiliation(s)
- Leigh K Hawkins
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762, USA.
| | - Marilyn L Warburton
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762, USA.
| | - Juliet Tang
- USDA FS Durability and Wood Protection Research Unit, Starkville, MS 39759, USA.
| | - John Tomashek
- Integrated Micro-Chromatography Systems LLC, Irmo, SC 29063, USA.
| | - Dafne Alves Oliveira
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762 USA.
| | - Oluwaseun F Ogunola
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS 39762, USA.
| | - J Spencer Smith
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762, USA.
| | - W Paul Williams
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762, USA.
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8
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Jorquera R, González C, Clausen P, Petersen B, Holmes DS. Improved ontology for eukaryotic single-exon coding sequences in biological databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-6. [PMID: 30239665 PMCID: PMC6146118 DOI: 10.1093/database/bay089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022]
Abstract
Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases.
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Affiliation(s)
- Roddy Jorquera
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile
| | - Philip Clausen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bent Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Centro de Genómica y Bioinformática Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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9
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Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, Sanusi NSNM, Jayanthi N, Ponomarenko P, Triska M, Solovyev V, Firdaus-Raih M, Sambanthamurthi R, Murphy D, Low ETL. Evidence-based gene models for structural and functional annotations of the oil palm genome. Biol Direct 2017; 12:21. [PMID: 28886750 PMCID: PMC5591544 DOI: 10.1186/s13062-017-0191-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Background Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Results Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. Conclusions We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops. Reviewers This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, California, 91750, USA.,Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Petr Ponomarenko
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Martin Triska
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, 90089, USA
| | - Victor Solovyev
- Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
| | - Mohd Firdaus-Raih
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Denis Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
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Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Res 2016; 45:1015-1020. [PMID: 27742820 PMCID: PMC5210635 DOI: 10.1093/nar/gkw935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.
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Affiliation(s)
- Yi Wang
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Roger Thilmony
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden R6M 1Y5 MB, Canada
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA .,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
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11
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Coleto I, Trenas AT, Erban A, Kopka J, Pineda M, Alamillo JM. Functional specialization of one copy of glutamine phosphoribosyl pyrophosphate amidotransferase in ureide production from symbiotically fixed nitrogen in Phaseolus vulgaris. PLANT, CELL & ENVIRONMENT 2016; 39:1767-1779. [PMID: 27004600 DOI: 10.1111/pce.12743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Purines are essential molecules formed in a highly regulated pathway in all organisms. In tropical legumes, the nitrogen fixed in the nodules is used to generate ureides through the oxidation of de novo synthesized purines. Glutamine phosphoribosyl pyrophosphate amidotransferase (PRAT) catalyses the first committed step of de novo purine synthesis. In Phaseolus vulgaris there are three genes coding for PRAT. The three full-length sequences, which are intron-less genes, were cloned, and their expression levels were determined under conditions that affect the synthesis of purines. One of the three genes, PvPRAT3, is highly expressed in nodules and protein amount and enzymatic activity in these tissues correlate with nitrogen fixation activity. Inhibition of PvPRAT3 gene expression by RNAi-silencing and subsequent metabolomic analysis of the transformed roots shows that PvPRAT3 is essential for the synthesis of ureides in P. vulgaris nodules.
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Affiliation(s)
- Inmaculada Coleto
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Almudena T Trenas
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Alexander Erban
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Joachim Kopka
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Manuel Pineda
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Josefa M Alamillo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
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Abstract
Background Intronless genes are a significant characteristic of prokaryotes. Systematic identification and annotation are primary and crucial steps for determining the functions of intronless genes and understanding their occurrence in eukaryotes. Description In this paper, we describe the construction of the Intronless Genes Database in Dicots (IGDD; available at http://bio.njfu.edu.cn/igdd/), which contains data for five well-annotated plants including Arabidopsis thaliana, Carica papaya, Populus trichocarpa, Salix suchowensis and Vitis vinifera. Using highly visual settings, IGDD displays the structural and functional annotations, the homolog groups, the syntenic relationships, the expression patterns, and the statistical characteristics of intronless genes. In addition, useful tools such as an advanced search and local BLAST are available through a user-friendly and intuitive web interface. Conclusion In conclusion, the IGDD provides a comprehensive and up-to-date platform for researchers to assist the exploration of intronless genes in dicot plants.
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Jorquera R, Ortiz R, Ossandon F, Cárdenas JP, Sepúlveda R, González C, Holmes DS. SinEx DB: a database for single exon coding sequences in mammalian genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw095. [PMID: 27278816 PMCID: PMC4897596 DOI: 10.1093/database/baw095] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 05/11/2016] [Indexed: 12/27/2022]
Abstract
Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.
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Affiliation(s)
- Roddy Jorquera
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Rodrigo Ortiz
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - F Ossandon
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Juan Pablo Cárdenas
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Rene Sepúlveda
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avda Zañartu 1482, Santiago, Chile
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Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas. Dev Genes Evol 2015; 225:287-303. [DOI: 10.1007/s00427-015-0513-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/03/2015] [Indexed: 10/23/2022]
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