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He J, Tian D, Li X, Wang X, Wang T, Wang Z, Zang H, He X, Zhang T, Yun Q, Zhang R, Jiang J, Jia S, Zhang Y. A chromosome-level genome assembly for Onobrychis viciifolia reveals gene copy number gain underlying enhanced proanthocyanidin biosynthesis. Commun Biol 2024; 7:19. [PMID: 38182881 PMCID: PMC10770414 DOI: 10.1038/s42003-023-05754-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024] Open
Abstract
Sainfoin (Onobrychis viciifolia), which belongs to subfamily Papilionoideae of Leguminosae, is a vital perennial forage known as "holy hay" due to its high contents of crude proteins and proanthocyanidins (PAs, also called condensed tannins) that have various pharmacological properties in animal feed, such as alleviating rumen tympanic disease in ruminants. In this study, we select an autotetraploid common sainfoin (2n = 4x = 28) and report its high-quality chromosome-level genome assembly with 28 pseudochromosomes and four haplotypes (~1950.14 Mb, contig N50 = 10.91 Mb). The copy numbers of genes involved in PA biosynthesis in sainfoin are significantly greater than those in four selected Fabales species, namely, autotetraploid Medicago sativa and three other diploid species, Lotus japonicus, Medicago truncatula, and Glycine max. Furthermore, gene expansion is confirmed to be the key contributor to the increased expression of these genes and subsequent PA enhancement in sainfoin. Transcriptomic analyses reveal that the expression of genes involved in the PA biosynthesis pathway is significantly increased in the lines with high PA content compared to the lines with medium and low PA content. The sainfoin genome assembly will improve our understanding of leguminous genome evolution and biosynthesis of secondary metabolites in sainfoin.
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Affiliation(s)
- Junyi He
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Danyang Tian
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xue Li
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xuemeng Wang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Tingting Wang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Ziyao Wang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Hui Zang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xiaofan He
- School of Grassland Science, Beijing Forestry University, 100083, Beijing, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, 100083, Beijing, China
| | - Quanzheng Yun
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261322, China
| | - Rengang Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261322, China
| | - Jishan Jiang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China.
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China.
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Eskier D, Arıbaş A, Karakülah G. PlanTEnrichment: A How-to Guide on Rapid Identification of Transposable Elements Associated with Regions of Interest in Select Plant Genomes. Methods Mol Biol 2023; 2703:59-70. [PMID: 37646937 DOI: 10.1007/978-1-0716-3389-2_5] [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] [Indexed: 09/01/2023]
Abstract
Transposable elements (TEs) are repeat elements that can relocate or create novel copies of themselves in the genome and contribute to genomic complexity and expansion, via events such as chromosome recombination or regulation of gene expression. However, given the large number of such repeats across the genome, identifying repeats of interest can be a challenge in even well-annotated genomes, especially in more complex, TE-rich plant genomes. Here, we describe a protocol for PlanTEnrichment, a database we created comprising information on 11 plant genomes to analyze stress-associated TEs using publicly available data. By selecting a genome and providing a list of genes or genomic regions whose TE associations the user wants to identify, the user can rapidly obtain TE subfamilies found near the provided regions, as well as their superfamily and class, and the enrichment values of the repeats. The results also provide the locations of individual repeat instances found, alongside the input regions or genes they are associated with, and a bar graph of the top ten most significant repeat subfamilies identified. PlanTEnrichment is freely available at http://tools.ibg.deu.edu.tr/plantenrichment/ and can be used by researchers with rudimentary or no proficiency in computational analysis of TE elements, allowing for expedience in the identification of TEs of interest and helping further our understanding of the potential contributions of TEs in plant genomes.
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Affiliation(s)
- Doğa Eskier
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İnciraltı, İzmir, Turkey
- Bioinformatics Platform, İzmir Biomedicine and Genome Center (IBG), İnciraltı, İzmir, Turkey
| | - Alirıza Arıbaş
- Bioinformatics Platform, İzmir Biomedicine and Genome Center (IBG), İnciraltı, İzmir, Turkey
| | - Gökhan Karakülah
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İnciraltı, İzmir, Turkey.
- Bioinformatics Platform, İzmir Biomedicine and Genome Center (IBG), İnciraltı, İzmir, Turkey.
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Song R, Wang Z, Wang H, Zhang H, Wang X, Nguyen H, Holding D, Yu B, Clemente T, Jia S, Zhang C. InMut-finder: a software tool for insertion identification in mutagenesis using Nanopore long reads. BMC Genomics 2021; 22:908. [PMID: 34923956 PMCID: PMC8684674 DOI: 10.1186/s12864-021-08206-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
Background Biological mutagens (such as transposon) with sequences inserted, play a crucial role to link observed phenotype and genotype in reverse genetic studies. For this reason, accurate and efficient software tools for identifying insertion sites based on the analysis of sequencing reads are desired. Results We developed a bioinformatics tool, a Finder, to identify genome-wide Insertions in Mutagenesis (named as “InMut-Finder”), based on target sequences and flanking sequences from long reads, such as Oxford Nanopore Sequencing. InMut-Finder succeeded in identify > 100 insertion sites in Medicago truncatula and soybean mutants based on sequencing reads of whole-genome DNA or enriched insertion-site DNA fragments. Insertion sites discovered by InMut-Finder were validated by PCR experiments. Conclusion InMut-Finder is a comprehensive and powerful tool for automated insertion detection from Nanopore long reads. The simplicity, efficiency, and flexibility of InMut-Finder make it a valuable tool for functional genomics and forward and reverse genetics. InMut-Finder was implemented with Perl, R, and Shell scripts, which are independent of the OS. The source code and instructions can be accessed at https://github.com/jsg200830/InMut-Finder. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08206-9.
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Affiliation(s)
- Rui Song
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ziyao Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Han Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xuemeng Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hanh Nguyen
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA
| | - David Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.,School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA
| | - Tom Clemente
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA. .,School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA.
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Jia S, Yobi A, Naldrett MJ, Alvarez S, Angelovici R, Zhang C, Holding DR. Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5880-5895. [PMID: 32667993 DOI: 10.1093/jxb/eraa325] [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: 04/07/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Opaque kernels in maize may result from mutations in many genes, such as OPAQUE-2. In this study, a maize null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4) showed an opaque kernel phenotype, as well as plant developmental delay, male sterility, and altered response to cold stress. We found that in opaque kernels, all zein proteins were reduced and amino acid content was changed, including increased lysine. Transcriptomic and proteomic analysis confirmed the zein reduction and proteomic rebalancing of non-zein proteins, which was quantitatively and qualitatively different from opaque-2. Global transcriptional changes were found in endosperm and leaf, including many transcription factors and tissue-specific expressed genes. Furthermore, of the more than 8000 significantly differentially expressed genes in wild type in response to cold, a significant proportion (25.9% in moderate cold stress and 40.8% in near freezing stress) were not differentially expressed in response to cold in rdm4, suggesting RDM4 may participate in regulation of abiotic stress tolerance. This initial characterization of maize RDM4 provides a basis for further investigating its function in endosperm and leaf, and as a regulator of normal and stress-responsive development.
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Affiliation(s)
- Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Pratacultural Science, Beijing Municipality, Beijing, China
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - Abou Yobi
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ruthie Angelovici
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - David R Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
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Yu J. A Time for Celebration: 40th Anniversary of GSC and 15th Anniversary of BIG, CAS. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:387-388. [PMID: 30743051 PMCID: PMC6411949 DOI: 10.1016/j.gpb.2019.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/24/2022]
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