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Sun R, Wu Y, Zhang X, Lv M, Yu D, Sun Y. Chromosome-level genome assembly and annotation of a potential model organism Gossypium arboreum ZB-1. Sci Data 2024; 11:620. [PMID: 38866802 PMCID: PMC11169495 DOI: 10.1038/s41597-024-03481-z] [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: 12/15/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Recent advancements in plant regeneration and synthetic polyploid creation have been documented in Gossypium arboreum ZB-1. These developments make ZB-1 a potential model within the Gossypium genus for investigating gene function and polyploidy. This work generated the sequence and annotation of the ZB-1 genome. The contig-level genome was constructed using the PacBio high-fidelity reads, encompassing 81 contigs with an N50 length of 112.12 Mb. The Hi-C data assisted the construction of the chromosome-level genome, which consists of 13 pseudo-chromosomes and 39 un-anchored contigs, with a total length of about 1.67 Gb. Repetitive sequences accounted for about 69.7% of the genome in length. Based on ab initio and evidence-based prediction, we have identified 48,021 protein-coding genes in the ZB-1 genome. Comparative genomics analysis revealed conserved gene content and arrangement between ZB-1 and G. arboreum SXY1. The single nucleotide polymorphism occurrence rate between ZB-1 and SXY1 was about 0.54 per 1,000 nucleotides. This study enriched the genomic resources for further exploration into cotton regeneration and polyploidy mechanisms.
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Affiliation(s)
- Rongnan Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Yuqing Wu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Xinyu Zhang
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Minghua Lv
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China
| | - Dongliang Yu
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
| | - Yuqiang Sun
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310008, China.
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Liu G, Zhang D, Zhao T, Yang H, Jiang J, Li J, Zhang H, Xu X, Hu X. Identification of Cladosporium fulvum infection responsive genes in tomato through cDNA-AFLP. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2116997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Guan Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, Heilongjiang, PR China
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, PR China
| | - Dongye Zhang
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, Heilongjiang, PR China
| | - Tingting Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Huanhuan Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Jingbin Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Jingfu Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - He Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Xiangyang Xu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Xiaohang Hu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, Heilongjiang, PR China
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Pozzi FI, Green GY, Barbona IG, Rodríguez GR, Felitti SA. CleanBSequences: an efficient curator of biological sequences in R. Mol Genet Genomics 2020; 295:837-841. [PMID: 32300860 DOI: 10.1007/s00438-020-01671-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
This work presents a new method and tool to solve a common problem of molecular biologists and geneticists who use molecular markers in their scientific research and developments: curation of sequences. Omic studies conducted by molecular biologists and geneticists usually involve the use of molecular markers. AFLP, cDNA-AFLP, and MSAP are examples of markers that render information at the genomics, transcriptomics, and epigenomics levels, respectively. These three types of molecular markers use adaptors that are the template for PCR amplification. The sequences of the adaptors have to be eliminated for the analysis of the results. Since a large number of sequences are usually obtained in these studies, this clean-up of the data could demand long time and work. To automate this work, an R package, named CleanBSequences, was created that allows the sequences to be curated massively, quickly, without errors and can be used offline. The curating is performed by aligning the forward and/or reverse primers or ends of cloning vectors with the sequences to be removed. After the alignment, new subsequences are generated without biological fragments not desired by the user, i.e., sequences needed by the techniques. In conclusion, the CleanBSequences tool facilitates the work of researchers, reducing time, effort, and working errors. Therefore, the present tool would respond to the problems related to the curation of sequences obtained from the use of some types of molecular markers. In addition to the above, being an open source, CleanBSequences is a flexible tool that has the potential to be used in future improvements to respond to new problems.
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Affiliation(s)
- Florencia I Pozzi
- Instituto de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km. 3, 2580, Marcos Juárez, Córdoba, Argentina. .,Cátedra de Microbiología, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina.
| | - Gisela Y Green
- Cátedra de Epidemiología, Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, S2170, Casilda, Santa Fe, Argentina
| | - Ivana G Barbona
- Cátedra de Estadística, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Gustavo R Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) (CONICET-UNR), Zavalla, Argentina.,Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Silvina A Felitti
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) (CONICET-UNR), Zavalla, Argentina
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