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Blume RY, Rabokon AM, Pydiura M, Yemets AI, Pirko YV, Blume YB. Genome-wide identification and evolution of the tubulin gene family in Camelina sativa. BMC Genomics 2024; 25:599. [PMID: 38877397 PMCID: PMC11177405 DOI: 10.1186/s12864-024-10503-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: 02/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. RESULTS We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. CONCLUSIONS For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.
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Affiliation(s)
- Rostyslav Y Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine.
| | - Anastasiia M Rabokon
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Mykola Pydiura
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
- JSC "Farmak", Kyiv, 04080, Ukraine
| | - Alla I Yemets
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav V Pirko
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav B Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
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Wang S, Blume RY, Zhou ZW, Lu S, Nazarenus TJ, Blume YB, Xie W, Cahoon EB, Chen LL, Guo L. Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:17. [PMID: 38291537 PMCID: PMC10829252 DOI: 10.1186/s13068-024-02466-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and β) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis between C. neglecta and C. sativa, we successfully used the method of calculating Ks to distinguish the three subgenomes of C. sativa and determined that C. neglecta was closest to the first subgenome (SG1) of C. sativa. Further, transcriptomic analysis revealed the key genes associated with seed oil biosynthesis and its transcriptional regulation, including SAD, FAD2, FAD3, FAE1, ABI3, WRI1 and FUS3 displaying high expression levels in C. neglecta seeds. The high representability of C. neglecta as a model species for Camelina-based biotechnology research has been demonstrated for the first time. In particular, floral Agrobacterium tumefaciens infiltration-based transformation of C. neglecta, leading to overexpression of CvLPAT2, CpDGAT1 and CvFatB1 transgenes, was demonstrated for medium-chain fatty acid accumulation in C. neglecta seed oil. This study provides an important genomic resource and establishes C. neglecta as a new model for oilseed biotechnology research.
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Affiliation(s)
- Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Rostislav Y Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Zhi-Wei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Tara J Nazarenus
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Yaroslav B Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
| | - Ling-Ling Chen
- College of Life Science and Technology, Guangxi University, Nanning, China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Blume RY, Kalendar R, Guo L, Cahoon EB, Blume YB. Overcoming genetic paucity of Camelina sativa: possibilities for interspecific hybridization conditioned by the genus evolution pathway. FRONTIERS IN PLANT SCIENCE 2023; 14:1259431. [PMID: 37818316 PMCID: PMC10561096 DOI: 10.3389/fpls.2023.1259431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023]
Abstract
Camelina or false flax (Camelina sativa) is an emerging oilseed crop and a feedstock for biofuel production. This species is believed to originate from Western Asian and Eastern European regions, where the center of diversity of the Camelina genus is located. Cultivated Camelina species arose via a series of polyploidization events, serving as bottlenecks narrowing genetic diversity of the species. The genetic paucity of C. sativa is foreseen as the most crucial limitation for successful breeding and improvement of this crop. A potential solution to this challenge could be gene introgression from Camelina wild species or from resynthesized allohexaploid C. sativa. However, both approaches would require a complete comprehension of the evolutionary trajectories that led to the C. sativa origin. Although there are some studies discussing the origin and evolution of Camelina hexaploid species, final conclusions have not been made yet. Here, we propose the most complete integrated evolutionary model for the Camelina genus based on the most recently described findings, which enables efficient improvement of C. sativa via the interspecific hybridization with its wild relatives. We also discuss issues of interspecific and intergeneric hybridization, aimed on improving C. sativa and overcoming the genetic paucity of this crop. The proposed comprehensive evolutionary model of Camelina species indicates that a newly described species Camelina neglecta has a key role in origin of tetra- and hexaploids, all of which have two C. neglecta-based subgenomes. Understanding of species evolution within the Camelina genus provides insights into further research on C. sativa improvements via gene introgression from wild species, and a potential resynthesis of this emerging oilseed crop.
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Affiliation(s)
- Rostyslav Y. Blume
- Institute of Food Biotechnology and Genomics of National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Ruslan Kalendar
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Edgar B. Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Yaroslav B. Blume
- Institute of Food Biotechnology and Genomics of National Academy of Science of Ukraine, Kyiv, Ukraine
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Wang F, Zhang R, Sun X, Wang J, Liu H, Zhang K, Wang C. An intelligent recognition method of chromosome rearrangement patterns based on information entropy. Sci Rep 2022; 12:19707. [PMID: 36385139 PMCID: PMC9668828 DOI: 10.1038/s41598-022-22046-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: 06/09/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Chromosome rearrangements play an important role in the speciation of plants and animals, and the recognition of chromosome rearrangement patterns is helpful to elucidate the mechanism of species differentiation at the chromosome level. However, the existing chromosome rearrangement recognition methods have some major limitations, such as low quality, barriers to parental selection, and inability to identify specific rearrangement patterns. Based on the whole genome protein sequences, we constructed the combined figure according to the slope of the collinear fragment, the number of homologous genes, the coordinates in the top left and bottom right of the collinear fragment. The standardized combination figure is compared with the four standard pattern figures, and then combined with the information entropy analysis strategy to automatically classify the chromosome images and identify the chromosome rearrangement pattern. This paper proposes an automatic karyotype analysis method EntroCR (intelligent recognition method of chromosome rearrangement based on information entropy), which integrates rearrangement pattern recognition, result recommendation and related chromosome determination, so as to infer the evolution process of ancestral chromosomes to the existing chromosomes. Validation experiments were conducted using whole-genome data of Gossypium raimondii and Gossypium arboreum, Oryza sativa and Sorghum bicolor. The conclusions were consistent with previous results. EntroCR provides a reference for researchers in species evolution and molecular marker assisted breeding as well as new methods for analyzing karyotype evolution in other species.
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Affiliation(s)
- Fushun Wang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530Hebei Key Laboratory of Agricultural Big Data, Baoding, 071000 People’s Republic of China
| | - Ruolan Zhang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Xiaohua Sun
- grid.484109.00000 0004 1758 9755Department of Digital Media, Hebei Software Institute, Baoding, 071000 People’s Republic of China
| | - Junhao Wang
- grid.274504.00000 0001 2291 4530College of Information Science and Technology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Hongquan Liu
- grid.274504.00000 0001 2291 4530Department of Urban and Rural Construction, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Kang Zhang
- grid.274504.00000 0001 2291 4530College of Life Science, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
| | - Chunyang Wang
- grid.274504.00000 0001 2291 4530College of Life Science, Hebei Agricultural University, Baoding, 071000 People’s Republic of China ,grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000 People’s Republic of China
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