Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research
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 tomore »
- Authors:
-
- Huazhong Agricultural University, Wuhan (China)
- National Academy of Sciences of Ukraine, Kiev (Ukraine)
- Huazhong Agricultural University, Wuhan (China); Hubei Hongshan Laboratory, Wuhan (China)
- University of Nebraska-Lincoln, NE (United States)
- Guangxi University, Nanning (China)
- Publication Date:
- Research Org.:
- Univ. of Nebraska, Lincoln, NE (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)
- OSTI Identifier:
- 2311522
- Grant/Contract Number:
- SC0023142
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biotechnology for Biofuels and Bioproducts
- Additional Journal Information:
- Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 2731-3654
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; camelina; biofuel; oilseed; genome; biotechnology
Citation Formats
Wang, Shuo, Blume, Rostislav Y., Zhou, Zhi-Wei, Lu, Shaoping, Nazarenus, Tara J., Blume, Yaroslav B., Xie, Weibo, Cahoon, Edgar B., Chen, Ling-Ling, and Guo, Liang. Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research. United States: N. p., 2024.
Web. doi:10.1186/s13068-024-02466-9.
Wang, Shuo, Blume, Rostislav Y., Zhou, Zhi-Wei, Lu, Shaoping, Nazarenus, Tara J., Blume, Yaroslav B., Xie, Weibo, Cahoon, Edgar B., Chen, Ling-Ling, & Guo, Liang. Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research. United States. https://doi.org/10.1186/s13068-024-02466-9
Wang, Shuo, Blume, Rostislav Y., Zhou, Zhi-Wei, Lu, Shaoping, Nazarenus, Tara J., Blume, Yaroslav B., Xie, Weibo, Cahoon, Edgar B., Chen, Ling-Ling, and Guo, Liang. Wed .
"Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research". United States. https://doi.org/10.1186/s13068-024-02466-9. https://www.osti.gov/servlets/purl/2311522.
@article{osti_2311522,
title = {Chromosome-level assembly and analysis of Camelina neglecta: a novel diploid model for Camelina biotechnology research},
author = {Wang, Shuo and Blume, Rostislav Y. and Zhou, Zhi-Wei and Lu, Shaoping and Nazarenus, Tara J. and Blume, Yaroslav B. and Xie, Weibo and Cahoon, Edgar B. and Chen, Ling-Ling and Guo, Liang},
abstractNote = {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.},
doi = {10.1186/s13068-024-02466-9},
journal = {Biotechnology for Biofuels and Bioproducts},
number = 1,
volume = 17,
place = {United States},
year = {Wed Jan 31 00:00:00 EST 2024},
month = {Wed Jan 31 00:00:00 EST 2024}
}
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