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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production

Chao-Qun Xu, Hui Liu, Shan-Shan Zhou, Dong-Xu Zhang, Wei Zhao, Sihai Wang, Fu Chen, Yan-Qiang Sun, Shuai Nie, Kai-Hua Jia, et al.
(2019) GIGASCIENCE. 8(2).
Author
Organization
Abstract
BACKGROUND: Malania oleifera, a member of the Olacaceae family, is an IUCN Red Listed tree, endemic and restricted to the Karst region of South West China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic make-up, and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. FINDINGS: We generated 51 Gigabases (Gb) and 135 Gb of raw DNA sequences, using PacBio Single-Molecule Real-Time (SMRT) and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Megabases (Mb) and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long chain fatty acid were identified and studied in detail. CONCLUSIONS: Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology, and for the functional genomics of nervonic acid biosynthesis.
Keywords
de novo genome assembly, vulnerable plant, Malania, nervonic acid, transcriptomes, GYPSY DATABASE GYDB, PROVIDES INSIGHTS, READ ALIGNMENT, ANNOTATION, IDENTIFICATION, CLASSIFICATION, TRANSCRIPTOME, METABOLISM, PREDICTION, EVOLUTION

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MLA
Xu, Chao-Qun, et al. “Genome Sequence of Malania Oleifera, a Tree with Great Value for Nervonic Acid Production.” GIGASCIENCE, vol. 8, no. 2, 2019, doi:10.1093/gigascience/giy164.
APA
Xu, C.-Q., Liu, H., Zhou, S.-S., Zhang, D.-X., Zhao, W., Wang, S., … Mao, J.-F. (2019). Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. GIGASCIENCE, 8(2). https://doi.org/10.1093/gigascience/giy164
Chicago author-date
Xu, Chao-Qun, Hui Liu, Shan-Shan Zhou, Dong-Xu Zhang, Wei Zhao, Sihai Wang, Fu Chen, et al. 2019. “Genome Sequence of Malania Oleifera, a Tree with Great Value for Nervonic Acid Production.” GIGASCIENCE 8 (2). https://doi.org/10.1093/gigascience/giy164.
Chicago author-date (all authors)
Xu, Chao-Qun, Hui Liu, Shan-Shan Zhou, Dong-Xu Zhang, Wei Zhao, Sihai Wang, Fu Chen, Yan-Qiang Sun, Shuai Nie, Kai-Hua Jia, Si-Qian Jiao, Ren-Gang Zhang, Quan-Zheng Yun, Wenbin Guan, Xuewen Wang, Qiong Gao, Jeffrey L Bennetzen, Fatemeh Maghuly, Ilga Porth, Yves Van de Peer, Xiao-Ru Wang, Yongpeng Ma, and Jian-Feng Mao. 2019. “Genome Sequence of Malania Oleifera, a Tree with Great Value for Nervonic Acid Production.” GIGASCIENCE 8 (2). doi:10.1093/gigascience/giy164.
Vancouver
1.
Xu C-Q, Liu H, Zhou S-S, Zhang D-X, Zhao W, Wang S, et al. Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. GIGASCIENCE. 2019;8(2).
IEEE
[1]
C.-Q. Xu et al., “Genome sequence of Malania oleifera, a tree with great value for nervonic acid production,” GIGASCIENCE, vol. 8, no. 2, 2019.
@article{8599187,
  abstract     = {{BACKGROUND: Malania oleifera, a member of the Olacaceae family, is an IUCN Red Listed tree, endemic and restricted to the Karst region of South West China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic make-up, and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.
FINDINGS: We generated 51 Gigabases (Gb) and 135 Gb of raw DNA sequences, using PacBio Single-Molecule Real-Time (SMRT) and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Megabases (Mb) and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long chain fatty acid were identified and studied in detail.
CONCLUSIONS: Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology, and for the functional genomics of nervonic acid biosynthesis.}},
  articleno    = {{giy164}},
  author       = {{Xu, Chao-Qun and Liu, Hui and Zhou, Shan-Shan and Zhang, Dong-Xu and Zhao, Wei and Wang, Sihai and Chen, Fu and Sun, Yan-Qiang and Nie, Shuai and Jia, Kai-Hua and Jiao, Si-Qian and Zhang, Ren-Gang and Yun, Quan-Zheng and Guan, Wenbin and Wang, Xuewen and Gao, Qiong and Bennetzen, Jeffrey L and Maghuly, Fatemeh and Porth, Ilga and Van de Peer, Yves and Wang, Xiao-Ru and Ma, Yongpeng and Mao, Jian-Feng}},
  issn         = {{2047-217X}},
  journal      = {{GIGASCIENCE}},
  keywords     = {{de novo genome assembly,vulnerable plant,Malania,nervonic acid,transcriptomes,GYPSY DATABASE GYDB,PROVIDES INSIGHTS,READ ALIGNMENT,ANNOTATION,IDENTIFICATION,CLASSIFICATION,TRANSCRIPTOME,METABOLISM,PREDICTION,EVOLUTION}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{14}},
  title        = {{Genome sequence of Malania oleifera, a tree with great value for nervonic acid production}},
  url          = {{http://doi.org/10.1093/gigascience/giy164}},
  volume       = {{8}},
  year         = {{2019}},
}
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