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- Jin, Yuqing, et al.
(author)
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Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)
- 2016
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Journal article (peer-reviewed)abstract
- Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average H-e = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.
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- Xu, Chao-Qun, et al.
(author)
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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
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In: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
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Journal article (peer-reviewed)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 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.
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3. |
- Yang, Tianquan, et al.
(author)
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The chromosome-level genome assembly and genes involved in biosynthesis of nervonic acid of Malania oleifera
- 2023
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In: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
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Journal article (peer-reviewed)abstract
- Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of ~4.9 Mb and a scaffold N50 of ~112.6 Mb. ~98.2% of the assembly was anchored into 13 pseudo-chromosomes. It contains ~1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.
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5. |
- Zhang, Yege, et al.
(author)
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Causation Identification and Control Measures of Deformation by Integrated Dewatering-Excavation Process Simulation of a T-Shaped Deep Foundation Pit
- 2022
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In: Water (Switzerland). - : MDPI AG. - 2073-4441. ; 14:4
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Journal article (peer-reviewed)abstract
- Construction of subway line intersection stations will become more and more popular in the future. Research on the deformation characteristics in the construction process is the best way to ensure the safety of the foundation pit itself, the surrounding buildings, and adjacent subway stations. In this paper, the deformation characteristics of a T-shaped subway foundation pit during construction are studied by an integrated dewatering-excavation three-dimensional numerical simulation method. The results show that the main causation of the surface settlement around the foundation pit is the stratum compression caused by dewatering, and the main causation of the deformation of the diaphragm wall and the existing subway station is the soil deformation caused by excavation unloading. It is suggested that constructing a high-quality diaphragm wall, controlling the water level within the excavation foundation pit, strengthening the monitoring, and timely cement pouring of the bottom plate are key countermeasures to reduce the deformation. The research results of this paper have reference significance for similar projects.
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