Suchergebnisse

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 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× 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. ; This study was funded by Fundamental Research Funds for the Central Universities (2018BLCB08), by the construction of the workstation for Academician Bennetzen (2015IC056) from Yunnan Provinical Science and Technology Department, by the Breeding of new variety for Malania oleifera and product development of nervonic acid (2015BB018) from the Science Fund of China's Yunnan government, and by the Natural hybridization and reproductive isolation among plants with high horticulture values (2018428) from Chinese Academy of Sciences. ; https://academic.oup.com/gigascience ; am2019 ; Biochemistry ; Genetics ; Microbiology and Plant Pathology

Abstract Background Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants. ; This work was supported by a grant from the Agricultural Genome Center of the Next Generation Biogreen 21 Program of RDA (Project No. PJ01127501) and by a grant from the Ministry of Science, ICT, and Future Planning (MSIP) of the Korean government through the National Research Foundation (NRF-2015R1A2A1A01002327) to DC.