PDF(Pubmed)
Abstract：
BACKGROUND: The finger lime (Citrus australasica), one of six Australian endemic citrus species shows a high natural phenotypic diversity and novel characteristics. The wide variation and unique horticultural features have made this lime an attractive candidate for domestication. Currently no haplotype resolved genome is available for this species. Here we present a high quality, haplotype-resolved reference genome for this species using PacBio HiFi and Hi-C sequencing.
RESULTS: Hifiasm assembly and SALSA scaffolding resulted in a collapsed genome size of 344.2 Mb and 321.1 Mb and 323.2 Mb size for the two haplotypes. The nine pseudochromosomes of the collapsed genome had an N50 of 35.2 Mb, 99.1% genome assembly completeness and 98.9% gene annotation completeness (BUSCO). A total of 41,304 genes were predicted in the nuclear genome. Comparison with C. australis revealed that 13,661 genes in pseudochromosomes were unique in C. australasica. These were mainly involved in plant-pathogen interactions, stress response, cellular metabolic and developmental processes, and signal transduction. The two genomes showed a syntenic arrangement at the chromosome level with large structural rearrangements in some chromosomes. Genetic variation among five C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identified in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome.
CONCLUSIONS: The genome of C. australasica present in this study is of high quality and contiguity. This genome helps deepen our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.
RESULTS: Hifiasm assembly and SALSA scaffolding resulted in a collapsed genome size of 344.2 Mb and 321.1 Mb and 323.2 Mb size for the two haplotypes. The nine pseudochromosomes of the collapsed genome had an N50 of 35.2 Mb, 99.1% genome assembly completeness and 98.9% gene annotation completeness (BUSCO). A total of 41,304 genes were predicted in the nuclear genome. Comparison with C. australis revealed that 13,661 genes in pseudochromosomes were unique in C. australasica. These were mainly involved in plant-pathogen interactions, stress response, cellular metabolic and developmental processes, and signal transduction. The two genomes showed a syntenic arrangement at the chromosome level with large structural rearrangements in some chromosomes. Genetic variation among five C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identified in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome.
CONCLUSIONS: The genome of C. australasica present in this study is of high quality and contiguity. This genome helps deepen our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.
摘要：
背景：指石灰（柑橘），澳大利亚六种特有柑橘之一表现出很高的自然表型多样性和新颖的特征。广泛的变化和独特的园艺特征使这种石灰成为驯化的有吸引力的候选者。目前没有单倍型解析基因组可用于该物种。在这里，我们提出了一个高质量的，使用PacBioHiFi和Hi-C测序对该物种进行单倍型解析的参考基因组。
结果：Hifiasm组装和SALSA支架导致两种单倍型基因组大小为344.2Mb和321.1Mb和323.2Mb。折叠基因组的九个假染色体的N50为35.2Mb，99.1%的基因组组装完全性和98.9%的基因注释完全性(BUSCO)。在核基因组中总共预测了41,304个基因。与澳大利亚梭菌的比较表明，假染色体中的13,661个基因在澳大利亚梭菌中是独特的。这些主要涉及植物-病原体相互作用，应激反应，细胞代谢和发育过程，和信号转导。这两个基因组在染色体水平上显示出同步排列，在某些染色体中具有较大的结构重排。分析了5个南方紫菜品种之间的遗传变异。与防御有关的基因，在基因组中鉴定了挥发性化合物的合成和红/黄着色。在澳大利亚梭菌基因组中发现了编码类囊体曲率蛋白的基因的主要扩展。
结论：本研究中存在的澳大利亚念珠菌基因组具有高质量和连续性。该基因组有助于加深我们对柑橘进化的理解，揭示抗病性和品质相关基因，有可能加速柑橘的遗传改良。
结果：Hifiasm组装和SALSA支架导致两种单倍型基因组大小为344.2Mb和321.1Mb和323.2Mb。折叠基因组的九个假染色体的N50为35.2Mb，99.1%的基因组组装完全性和98.9%的基因注释完全性(BUSCO)。在核基因组中总共预测了41,304个基因。与澳大利亚梭菌的比较表明，假染色体中的13,661个基因在澳大利亚梭菌中是独特的。这些主要涉及植物-病原体相互作用，应激反应，细胞代谢和发育过程，和信号转导。这两个基因组在染色体水平上显示出同步排列，在某些染色体中具有较大的结构重排。分析了5个南方紫菜品种之间的遗传变异。与防御有关的基因，在基因组中鉴定了挥发性化合物的合成和红/黄着色。在澳大利亚梭菌基因组中发现了编码类囊体曲率蛋白的基因的主要扩展。
结论：本研究中存在的澳大利亚念珠菌基因组具有高质量和连续性。该基因组有助于加深我们对柑橘进化的理解，揭示抗病性和品质相关基因，有可能加速柑橘的遗传改良。
