Singh Khushwant, Huff Matthew, Liu Jianyang, Park Jong-Won, Rickman Tara, Keremane Manjunath, Krueger Robert R, Kunta Madhurababu, Roose Mikeal L, Dardick Chris, Staton Margaret, Ramadugu Chandrika
Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA.
Plants (Basel). 2024 May 24;13(11):1460. doi: 10.3390/plants13111460.
Huanglongbing (HLB) is a severe citrus disease worldwide. Wild Australian limes like , , and possess beneficial HLB resistance traits. Individual trees of the three taxa were extensively used in a breeding program for over a decade to introgress resistance traits into commercial-quality citrus germplasm. We generated high-quality, phased, de novo genome assemblies of the three Australian limes using PacBio long-read sequencing. The genome assembly sizes of the primary and alternate haplotypes were determined for (337 Mb/335 Mb), (304 Mb/299 Mb), and (376 Mb/379 Mb). The nine chromosome-scale scaffolds included 86-91% of the genome sequences generated. The integrity and completeness of the assembled genomes were estimated to be at 97.2-98.8%. Gene annotation studies identified 25,461 genes in , 27,665 in , and 30,067 in . Genes belonging to 118 orthogroups were specific to Australian lime genomes compared to other citrus genomes analyzed. Significantly fewer canonical resistance () genes were found in and (319 and 449, respectively) compared to (576), (579), and (651). Similar patterns were observed for other gene families associated with potential HLB resistance, including Phloem protein 2 () and Callose synthase () genes predicted in the Australian lime genomes. The genomic information on Australian limes developed in the present study will help understand the genetic basis of HLB resistance.
黄龙病（HLB）是一种在全球范围内严重危害柑橘的病害。野生澳大利亚酸橙如、和具有有益的抗黄龙病特性。在长达十多年的育种计划中，广泛使用这三个分类群的单株树木，将抗性性状导入商业品质的柑橘种质中。我们使用PacBio长读长测序技术生成了这三种澳大利亚酸橙的高质量、分阶段、从头基因组组装。确定了、和的主要和替代单倍型的基因组组装大小（分别为337 Mb/335 Mb、304 Mb/299 Mb和376 Mb/379 Mb）。九个染色体规模的支架包含了所生成基因组序列的86 - 91%。组装基因组的完整性和完整性估计在97.2 - 98.8%。基因注释研究在中鉴定出25461个基因，在中鉴定出27665个基因，在中鉴定出30067个基因。与其他分析的柑橘基因组相比，属于118个直系同源组的基因是澳大利亚酸橙基因组特有的。与（576个）、（579个）和（651个）相比，在和中发现的典型抗性（）基因显著更少（分别为319个和449个）。在与潜在抗黄龙病相关的其他基因家族中也观察到类似模式，包括在澳大利亚酸橙基因组中预测的韧皮部蛋白2（）和胼胝质合酶（）基因。本研究中开发的澳大利亚酸橙的基因组信息将有助于理解抗黄龙病的遗传基础。
