Supporting data for "A high-quality pseudo-phased genome for <i>Melaleuca quinquenervia</i> shows allelic diversity of NLR-type resistance genes"

The coastal wetland tree species <i>Melaleuca quinquenervia</i> (broad-leaved paperbark), is a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. The species has been widely grown as an ornamental, becoming invasive in areas such as Florida in the United States. Long-lived trees must respond to a wide range pests and pathogens, and immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family play a key role in plant stress responses. Expansion of this family is driven largely by tandem duplication, resulting in a clustering arrangement on chromosomes. Due to this clustering and their highly repetitive domain structure, comprehensive annotation of NLR encoding genes within genomes has been difficult. Additionally, as many genomes are presented in their haploid, collapsed state, the allelic diversity of the NLR gene family has not been widely published for outcrossing tree species. <br>We assembled a chromosome-level pseudo-phased genome for <i>M. quinquenervia</i> and describe the allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, differences in clusters and in the types and numbers of novel integrated domains. <br>We anticipate that the high quality of the <i>M. quinquenervia</i> genome will provide a new framework for functional and evolutionary studies into this important tree species. Our results indicate a likely role for maintenance of NLR allelic diversity to enable response to environmental stress, and we suggest that this allelic diversity may be even more important for long-lived plants.

滨海湿地树种宽叶白千层（*Melaleuca quinquenervia*，broad-leaved paperbark）是澳大利亚东部、印度尼西亚、巴布亚新几内亚以及新喀里多尼亚的建群种。该物种被广泛作为观赏植物栽培，在美国佛罗里达州等地区已成为入侵物种。长寿树木需应对多种害虫与病原菌，而由核苷酸结合富亮氨酸重复（nucleotide-binding leucine-rich repeat, NLR）基因家族编码的免疫受体在植物胁迫响应中发挥关键作用。该基因家族的扩张主要由串联重复事件驱动，使其在染色体上呈现簇状排列模式。受限于这种簇状结构以及其高度重复的结构域特征，对基因组中编码NLR的基因开展全面注释始终存在挑战。此外，由于多数基因组以单倍体压缩状态提交，针对异交树木物种的NLR基因家族等位基因多样性研究尚未得到广泛报道。
本研究组装了宽叶白千层的染色体级假相基因组，并借助新型FindPlantNLRs流程解析了植物NLR的等位基因多样性。分析结果显示，不同单倍型上的NLR基因数量存在差异，基因簇结构以及新型整合结构域的类型与数量亦存在显著区别。
我们认为，高质量的宽叶白千层基因组将为这一重要树种的功能与进化研究提供全新的研究框架。本研究结果表明，维持NLR等位基因多样性或可帮助植物应对环境胁迫，且我们推测此类等位基因多样性对于长寿植物而言可能更为关键。