Publication
A high-quality pseudo-phased genome forMelaleuca quinquenerviashows allelic diversity of NLR-type resistance genes
Publisher:
Cold Spring Harbor Laboratory
Date:
28-04-2023
DOI:
10.1101/2023.04.27.538497
Abstract: The coastal wetland tree species Melaleuca quinquenervia (Cav.) S.T.Blake (Myrtaceae), commonly named the 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 throughout their lifespan, and immune receptors encoded by the nucleotide- binding domain and leucine-rich repeat containing (NLR) gene family play a key role in plant stress responses. Expansion of this gene 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 still presented in their haploid, collapsed state, the full allelic ersity of the NLR gene family has not been widely published for outcrossing tree species. We assembled a chromosome-level pseudo-phased genome for M . quinquenervia and describe the full allelic ersity 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. We anticipate that the high quality of the genome for M. quinquenervia 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 ersity to enable response to environmental stress, and we suggest that this allelic ersity may be even more important for long-lived plants.