A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

Chen SH, Martino AM, Luo Z, Schwessinger B, Jones A, Tolessa T, Bragg JG, Tobias PA, Edwards RJ (2023): A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes. GigaScience 12:giad102. [Gigascience] [PubMed]

Background. Melaleuca quinquenervia (broad-leaved paperbark) is a coastal wetland tree species that serves as a foundation species in eastern Australia, Indonesia, Papua New Guinea, and New Caledonia. While extensively cultivated for its ornamental value, it has also become invasive in regions like Florida, USA. Long-lived trees face diverse pest and pathogen pressures, and plant stress responses rely on immune receptors encoded by the nucleotide-binding leucine-rich repeat (NLR) gene family. However, the comprehensive annotation of NLR encoding genes has been challenging due to their clustering arrangement on chromosomes and highly repetitive domain structure; expansion of the NLR gene family is driven largely by tandem duplication. Additionally, the allelic diversity of the NLR gene family remains largely unexplored in outcrossing tree species, as many genomes are presented in their haploid, collapsed state.

Results. We assembled a chromosome-level pseudo-phased genome for M. quinquenervia and described the allelic diversity of plant NLRs using the novel FindPlantNLRs pipeline. Analysis reveals variation in the number of NLR genes on each haplotype, distinct clustering patterns, and differences in the types and numbers of novel integrated domains.

Conclusions. The high-quality M. quinquenervia genome assembly establishes a new framework for functional and evolutionary studies of this significant tree species. Our findings suggest that maintaining allelic diversity within the NLR gene family is crucial for enabling responses to environmental stress, particularly in long-lived plants.

Dr Collin Ahrens (Postdoc)

Dr Collin Ahrens joined the Edwards lab as a postdoctoral researcher in January of 2021. He studies local adaptation to environmental variation (e.g. pathogens, drought, heatwaves etc.), and investigates how these adaptive patterns can be used to manage plant populations.

Local adaptation is often driven by differential physiological responses to environmental stress, controlled by genetic mechanisms. Therefore, he focuses on the E + G = P paradigm to ask questions such as how do populations evolve such different responses to different environmental conditions? And how do species evolve such different responses to the same environmental conditions? To answer these fundamental questions, he leverages several computational techniques to disentangle patterns of adaptation. At the Edwards lab, he will use whole genome sequencing, quantitative genetics, and physiological experimentation to explore how myrtle rust resistance segregates within Melaleuca quinquenervia populations to assist in broader conservation programs, including applied outcomes such as seed collection and ex situ breeding programs.