Friday 15 March 2024

Towards telomere-to-telomere fish genomes with Oxford Nanopore Technologies gap-filling

It was a pleasure to be invited to the “What You’re Missing Matters” tour at Perth, and present some ongoing work investigating the best way to incorporate Oxford Nanopore Technologies data into our high-quality HiFi+HiC fish genomes. The results are too preliminary to share here (and will soon be superseded) but do get in touch if it sounds interesting to you.

Thursday 7 March 2024

Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)?

Second cane toad paper of the week! This time, we're revisiting invasive epigenomics.

Yagound B, Sarma RR, Edwards RJ, Richardson MF, Rodriguez Lopez CM, Crossland MR, Brown GP, DeVore JL, Shine R & Rollins LA (2024): Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)? Ecology and Evolution 14:e11127. [Ecol Evol] [PubMed] [bioRxiv]

Many organisms can adjust their development according to environmental conditions, including the presence of conspecifics. Although this developmental plasticity is common in amphibians, its underlying molecular mechanisms remain largely unknown. Exposure during development to either ‘cannibal cues’ from older conspecifics, or ‘alarm cues’ from injured conspecifics, causes reduced growth and survival in cane toad (Rhinella marina) tadpoles. Epigenetic modifications, such as changes in DNA methylation patterns, are a plausible mechanism underlying these developmental plastic responses. Here we tested this hypothesis, and asked whether cannibal cues and alarm cues trigger the same DNA methylation changes in developing cane toads. We found that exposure to both cannibal cues and alarm cues was associated with local changes in DNA methylation patterns. These DNA methylation changes affected genes putatively involved in developmental processes, but in different genomic regions for different conspecific-derived cues. Genetic background explains most of the epigenetic variation among individuals. Overall, the molecular mechanisms triggered by exposure to cannibal cues seem to differ from those triggered by alarm cues. Studies linking epigenetic modifications to transcriptional activity are needed to clarify the proximate mechanisms that regulate developmental plasticity in cane toads.

Monday 4 March 2024

Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory

Congratulations to Kelton Cheung for getting her first PhD paper out. This one has been a long time brewing and involved quite a lot of data wrangling, but we got there in the end. Invasive cane toads might be a little more complex than we thought.

Cheung K, Amos TG, Shine R, DeVore JL, S Ducatez S, Edwards RJ & Rollins LA (2024): Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory. Ecology and Evolution 14:e11115. [Ecol Evol] [PubMed] [bioRxiv]

Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai’ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai’i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai’ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai’ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.

Sunday 28 January 2024

Toward genome assemblies for all marine vertebrates: current landscape and challenges

The first Ocean Genomes paper is now out! This one is a small commentary piece, but some high-quality genomes are on their way - watch this space. Well, actually, watch this space at Genomes on a Tree!

de Jong E, Parata L, Bayer PE, Corrigan S & Edwards RJ (2024): Toward genome assemblies for all marine vertebrates: current landscape and challenges. Gigascience 13:giad119. [Gigascience] [PubMed]

Marine vertebrate biodiversity is fundamental to ocean ecosystem health but is threatened by climate change, overharvesting, and habitat degradation. High-quality reference genomes are valuable foundational scientific resources that can inform conservation efforts. Consequently, global consortia are striving to produce reference genomes for representatives of all life. Here, we summarize the current landscape of available marine vertebrate reference genomes, including their phylogenetic diversity and geographic hotspots of production. We discuss key logistical and technical challenges that remain to be overcome if we are to realize the vision of a comprehensive reference genome library of all marine vertebrates.

Thursday 4 January 2024

Happy New Year! Updates coming soon...

It's been a really busy year or so, getting the Minderoo OceanOmics Centre at UWA fully staffed and operational, and blog content has suffered as a result. Stay tuned for a backlog of publications (see Publications tab) and other news - including some of the first outputs to come out of Ocean Genomes, and exciting updates to the Oceans Insitute strategy.

Friday 15 December 2023

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.

Thursday 21 September 2023

PAG Australia 2023: Exploring Dingo Ecology and Evolution with Chromosome-Level Canid Genomes

Richard J Edwards, Matt F Field and J William O Ballard - PAG Australia 2023

Dogs are uniquely associated with human dispersal and bring novel insight into human migration and the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. The exact origin(s) and people(s) who transported the canines that became dingoes to Australia is debated, but it has been suggested they arrived by boat ~5,000-8,000 BP. Published morphological and genetic evidence has established the presence of at least two dingo lineages. The Alpine dingo is commonly found in south-eastern Australia while the Desert ecotype is found in the north, central and western Australia. The relationship of dingoes to modern dogs, and the ecotypes to each other, has important implications management and protection of this top predator, as well as providing interesting perspectives on human colonisation and canine domestication.

We have generated chromosome-level assemblies of both dingo ecotypes, along with domesticated dogs representing both ancient (Basenji) and derived (German Shepherd) breeds. In each case, long-read sequencing and Hi-C scaffolding have been combined to produce genome assemblies with high contiguity and structural completeness. Comparison of these assemblies with additional dog breeds, using the Greenland wolf as an outgroup, places the dingo as an early offshoot of modern dogs, situated between the grey wolf and the domesticated dogs of today. This is supported by patterns of genetic variation, and chromosome structure. Furthermore, we confirm that dingoes have not experienced the expansion of the AMY2B pancreatic amylase gene that occurred during domestication of modern dogs. This has important implications for dingo ecology and behaviour, and raises the prospect of using AMY2B copy number as a novel and reliable in-field discriminator between dingoes and feral dogs.