Biology subjects

Fraser, C. I.

Publications and source records attributed to Fraser, C. I..

3 recordsLinked to original sources

bioRxiv2024

A Cry For Kelp: Evidence for Polyphenolic Inhibition of Oxford Nanopore Sequencing of Brown Algae

Genomic resources for macroalgae are increasingly important for conservation and commercial management, however the generation of such resources continues to be hampered by difficulties in the isolation of suitable DNA. Even when DNA has been isolated that otherwise appears high quality, such samples may not perform well during the sequencing process. We here compare Oxford Nanopore long-read sequencing results for three species of macroalgae to those of non-macroalgal species and find that macroalgal samples tend to lead to rapid decline in the number of available sequencing pores resulting in reduced sequencing yield. LC-MS analysis of macroalgal DNA that would be considered suitable for sequencing reveals that DNA derived from dried macroalgae is enriched for polyphenol-DNA adducts - which may lead to sequencing inhibition. Our findings have wide-ranging implications for the generation of genomic resources from macroalgae, for example long read sequencing of dried herbarium specimens, and suggest a need to use fresh tissue wherever possible for genome sequencing.

molecular biology↗

bioRxiv2023

Population genomic analysis reveals genetic structure and thermal-tolerant genotypes in remnant Tasmanian giant kelp populations

Giant kelp, Macrocystis pyrifera, is a foundation species that forms dense forests of complex physical habitat and supports coastal biodiversity, productivity, and other essential ecosystem services. Tasmanian coasts have suffered a massive decline in giant kelp forests due to changes in regional oceanography and environmental conditions, but efforts are being made to restore these disappearing populations using identification and selective breeding for lineages that are more tolerant to warmer temperatures. Here, we used gametophytes that originated from remnant populations collected at three sites in northeastern and three sites in southeastern Tasmania to determine the genetic structure of the giant kelp population via genotyping-by-sequencing (GBS) and assembled a draft genome from a Tasmanian giant kelp sporophyte individual. Previous research identified seven strain lines that were tolerant to warm temperatures, and we used the GBS data to test whether genotypes were associated with warm tolerance. Kelps from the north were genetically distinct from the southern ones, with much lower gene flow between regions than within regions. These results revealed that giant kelp populations from Tasmania are more genetically structured than previously thought. Two loci were significantly associated with warm temperature tolerance. They are population-specific: the alternative allele from one of the loci was found only in the northern populations, while the other was found in the southern populations. This could suggest that thermal tolerance is adapting locally or drifting given large changes in population demography, but further research is needed to confirm this hypothesis. Our research sheds light on genetic patterns in this critical habitat-forming kelp and will help inform conservation management, including selective breeding.

genetics↗

bioRxiv2023

Differences in density: taxonomic but not functional diversity in seaweed microbiomes affected by an earthquake

Host-associated microbial communities can make important contributions to host health, and are shaped by a range of different factors ranging from host condition, environmental conditions, and other microbes. Disentangling the roles of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host density to identify the influence of host density on microbiome composition. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6m, sufficient to locally extirpate some intertidal kelp populations. These uplifted populations are slowly recovering, but intertidal kelps remain at much lower densities than at nearby, less uplifted sites. By comparing the microbiome of the low and high density sites using 16S amplicon sequencing, we observed that low density populations had higher beta-diversity than high density populations with regards to taxonomic variability, while no beta-diversity differences were observed between functional categories. Using phylogenetic and taxonomic turnover approaches, we determined that dispersal limitation shapes low density populations to a greater extent, while homogeneous selection shapes high density populations to a greater extent. Our findings shed light on microbiome assembly processes, particularly highlighting that large-scale disturbances that affect host density can dramatically influence microbiome structure.

microbiology↗