Biology subjects

Johnson, H. A.

Publications and source records attributed to Johnson, H. A..

3 recordsLinked to original sources

bioRxiv2021

Genome assembly, transcriptome and SNP database for chum salmon (Oncorhynchus keta)

Chum salmon (Oncorhynchus keta) is the species with the widest geographic range of the anadromous Pacific salmonids. Chum salmon is the second largest of the Pacific salmon, behind Chinook salmon, and considered the most plentiful Pacific salmon by overall biomass. This species is of significant commercial and economic importance: on average the commercial chum salmon fishery has the second highest processed value of the Pacific salmon within British Columbia. The aim of this work was to establish genomic baseline resources for this species. Our first step to accomplish this goal was to generate a chum salmon reference genome assembly from a doubled-haploid chum salmon. Gene annotation of this genome was facilitated by an extensive RNA-seq database we were able to create from multiple tissues. Range-wide resequencing of chum salmon genomes allowed us to categorize genome-wide geographic variation, which in turn reinforced the idea that genetic differentiation was best described on a regional, rather than at a stock-specific, level. Within British Columbia, chum salmon regional groupings were described at the conservation unit (CU) level, and there may be substructure within particular CUs. Genome wide associations of phenotypic sex to SNP genetic markers identified two clear peaks, a very strong peak on Linkage Group 15, and another on Linkage Group 3. With these new resources, we were better able to characterize the sex-determining region and gain further insights into sex determination in chum salmon and the general biology of this species.

genomics↗

bioRxiv2020

Population genomics of North American northern pike: variation and sex-specific signals from a chromosome-level, long read genome assembly

The northern pike Esox lucius is a freshwater fish renowned for having low genetic diversity but ecological success throughout the Northern Hemisphere. Here we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds using long-reads and chromatin capture technology. We then align whole-genome resequencing data against this reference to genotype northern pike from Alaska through New Jersey (n = 47). A striking decrease in genetic diversity occurs along the sampling range, whereby samples to the west of the North American Continental Divide have substantially higher diversity than populations to the east. As an example, individuals from Interior Alaska in the west and St. Lawrence River in the east have on average 181K and 64K heterozygous SNPs per individual, respectively (i.e., a SNP variant every 3.2 kbp and 11.2 kbp, respectively). Even with such low diversity, individuals clustered with strong support within each population, and this may be related to numerous private alleles in each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajimas D = -1.07 and -1.30, respectively). Non-uniform patterns of diversity were observed across the genome, with large regions showing elevated diversity in several chromosomes, including LG24. In populations with the master sex determining gene amhby still present in the genome, amhby is in LG24. As expected, amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we also document some amhby(-) males in Alaska and amhby(+) males in the Columbia River. This indicates that rather than a discrete boundary after which amhby was lost in North America, there is a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity including the loss of the sex determination system.

genomics↗

bioRxiv2018

The Metabolic Capability and Phylogenetic Diversity of Mono Lake During a Bloom of the Eukaryotic Phototroph Picocystis strain ML

Algal blooms in lakes are often associated with anthropogenic eutrophication; however, they can occur naturally. In Spring of 2016 Mono Lake, a hyperalkaline lake in California, was near the height of a rare bloom of the algae Picocystis strain ML and at the apex of a multi-year long drought. These conditions presented a unique sampling opportunity to investigate microbiological dynamics during an intense natural bloom. We conducted a comprehensive molecular analysis along a depth transect near the center of the lake from surface to 25 m depth during June 2016. Across sampled depths, rRNA gene sequencing revealed that Picocystis associated chloroplast were found at 40-50 % relative abundance, greater than values recorded previously. Despite the presence of the photosynthetic oxygenic algal genus Picocystis, oxygen declined below detectible limits below 15 m depth, corresponding with an increase in microorganisms known to be anaerobic. In contrast to previously sampled years, metagenomic and metatranscriptomic data suggested a loss of sulfate reducing microorganisms throughout the lakes water column. Gene transcripts associated with Photosystem I and II were expressed at both 2 m and 25 m, suggesting that limited oxygen production may occur at extremely low light levels at depth within the lake. Oxygenic photosynthesis under low light conditions, in the absence of potential grazing by the brine shrimp Artemia, may allow for a cryptic redox cycle to occur in an otherwise anoxic setting at depth in the lake with the following effects: enhanced productivity, reduced grazing pressure on Picocystis, and an exacerbation of bloom.\n\nIMPORTANCEMono Lake, California provides habitat to a unique ecological community that is heavily stressed due to recent human water diversions and a period of extended drought. To date, no baseline information exists about Mono Lake to understand how the microbial community responds to drought, bloom, and what genetic functions are lost in the water column. While previously identified anaerobic members of the microbial community disappear from the water column during drought and bloom, sediment samples suggest these microorganisms seek refuge at lake bottom or in the subsurface. Thus, the sediments may represent a type of seed bank which could restore the microbial community as a bloom subsides. Our work also sheds light on the activity of the halotolerant algae Picocystis strain ML during a bloom at Mono Lake, its ability to potentially produce oxygen via photosynthesis even under extreme low-light conditions, and how the remainder of the microbial community responds.

microbiology↗