As part of its scope, G3 Genes|Genomes|Genetics is dedicated to reporting new methods and technologies of significant benefit to the genetics community. Here, we highlight a selection of new analysis pipelines and software developments from the August 2024 issue that promise to improve research and practical applications in their respective subfields. These advances include easy and ready-to-use genomics tools that improve data management and analysis and overcome long-time challenges, emphasizing the ongoing progress and innovation happening in genomics.

An easy-to-use phylogenetic analysis pipeline

A new turn-key pipeline called OrthoPhyl has answered the call to improve the phylogenetic analysis of bacterial genomes. Developed by Middlebrook et al., OrthoPhyl can analyze up to 1,200 input genomes and reconstruct high-resolution phylogenetic trees based on whole genome codon alignments from diverse bacterial clades.

The beauty of OrthoPhyl is that it streamlines a usually complex, multi-step process requiring extensive bioinformatics expertise and computing resources into a multi-threaded tool that runs from a single command.

With more than 2 million publicly available bacterial genomes in NCBI’s GenBank database, OrthoPhyl can help research groups in the fields of bacterial phylogenetics and taxonomy take advantage of existing datasets to inform their ongoing analyses amid the ever-expanding sea of bacterial diversity.

Accurate genotype phasing and inference of grandparental haplotypes

To improve the analysis of complex plant genomes, Montero-Tena et al. have developed a new computational pipeline called haploMAGIC, which lets researchers identify locations of recombination known as genome-wide crossovers (COs) in multi-parent populations. haploMAGIC uses single-nucleotide polymorphism (SNP) data and known pedigree information to accurately phase genotypes, i.e., determine which alleles were inherited from each parent, and to reconstruct grandparental haplotypes, i.e., determine which alleles were inherited from each grandparent.

When tested on real-world data, haploMAGIC improved upon existing methods by using different levels of haploblock filtering to prevent false-positive COs—a common limitation—even as rates of genotyping errors increased. haploMAGIC can also distinguish between COs and gene conversions. By learning more about the position and frequency of genetic recombination events in complex plant genomes, breeders can better manage and expand genetic variation in their breeding programs.

A complete HiC/HiFi assembly pipeline

The USDA-ARS AgPest100 Initiative aims to create high-quality genome assemblies of pest insects that threaten agricultural production. However, the high cost and time currently needed to produce and manage these assemblies often hinders progress.

Molik et al. set out to address this challenge by developing a new Hi-C/high-fidelity (HiFi) sequencing genomic assembly pipeline called only the best (otb) using the Nextflow programming language. They then used otb to create a HiC/HiFi genome of the two-lined spittlebug, a significant agricultural pest that is not well understood. Overall, otb was able to streamline the process and reduce manual input and analysis time—including time spent organizing data and installing and calibrating bioinformatic tools.

By saving time, otb can significantly reduce costs for large genomic projects like AgPest100 and pave the way for new discoveries. Indeed, the HiC/HiFi assembly of the spittlebug genome represents a first step toward better understanding this plant-eating pest, which may lead to new, sustainable ways to manage it.

Assigning triploids to their diploid parents

Roche et al. have developed the first publicly-available, ready-to-use software for assigning triploid fish to their diploid parents. Triploidy means that an organism has three sets of chromosomes instead of two, and sterile triploids are commonly used in aquaculture breeding programs for their better yield and growth and to prevent genetic contamination of wild fish populations. The authors improve upon existing frameworks by updating the parentage assignment R package APIS to support triploids with diploid parentage.

When assessed with simulated and real datasets, APIS accurately assigned triploid offspring to their diploid parents using both likelihood and exclusion methods. The new software represents a key tool for establishing pedigrees in fish farming.

University of Minnesota researchers have successfully mapped the complete genome of the endangered Przewalski’s horse. Once extinct in the wild, the species now has a population of around 2,000 animals thanks to conservation efforts.

The study, published in the journal G3, was led by Nicole Flack and Lauren Hughes, researchers at the College of Veterinary Medicine, along with Christopher Faulk, a professor in the College of Food, Agricultural and Natural Resource Sciences. University of Minnesota students contributed to the genome sequencing through Faulk’s animal science course. 

“The genome is the basic blueprint for an animal and tells us what makes a species unique and also tells us about the health of a population,” said Faulk. “My students worked together to produce the highest quality Przewalski’s horse genome in the world.”

Researchers can now use this as a tool to make accurate predictions about what gene mutations mean for Przewalski’s horse health and conservation.  

“Studying genes without a good reference is like doing a 3 billion-piece puzzle without the picture on the box,” said Flack. “Przewalski’s horse researchers studying mutations in an important gene need a good reference picture to compare their puzzle with.” 

Researchers used a blood sample from Varuschka, a 10-year-old Przewalski’s mare at the Minnesota Zoo, to construct a representative map of genes for the species. The zoo has long been active in Przewalski’s horse breeding and management, with over 50 foals born since the 1970s. 

“We were excited to partner with the University of Minnesota to preserve the genetic health of the species as their populations continue to recover, both in zoos and in the wild,” said Anne Rivas, doctor of veterinary medicine at the Minnesota Zoo. “We are thrilled to offer our community the opportunity to see the horse as the results of our conservation efforts.” 

The cutting-edge technology sequencing used to construct the genome uses a small machine about the size of a soda can. Its portability means this method could be adapted for further study of wild Przewalski’s horses in remote locations.

Future applications of the reference genome may include studying genes that help the horse adapt to environmental changes, identifying mutations associated with specific traits or diseases, and informing future breeding decisions to help improve upon genetic diversity. Given the extreme population bottleneck that occurred during the near-extinction of Przewalski’s horse, such understanding is crucial for continued breeding efforts.

Aquaculture experts at the Roslin Institute have collaborated with industry partner Atlantic Aqua Farms to map the complete set of chromosomes for the blue mussel, an important commercial species in Europe and North America.

Researchers aim to support mussel farming and improve disease resistance using advanced gene sequencing technologies.

The high-quality genome map identifies over 65,000 genes, providing a comprehensive blueprint of the mussel’s genetic makeup.

This development is particularly important for the aquaculture industry, which relies on efficient and sustainable breeding practices to meet the growing demand for mussels.

Aquaculture Breeding

In Prince Edward Island, Canada, where the world’s only commercial mussel hatchery exists, this information will allow farmers to select mussels with desirable traits.

For instance, the new data will enable farmers to breed mussels with stronger byssus threads, which are crucial for the mussels to attach securely to ropes, ensuring a more stable yield.

Additionally, the genomic insights will help in selecting mussels that grow faster and produce more meat, enhancing overall productivity for mussel farms.

Disease Resistance

The mapped genome allows scientists to study the immune responses of different mussel populations, enabling researchers to identify how certain populations are better able to withstand threats posed by climate change and emerging diseases. This can lead to targeted breeding programmes that enhance disease resistance.

This will help reduce losses due to illness and improve the health and sustainability of mussel populations, the research team says.

Ecosystem conservation

This research not only benefits commercial aquaculture, but also contributes to the conservation of wild mussel populations by ensuring their health and genetic diversity, researchers explain.

Blue mussels can spread and establish themselves in non-native regions, affecting local ecosystems. Accessing detailed genomic data will enable scientists to track and mitigate the impact of these invasive populations, preserving the balance of marine environments.

In the coming months, the research team plans to explore the genetic diversity of blue mussels in Scotland, leveraging the complete genome map for more detailed analyses.

This research was published in the G3 Genes, Genomes, Genetics journal. The project was funded by Genome Canada and carried out in close collaboration with Atlantic Aqua Farms.

“This research project marks a significant advancement in aquaculture. It showcases how genomic research can provide practical solutions for commercial aquaculture and environmental conservation,” says Dr. Tim Regan, Career Track Fellow, Roslin Institute.