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Volume 14, Issue 8, August 2024
Investigation
The genetic architecture of dog ownership: large-scale genome-wide association study in 97,552 European-ancestry individuals
Widespread changes in gene expression accompany body size evolution in nematodes
Comprehensive analysis of CXXX sequence space reveals that Saccharomyces cerevisiae GGTase-I mainly relies on a2X substrate determinants
QTL analysis of divergent floral morphology traits between Gilia yorkii and G. capitata
haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors
Neurexin drives Caenorhabditis elegans avoidance behavior independently of its post-synaptic binding partner neuroligin
Genome-wide association analyses using multilocus models on bananas (Musa spp.) reveal candidate genes related to morphology, fruit quality, and yield
A temporal sequence of heterochronic gene activities promotes stage-specific developmental events in Caenorhabditis elegans
Whole-genome sequencing analysis of soybean diversity across different countries and selection signature of Korean soybean accession
This study investigated the genomic characteristics and population structures of 2,317 soybean public whole-genome sequencing data from different regions. Soybean accessions from China, Korea, and North America exhibited landrace characteristics, indicating higher genetic diversity and adaptation to local environments. In Korean soybean accession, strong selection signals for isoflavone synthesis were observed. Key genetic variants and genes influencing adaptability were identified, laying the foundation for future advances in genomics-based breeding programs and crop improvement efforts.
Use of simulation to optimize a sweet corn breeding program: implementing genomic selection and doubled haploid technology
The generation of stable transgenic lines in the human-infective nematode Strongyloides stercoralis
OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales
Understanding the evolutionary history of organisms is fundamental to biology. However, bacterial phylogenomic analyses require highly specialized software tools and extensive time and computational investments, so getting it right is difficult and errors are costly. These bottlenecks become even more pronounced when inferring trees with hundreds to thousands of leaves. Here, Middlebrook et al. present OrthoPhyl, which takes much of the guesswork and troubleshooting out of inferring orthologs, generating codon alignments, and finally, producing phylogenetic trees.
The putative prenyltransferase Nus1 is required for filamentation in the human fungal pathogen Candida albicans
otb: an automated HiC/HiFi pipeline assembles the Prosapia bicincta Genome
Regulation of thiamine and pyruvate decarboxylase genes by Pdc2 in Nakaseomyces glabratus (Candida glabrata) is complex
Novel metagenomics analysis of stony coral tissue loss disease
Genomic structural variation in Barramundi Perch Lates calcarifer and potential roles in speciation and adaptation
Barramundi Perch, aka Asian Sea Bass or ‘Barramundi’, are widely distributed in the tropical Indo-Pacific and are a popular recreational and important aquaculture fish. Molecular data has identified three divergent genetic lineages and indicate that Barramundi Perch is better described as a species complex. Campbell and Hale identify genetic architecture that may underpin the speciation and adaptation of this species complex across its broad range. Their results may be leveraged for evolutionary study, aquaculture development, management, and conservation.
Genome Report
Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery
Genome assembly of Hibiscus sabdariffa L. provides insights into metabolisms of medicinal natural products
The genome of Przewalski’s horse (Equus ferus przewalskii)
Przewalski’s horse is an endangered wild horse native to central Asia. After becoming extinct in the wild, multiple conservation efforts were used to rescue the species, including zoo breeding programs, reintroduction into the wild, protected lands, and cloning. Flack et al. used a blood sample to build a representative set of genes for Przewalski’s horse. This digital resource will aid species conservation.
A robust genome assembly with transcriptomic data from the striped bark scorpion, Centruroides vittatus
The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California
McEvoy et al. introduce a scaffold-quality reference genome for the endangered Gaviota tarplant. The assembly is 1.67 Gbp with 96% BUSCO completeness, 33 K genes and 75% repeat content. The authors find extensive Copia long terminal repeat sequences and duplicate genes that suggest environmental adaptation strategies. Comparisons with sunflower suggest a shared polyploidization event around 27 million years ago, close to the date of the common ancestor divergence. This work underlines the importance of genomic studies in accurately understanding adaptations and conservation needs.
