Rahman, S. R. | bioRxiv Science

bioRxiv2022

fastman: A fast algorithm for visualizing GWAS results using Manhattan and Q-Q plots

Visualisation of GWAS summary statistics, specifically P-values, as Manhattan plots are widespread in GWAS publications, and many popular software tools are available, such as the R package qqman. However, there is a substantial need for further development, such as handling datasets from non-model organisms. We provide a new R package, fastman, with major additional capabilities compared to currently available packages. For example, it handles datasets involving genomes from non-model organisms, even at a draft stage consisting of numerous contigs and scaffolds (shorter stretches of assembled DNA sequences) that have not been compiled into chromosomes. Non-numeric chromosome IDs are also supported. Additionally, our package has the capability of plotting other genetic scores, such as other GWAS statistics (e.g. regression betas or odds ratios), fixation index(FST), D-statistics, and various selection statistics, such as PBS. Importantly, negative or two-tailed values are supported in this package. In our package, we implement a heuristic algorithm that drastically reduces plotting time for huge datasets without losing visual precision, allowing for many different data types and missing data. We also provide substantial additional flexibility in highlighting and annotation. The package can produce plots directly from association outputs by PLINK. Alternatively, it can produce plots from any R data frame with custom columns and can handle large datasets to generate plots rapidly. It is available for public use at https://github.com/adhikari-statgen-lab/fastman.

bioinformatics↗

bioRxiv2020

A combined RAD-Seq and WGS approach reveals the genomic basis of yellow colour variation in bumble bee Bombus terrestris

BackgroundIn the model bumble bee species B. terrestris, both males and females exhibit black coloration on the third thoracic and first metasomal segments. We discovered a fortuitous lab-generated mutant in which this typical black coloration is replaced by yellow. As this same color variant is found in several sister lineages to B. terrestris within the Bombus s.s. subgenus, this could be a result of ancestral allele sorting. ResultsUtilizing a combination of RAD-Seq and whole-genome re-sequencing approaches, we localized the color-generating variant to a single SNP in the protein-coding sequence of a homeobox transcription factor, cut. Sanger sequencing confirmed fixation of this SNP between wildtype and yellow mutants. Protein domain analysis revealed this SNP to generate an amino acid change (Ala38Pro) that modifies the conformation of coiled-coil structural elements which lie outside the characteristic DNA binding domains. We found all Hymenopterans including B. terrestris sister lineages possess the non-mutant allele, indicating different mechanism(s) are involved in the same black to yellow transition in nature. ConclusionsCut is a highly pleiotropic gene important for multiple facets of development, yet this mutation generated no noticeable external phenotypic effects outside of setal characteristics. Reproductive capacity was observed to be reduced, however, with queens being less likely to mate and produce female offspring, in a manner similar to workers. Our research implicates a novel developmental player in pigmentation, and potentially caste as well, thus contributing to a better understanding of the evolution of diversity in both of these processes.

genomics↗