Biology subjects

Rieseberg, L.

Publications and source records attributed to Rieseberg, L..

6 recordsLinked to original sources

bioRxiv2025

Phylogenomic synteny analysis tracks conserved ancient polyploid-derived triplicated genomic blocks across Asteraceae genomes

The Asteraceae (Compositae) is the largest flowering plant family, ubiquitous in most terrestrial communities, and morphologically hyper-diverse. An ancient whole genome triplication (paleo-hexaploidization) occurred at approximately the same time as the evolutionary innovation and adaptive radiation of the family during the middle Eocene. Despite its importance, the genomic contents arising from this triplication have yet to be tracked in context of the Asteraceae genome evolution. We applied a synteny oriented phylogenomic analysis of 21 Asterales genomes and to study the paleo-hexaploidization and its consequences to gene, trait, and genome evolution. We identified 15 ancestral linkage groups (ALGs) that date back to the common diploid ancestor of all Asteraceae. Each of these groups was triplicated, resulting in 45 genomic blocks (3x15), which serve as the foundation for cross-family analyses. We demonstrate the complex evolutionary dynamics of the 45 genomic blocks across the Asteraceae phylogeny. We found that modern genomes are genetic mosaics of three progenitor genomes by extensive genomic exchange, chromosomal shuffling and gene fractionation. 157 genes retained three paleo-hexaploid derived syntenic paralogs across most Asteraceae species. Transcription factors (TFs) and auxin-related genes are significantly overrepresented in the conserved triplets, and expression of the paleo-hexaploidy paralogs is spatiotemporally differentiated. These genes are involved in the development of floral capitulum, a remarkable morphological innovation of the family. The discovery of conserved triplicated genes can direct further study to understand the evolutionary innovation, and the synteny-phylogenomic framework and ALGs provide a comparative framework to characterize newly sequenced Asteraceae genomes.

genomics↗

bioRxiv2024

Climate resilience conserved in global germplasm repositories: Picking the most promising parents for agile plant breeding

Crop diversity is an essential resource for national and international breeding programs aimed at preparing global agriculture for a changing climate to ensure global food security. To do this there are related risks that need to be evaluated (1) does the genetic diversity needed for climate adaptation exist somewhere? And (2) is such genetic diversity accessible? To evaluate these risks, we consider the test case of publicly available genotyped and georeferenced sorghum landraces (n = 1,937) to ask if diversity is sufficient to support breeding for climate change adaptation. Answering these questions allows for characterization of the best potential parents and the geographies that harbor the most potentially promising genetypes for crop improvement. We subset this data into national, regional, and global geographic regions, and complete/mini core collections to understand the potential for climate adaptation in regional germplasm. Study accessions were given a future climate resilience score based on future climatic projections and a genomic adaptive capacity score using genomic estimated adaptive values (GEAVs) generated from environmental genomic selection - EGS) to ask whether this accessible diversity stored in germplasm repositories is potentially sufficient to meet forecasted changes in growing environments under climate change. We find that genomic resilience capacity is highly variable among countries and regions. High geographical variability was also found for climate resilience. To equitably adapt agriculture to future climate conditions, increased accessibility to plant genetic resources is essential.

genomics↗

bioRxiv2023

RepeatOBserver: tandem repeat visualization and centromere detection

Tandem repeats can play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination, and the regulation of gene activity. There is a growing need for bioinformatics tools that can visualize and explore chromosome-scale repeats. Here we present RepeatOBserver, a new tool for visualizing tandem repeats and clustered transposable elements and for identifying potential natural centromere locations, using a Fourier transform of DNA walks: https://github.com/celphin/RepeatOBserverV1. RepeatOBserver can identify a broad range of repeats (3-20, 000bp long) in genome assemblies without any a priori knowledge of repeat sequences or the need for optimizing parameters. RepeatOBserver allows for easy visualization of the positions of both perfect and imperfect repeating sequences across each chromosome. We use RepeatOBserver to compare DNA walks, repeat patterns and centromere positions across genome assemblies in a wide range of well-studied species (e.g., human, mouse-ear cress), crops, and non-model organisms (e.g., fern, yew). Analyzing 107 chromosomes with known centromere positions, we find that centromeres consistently occur in regions that have the least diversity in repeat types (i.e. one or a few repeated sequences are present in very high numbers). Taking advantage of this information, we use a genomic Shannon diversity index to predict centromere locations in several other chromosome-scale genome assemblies. The Fourier spectra produced by RepeatOBserver can help visualize historic centromere positions, potential neocentromeres, retrotransposon clusters and gene copy variation. Identification of patterns of split and inverted tandem repeats at inversion boundaries suggests that at least some chromosomal inversions or misassemblies can be predicted with RepeatOBserver. RepeatOBserver is therefore a flexible tool for comprehensive characterization of tandem repeat patterns that can be used to visualize and identify a variety of regions of interest in genome assemblies.

bioinformatics↗

bioRxiv2022

The genomic basis of the plant island syndrome in Darwin's giant daisies

Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galapagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galapagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwins giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.

evolutionary biology↗

bioRxiv2021

ePlant in 2021: New Species, Viewers, Data Sets, and Widgets

ePlant was introduced in 2017 for exploring large Arabidopsis thaliana data sets from the kilometre to nanometre scales. In the past four years we have used the ePlant framework to develop ePlants for 15 agronomically-important species: maize, poplar, tomato, Camelina sativa, soybean, potato, barley, Medicago truncatula, eucalyptus, rice, willow, sunflower, Cannabis sativa, wheat and sugarcane. We also updated the interface to improve performance and accessibility, and added two new views to the Arabidopsis ePlant - the Navigator and Pathways viewers. The former shows phylogenetic relationships between homologs in other species and their expression pattern similarities, with links to view data for those genes in the respective ePlants. The latter shows Plant Reactome metabolic reactions. We also describe new Arabidopsis data sets including single cell RNA-seq data from roots, and how to embed ePlant eFP expression pictographs into any web page.

bioinformatics↗

bioRxiv2021

Image processing and genome-wide association studies in sunflower identify loci associated with seed-coat characteristics

Sunflower seeds (technically achenes) are characterized by a wide spectrum of sizes, shapes, and colors. These traits are genetically correlated with the branching plant architecture loci, which were introgressed into restorer lines to facilitate efficient hybrid production. To break this genetic correlation between branching and seed traits, high resolution mapping of the genes that regulate seed traits is necessary. Recent progress in genomics permits acquisition of comprehensive genotyping data for a large diversity panel, yet a major constraint for exploring the genetic basis of important phenotypes across large diversity panels is the ability to screen and characterize them efficiently. Here, we implement a cost-effective image analysis pipeline to phenotype seed characteristics in a large sunflower diversity panel comprised of 287 individuals that represents most of the genetic variation in cultivated sunflower. A genome-wide association analysis was performed for seed-coat size and shape traits and significant signals were identified around genes regulating phytohormone activity. In addition, significant seed-coat color QTLs were identified and candidate genes that effect pigmentation were detected including a phytomelanin regulating gene on chromosome 17. Finally, QTLs associated with the seed-coat striped pattern were identified and phytohormone regulating candidate genes were detected. The implementation of image analysis phenotyping for GWAS allowed efficient screening of a large diversity panel and identification of valuable genetic factors effecting seed characteristics at the finest resolution to date.

genetics↗