Biology subjects

Silva Arias, G. A.

Publications and source records attributed to Silva Arias, G. A..

4 recordsLinked to original sources

bioRxiv2023

Contrasting patterns of presence-absence variation of NLRS within S. chilense are mainly shaped by past demographic history

Understanding the evolution of pathogen resistance genes (nucleotide-binding site-leucine-rich repeats, also known as NLRs) within a species requires a comprehensive examination of factors that affect gene loss and gain. We present a new reference genome of Solanum chilense, that leads to an increased number and more accurate annotation of NLRs. Next, using a target-capture approach, we quantify the presence-absence variation (PAV) of NLR loci across 20 populations from different habitats. We build a rigorous pipeline to validate the identification of PAV of NLRs, then show that PAV is larger within populations than between populations, suggesting that maintenance of NLR diversity is linked to population dynamics. Furthermore, the amount of PAV is not correlated with the NLR presence in gene clusters in the genome, but rather with the past demographic history of the species, with loss of NLRs in diverging populations at the distribution edges and smaller population sizes. Finally, using a redundancy analysis, we find limited evidence of PAV being linked to environmental gradients. Our results contradict the classic assumptions of the important selective role of PAV for NLRs, and suggest that NLRs PAV is driven by random processes (and weak selection) in an outcrossing plant with high nucleotide diversity.

evolutionary biology↗

bioRxiv2023

Copy number variations shape genomic structural diversity underpinning ecological adaptation in the wild tomato Solanum chilense

Copy Number Variation (CNV) is a prevalent type of variation affecting large genomic regions which contributes to both genetic diversity and ecological adaptation in plants. The target genes involved in adaptation through CNV in tomato and its wild relatives remain unexplored at the population level. Therefore, we characterized the CNV landscape of Solanum chilense, a wild tomato species adapted to dry habitats, using whole-genome short-read data of 35 individuals from seven populations. We identified 212,207 CNVs, including 160,926 deletions and 51,281 duplications. We found a higher number of CNVs in diverging populations occupying stressful habitats. CNVs and single nucleotide polymorphisms analyses concordantly revealed the known species population structure, underscoring the impact of historical demographic and recent colonization events shaping genome-wide CNVs. Furthermore, we identified 3,539 candidate genes with highly divergent CNV profiles across populations. Interestingly, these genes are functionally associated with response to abiotic stress and linked to multiple pathways of flowering time regulation. Gene CNVs in S. chilense exhibit two evolutionary trends: gene loss in ancestral lineages distributed in central and southern coast populations and gene gain in the most recent diverged lineage from the southern highland region. Environmental association of the CNVs ultimately linked the dynamics of gene copy number to six climatic variables. It suggests that natural selection has likely shaped CNV patterns in stress-response genes promoting the colonization of contrasting habitats. Our findings provide insights into the role of CNV underlying adaptation during recent range expansion.

evolutionary biology↗

bioRxiv2023

Evolution of two gene networks underlying adaptation to drought stress in the wild tomato Solanum chilense

Drought stress is a key factor limiting plant growth and the colonization of arid habitats by plants. Here, we study the evolution of gene expression response to drought stress in a wild tomato, Solanum chilense naturally occurring around the Atacama Desert in South America. We conduct a transcriptome analysis of plants under standard and drought experimental conditions to understand the evolution of drought-response gene networks. We identify two main regulatory networks corresponding to two typical drought-responsive strategies: cell cycle and fundamental metabolic processes. We estimate the age of the genes in these networks and the age of the gene expression network, revealing that the metabolic network has a younger origin and more variable transcriptome than the cell-cycle network. Combining with analyses of population genetics, we found that a higher proportion of the metabolic network genes show signatures of recent positive selection underlying recent adaptation within S. chilense, while the cell-cycle network appears of ancient origin and is more conserved. For both networks, however, we find that genes showing older age of selective sweeps are the more connected in the network. Adaptation to southern arid habitats over the last 50,000 years occurred in S. chilense by adaptive changes core genes with substantial network rewiring and subsequently by smaller changes at peripheral genes.

evolutionary biology↗

bioRxiv2021

Local and temporal adaptation to climatic change in a wild tomato species via selective sweeps.

O_LIPositive selection is the driving force underpinning local adaptation, and leaves footprints of selective sweeps at the underlying major genes. Quantifying the timing of selection and revealing the genetic bases of adaptation in plants species occurring in steep and varying environmental gradients is crucial to predict a species ability colonize new niches. C_LIO_LIWe use whole genome sequence data from six populations across three different habitats of the wild tomato species Solanum chilense to infer the past demographic history and search for genes under strong positive selection. We then correlate current and past climatic projections with the demographic history, allele frequencies, the age of selection events, and distribution shifts. C_LIO_LIWe find evidence for several selective sweeps targeting regulatory networks involved in root hair development in low altitude, and response to photoperiod and vernalization in high altitude populations. These sweeps occur in a concerted fashion in a given regulatory gene network at particular periods of substantial climatic change. C_LIO_LIWe decipher the genetic bases and the timing of local adaptation during plant colonization of semi-arid habitats using a unique combination of genome scans for selection and modelling of past climatic data. C_LI

evolutionary biology↗