Biology subjects

Purugganan, M.

Publications and source records attributed to Purugganan, M..

9 recordsLinked to original sources

bioRxiv2025

Foundational genomic resources for date palm: A gap-free, telomere-to-telomere phased assembly of Ajwa and 19 high-quality genome assemblies of Phoenix dactylifera.

Phoenix dactylifera L. is an economically, nutritionally, and culturally important fruit crop in the arid and semi-arid regions of the Middle East and North Africa. Here, we present a gap-free, telomere-to-telomere reference genome of the variety Ajwa, along with 19 additional high-quality assemblies (18 female and 1 male). These assemblies reveal novel chromosomal structures validated through cytogenetics, Hi-C, optical mapping, and synteny analyses with other palm genomes. Chromosome names were revised based on average lengths across all sequenced genomes. The Sex Determination Region (SDR) on chromosome 14 was confirmed through male-specific k-mer analysis, spanning approximately 14.7 Mb. Nucleolar organizing regions (NORs) were localized on chromosome 10, where a large 45S rDNA locus displayed unique repeat spacer motifs containing transposon-like sequences. In some accessions, a second NOR was identified on the female sex chromosome. This collection of date palm assemblies, anchored by the Ajwa reference genome, provides a critical resource for advancing breeding strategies aimed at enhancing the genetic resilience and productivity of date palm.

genomics↗

bioRxiv2022

Nascent transcription and the associated cis-regulatory landscape in rice

BackgroundPlant genomes encode transcripts that require spatio-temporal regulation for proper cellular function, and a large fraction of the regulators can be found in intergenic regions. In animals, distal intergenic regions described as enhancer regions are actively transcribed as enhancer RNAs (eRNAs); the existence of eRNAs in plants has only been fairly recently documented. In this study, we evaluated with high sensitivity the synthesis of eRNAs that arise at genomic elements both distal and proximal to genes by combining PRO-seq with chromatin accessibility, histone modification, and methylation profiles in rice. ResultsWe found that regions defined as transcribed intergenic regions are widespread in the rice genome, and many likely harbor transcribed regulatory elements. In addition to displaying evidence of selective constraint, the presence of these transcribed regulatory elements are correlated with an increase in nearby gene expression. We further identified molecular interactions between genic regions and intergenic transcribed regulatory elements using 3D chromosomal contact data, and found that these interactions were both associated with eQTLs as well as promoting transcription. We also compared the profile of accessible chromatin regions to our identified transcribed regulatory elements, and found less overlap than expected. Finally, we also observed that transcribed intergenic regions that overlapped partially or entirely with repetitive elements had a propensity to be enriched for cytosine methylation, and were likely involved in TE silencing rather than promoting gene transcription. ConclusionThe characterization of eRNAs in the rice genome reveals that many share features of enhancers and are associated with transcription regulation, which could make them compelling candidate enhancer elements.

plant biology↗

bioRxiv2021

Fitness costs and benefits of gene expression plasticity in rice under drought

Genome-wide gene expression changes in response to environmental variability have been widely documented, but we lack detailed and comprehensive understanding of the interplay between this form of phenotypic plasticity and natural selection. Selection on expression plasticity may be limited by environment-specific costs, and plasticity may in turn affect selection on baseline expression levels. Here, we address this fundamental issue by measuring selection on drought-induced plasticity of leaf transcripts in field-grown rice populations. Selection disfavored switching off housekeeping genes under drought. This stress-induced dysregulation did not constrain selection on baseline transcript levels, suggesting compensatory evolution may be possible. Selection rarely acted strongly on individual transcripts but worked polygenically on gradual (continuous) plasticity of co-expressed gene modules regulating photosynthesis via known drought-responsive transcription factors. Finally, selection was tied to inefficient gene architectural features and metabolic costs of expression. Our study provides a genome-wide view of costs and benefits of gene expression plasticity.

evolutionary biology↗

bioRxiv2020

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

O_LIThe date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies. C_LIO_LIWe addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species. C_LIO_LIThe ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris. C_LIO_LIOur study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species. C_LI

evolutionary biology↗

bioRxiv2020

Selection on ancient variations drives the adaptive radiation of Metrosideros across the Hawaiian archipelago

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomic analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for M. polymorpha var. incana and analyzed wholegenome sequences of 131 individuals from 11 taxa sampled across the islands. We found evidence of population structure that grouped taxa by island. Demographic modeling showed concordance between the divergence times of island-specific lineages and the geological formation of individual islands. Gene flow was also detected within and between island taxa, suggesting a complex reticulated evolutionary history. We investigated genomic regions with increased differentiation as these regions may harbor variants involved in local adaptation or reproductive isolation, thus forming the genomic basis of adaptive radiation. We discovered differentiation outliers have arisen from balancing selection on ancient divergent haplotypes that formed before the initial colonization of the archipelago. These regions experienced recurrent divergent selection as lineages colonized and diversified on new islands, and hybridization likely facilitated the transfer of these ancient variants between taxa. Balancing selection on multiple ancient haplotypes-or time-tested variants-may help to explain how lineages with limited gene pools can rapidly diversify to fill myriad ecological niches on remote islands. Significance statementSome of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is not known. We generated novel genomic resources for Hawaiian Metrosideros--a hyper-variable incipient adaptive radiation of woody taxa--for insights into the paradox of remote island radiations. We found that Metrosideros colonized each island shortly after formation and diversified within islands through recurrent selection on ancient variations that predate the radiation. Recurring use of ancient variants may explain how genetically depauperate lineages can diversify to fill countless niches on remote islands.

evolutionary biology↗

bioRxiv2020

Telomere lengths in plants are correlated with flowering time variation

Telomeres are highly repetitive tandemly repeating DNA sequences found at chromosomal ends that protect chromosomes from deterioration during cell division. Using whole genome re-sequencing data, we found substantial natural intraspecific variation in telomere lengths in Arabidopsis thaliana, Oryza sativa (rice) and Zea mays (maize). Genome-wide association mapping in A. thaliana identifies a region that includes the telomerase reverse transcriptase (TERT) gene as underlying telomere length variation. TERT appears to exist in two haplotype groups (L and S), of which the L haplogroup allele shows evidence of a selective sweep in Arabidopsis. We find that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life history traits and chromosome integrity. We suggest that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier), and that chromosomal structure itself is an adaptive trait associated with plant life history strategies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2019

Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island

A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hyper-variable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newelliis origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 million years. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e. secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e. primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.\n\nAuthor summaryA long-standing question in evolution is whether or not new species can arise in the presence of gene flow, which is expected to inhibit the formation of reproductive isolating barriers. We investigated the genomics underlying the origin of a Hawaii Island-endemic riparian tree and purported case of incipient sympatric speciation due to disruptive selection across a sharp forest-riparian ecotone. We find extensive evidence of ongoing gene flow between the riparian tree and its closest relative along with local genomic regions resistant to admixture that likely formed through selection on genes for ecological adaptation and/or reproductive isolation. These results strongly suggest that where disruptive selection is strong, incipient speciation with gene flow is possible even in long-lived, highly dispersible trees.

evolutionary biology↗

bioRxiv2018

Nanopore sequence-based genome assembly of the basmati rice

BACKGROUNDThe circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the groups evolutionary history is not fully resolved. To address these gaps, we used long-read nanopore sequencing and assembled the genomes of two circum-basmati rice varieties, Basmati 334 and Dom Sufid.\n\nRESULTSWe generated two high-quality, chromosome-level reference genomes that represented the 12 chromosomes of Oryza. The assemblies showed a contig N50 of 6.32Mb and 10.53Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies we characterized structural variations segregating across circum-basmati genomes. We discovered repeat expansions not observed in japonica--the rice group most closely related to circum- basmati--as well as presence/absence variants of over 20Mb, one of which was a circum- basmati-specific deletion of a gene regulating awn length. We further detected strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow had its greatest effect on chromosome 10, causing both structural variation and single nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties showed three major geographically structured genetic groups: (1) Bhutan/Nepal group, (2) India/Bangladesh/Myanmar group, and (3) Iran/Pakistan group.\n\nCONCLUSIONAvailability of high-quality reference genomes from nanopore sequencing allowed functional and evolutionary genomic analyses, providing genome-wide evidence for gene flow between circum-aus and circum-basmati, the nature of circum-basmati structural variation, and the presence/absence of genes in this important and iconic rice variety group.

evolutionary biology↗

bioRxiv2017

Multiple origin but single domestication led to domesticated Asian rice

The domestication scenario that led to Asian rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated rice dataset, which were also analyzed by two studies but resulted in two contrasting domestication models. We suggest the analysis of false positive selective sweep regions and phylogenetic analysis of concatenated genomic regions may have been the sources that contributed to the different results. In the end, our result indicates Asian rice originated from multiple wild progenitor subpopulations; however, de novo domestication appears to have occurred only once and the domestication alleles were transferred between rice subpopulation through introgression.

evolutionary biology↗