Biology subjects

Leitch, I.

Publications and source records attributed to Leitch, I..

5 recordsLinked to original sources

bioRxiv2026

Horizontal gene transfer fuels metabolic innovation in the grass Zuloagaea bulbosa

Horizontal gene transfer (HGT) allows the movement of DNA across broad evolutionary distances without sexual reproduction. In grasses, HGT is widespread and although a few horizontally transferred genes (HTG) are adaptive, most are purged over time. Within the adaptive HTG, biosynthetic genes encoding enzymes that act together in the same pathway and physically co-localise in clusters have been reported multiple times. The aims of this study are to test whether HGT is bidirectional in a pair of grass species, maize and Zuloagaea bulbosa, and if HTGs are found more than expected by chance in biosynthetic genes organised in clusters. To achieve this, we firstly generated a phased reference genome for Z. bulbosa. Then we identified 56 candidate horizontally transferred genes, of which 45% were from Andropogoneae, including two likely to be of maize origin. Since transfers from Z. bulbosa to maize were previously described, our results show that HGT is bidirectional, although the balance might not be even. After predicting all biosynthetic gene clusters in the Z. bulbosa genome, we found that HTGs are enriched in biosynthetic genes organised in clusters. This correlation between HGT and gene clustering is likely to be a consequence of selection due to the immediate adaptive benefit a whole pathway can provide. Two of the HTGs from Andropogoneae belong to the benzoxazinoid BGC, which previously underwent an ancestral transfer from Panicoideae into Pooideae. The dynamism of biosynthetic gene clusters, including recurrent horizontal gene transfers, contributes to the extraordinary metabolic diversity present in plants. Significance statementHorizontal gene transfer (HGT) is a significant driver of evolution that is widespread in grasses. In this study, we show for the first time reciprocal transfer of DNA between maize and another Mexican grass, Zuloagaea bulbosa. This result represents a proof of concept of bidirectional HGT which allows for limited, recurrent gene flow among distant species. Furthermore, we show that horizontally transferred genes are enriched for biosynthetic genes organised in biosynthetic gene clusters, regions of the genome that encode for multiple enzymes that act in the same biosynthetic pathway. We hypothesise that the transfer of a complete multi-genic pathway, ready to be used and potentially offering an evolutionary advantage, might promote a predominant retention of gene clusters in comparison with background HGT.

genomics↗

bioRxiv2025

Functional traits drive speciation in tropical palms through complex interactions between genome size, adaptation and allometry

O_LIThe importance of functional trait evolution and genome size on plant speciation are well established, but their interactive effects remain untested in a single comparative macroevolutionary framework. C_LIO_LIWe integrated phylogenetic, trait and genome size data for palms (Arecaceae) - a large pantropical family (>2600 species) with 167-fold variation in trait and 60-fold variation in genome size. We used structural equation modelling to test three key hypotheses: trait evolution promotes speciation (H1: trait flexibility hypothesis), and, speciation and trait evolution rates are constrained by allometry (H2: allometric constraint hypothesis) and genome size (H3: large genome constraint hypothesis). C_LIO_LIWe detected seven major speciation rate shifts during the ca. 110-million-year history of palms. Tip-derived speciation rates increased with faster evolution in leaves and plant height, supporting H1, whereas correlated evolution between trait evolution rates indirectly influenced speciation, supporting H2. Large genomes decreased plant height and stem diameter evolutionary rates, but increased leaf size evolution and speciation rates, thus partly supporting H3. C_LIO_LIOur findings illustrate how the complex interplay between genome size, allometry and trait evolvability affect speciation, emphasizing the importance of holistic approaches in macroevolution. Furthermore, our results point to potential general mechanisms driving speciation rates throughout the plant Tree of Life. C_LI

evolutionary biology↗

bioRxiv2024

Assessing male reproductive investment in Papaveraceae using flow cytometry reveals lineage-specific trajectories to pollen-to-ovule ratio reduction

Male reproductive investment, in particular pollen production, is a crucial and ecologically relevant component of a plants phenotype and reproductive success. Its evolutionary trajectory, however, remains understudied, partly due to a lack of convenient methods to assess it. We developed a protocol for pollen quantification by flow cytometry and applied it to 107 flowers from 38 Papaveraceae species differing widely in floral traits (e.g., floral symmetry, stamen number), pollination syndromes (e.g., wind and insect pollination) and reproductive systems (e.g., degree of autogamy). We phylogenetically tested whether pollen number evolved in association with ovule, carpel, stamen and flower numbers per inflorescence, and if there were interacting effects between floral symmetry and/or self-compatibility with pollen and ovule production. Compared to manual counts, results using flow cytometry were similar, but much faster to obtain and more precise. Pollen and ovule numbers per flower varied > 39,000x and > 550x, respectively, among species. Pollen production correlated positively with ovule, carpel and stamen numbers. Lineage-specific trajectories to pollen-to-ovule ratio reduction (to values < 300) are observed. One involved increased female investment in ruderal species belonging to the subfamily Papaveroideae, while the other occurs through decreased male investment and is associated with the evolution of floral traits towards greater specialisation. The impact of reproductive systems on male and female investment is limited to ovule production in non-actinomorphic flowers. Taken together, these results revealed that the evolutionary associations between reproductive systems, floral traits, and pollen and ovule production are lineage-specific. Given the profound contrasts at the subfamily level of Papaveraceae, broader surveys across the diversity of flowering plants are clearly needed to better understand factors driving the evolution of reproductive investment. Such studies will certainly be facilitated by our new high-throughput pollen counting method outlined here.

plant biology↗

bioRxiv2022

Building a novel nuclear-organelle genomic framework for the fever tree (Cinchona pubescens Vahl) through short and long-read DNA data assemblies

BackgroundThe Andean Fever tree (Cinchona L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids, which have been vital to treating malaria for centuries. C. pubescens Vahl, in particular, has been an essential source of income for several countries within its native range in north-western South America. However, an absence of available genomic resources is essential for placing the Cinchona species within the tree of life and setting the foundation for exploring the evolution and biosynthesis of quinine alkaloids. FindingsWe address this gap by providing the first highly contiguous and annotated nuclear and organelle genome assemblies for C. pubescens. Using a combination of [~]120 Gb of long sequencing reads derived from the Oxford Nanopore PromethION platform and 142 Gb of short-read Illumina data. Our nuclear genome assembly comprises 603 scaffolds comprising a total length of 904 Mb, and the completeness represents [~]85% of the genome size (1.1 Gb/1C). This draft genome sequence was complemented by annotating 72,305 CDSs using a combination of de novo and reference-based transcriptome assemblies. Completeness analysis revealed that our assembly is moderately complete, displaying 83% of the BUSCO gene set and a small fraction of genes (4.6%) classified as fragmented. Additionally, we report C. pubescens plastome with a length of [~]157 Kb and a GC content of 37.74%. We demonstrate the utility of these novel genomic resources by placing C. pubescens in the Gentianales order using additional plastid and nuclear datasets. ConclusionsOur study provides the first genomic resource for C. pubescens, thus opening new research avenues, including the provision of crucial genetic resources for analysis of alkaloid biosynthesis in the Fever tree.

bioinformatics↗

bioRxiv2020

Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species

O_LIC4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this single species encompasses C4 and non-C4 populations. C_LIO_LIUsing phylogenomics and population genomics, we infer the history of dispersal and secondary exchanges before, during, and after photosynthetic divergence in A. semialata. We further establish the genetic origins of polyploids in this species. C_LIO_LIOrganelle phylogenies indicate limited seed dispersal within the Central Zambezian region of Africa, where the species originated [~] 2-3 Ma. Outside this region, the species spread rapidly across the paleotropics to Australia. Comparison of nuclear and organelle phylogenies and analyses of whole genomes reveal extensive secondary gene flow. In particular, the genomic group corresponding to the C4 trait was swept into seeds from distinct geographic regions. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. C_LIO_LILimited dispersal and isolation allowed lineage divergence, while episodic secondary exchanges led to the pollen-mediated, rapid spread of the derived C4 physiology. Overall, our study suggests that local adaptation followed by recurrent secondary gene flow promoted physiological diversification in this grass species. C_LI

evolutionary biology↗