Biology subjects

Perfectti, F.

Publications and source records attributed to Perfectti, F..

9 recordsLinked to original sources

bioRxiv2026

Benchmarking long-read RNA sequencing for de novo transcriptome assembly in non-model plant species: insights from Moricandia arvensis

De novo transcriptome assembly is the standard approach for constructing a reference transcriptome in non-model plants that lack a high-quality genome, yet short-read assemblies struggle to resolve full-length isoforms. Long-read Iso-Seq (PacBio) captures full-length transcripts directly, but its use as a primary reference and the choice of downstream assembly pipeline remains poorly benchmarked. Here, we construct genome-free Iso-Seq reference transcriptomes for two organs, flower and leaf, of the non-model species Moricandia arvensis (L.) DC. (Brassicaceae), and systematically compare pipeline strategies combining Iso-Seq clustering, CD-HIT redundancy reduction, and Cogent graph-based reconstruction, benchmarked by BUSCO completeness, RSEM short-read mapping, and TransDecoder ORF completeness. We find that the optimal pipeline is organ specific. For flower, CD-HIT pre-filtering followed by Cogent reconstruction produced a high-quality reference (95.3% BUSCO complete). For the leaf, the same Cogent step was detrimental, reducing BUSCO completeness from 90.1% to 78.0% by incorrectly merging distinct genes; therefore, CD-HIT at 95% identity without reconstruction was retained. We trace this divergence to organ-specific input-data characteristics: leaf transcripts show extreme full-length-read expression skew and predominantly single-isoform gene support, depriving Cogent's graph algorithm of the multi-isoform evidence it requires. We find that the concentration of full-length reads among the most highly expressed transcripts predicts pipeline suitability before reconstruction, with per-transcript read depth acting as a necessary but non-discriminating floor. Because the leaf reference lacked gene-level structure, we further recovered gene-isoform grouping using expression-aware read-clustering (Corset), which preserved completeness while restoring the paralog structure expected of a paleopolyploid genome and outperformed sequence-only clustering. Our results provide a robust, genome-free framework for constructing full-length reference transcriptomes in non-model plant species and demonstrate that pipeline choice must be evaluated per organ rather than assuming one size fits all.

bioinformatics↗

bioRxiv2024

An accelerating, decreasing phylogenetic trend in SARS-CoV-2 genome compositional heterogeneity during the pandemic

The rapid evolution of SARS-CoV-2 during the pandemic, driven by a plethora of mutations, many of which enable the virus to evade host resistance, has likely altered its genomes compositional structure (i.e. the arrangement of compositional domains of varying lengths and nucleotide frequencies within the genome). To explore this hypothesis, we summarize the evolutionary effects of these mutations by computing the Sequence Compositional Complexity (SCC) in random datasets of fully sequenced genomes. Phylogenetic ridge regression of SCC against time reveals a striking downward evolutionary trend, as well as an increasing rate of change, suggesting the ongoing adaptation of the viruss genome structure to the human host. Other genomic features, such as strand asymmetry, the effective number of K-mers, and the depletion of CpG dinucleotides, each linked to the viruss adaptation to its human host, also exhibit decreasing phylogenetic trends over the course of the pandemic, along with strong phylogenetic correlations to SCC. Overall, our findings suggest an accelerated, genome-wide evolutionary trend toward a more symmetric and homogeneous genome compositional structure in SARS-CoV-2.

evolutionary biology↗

bioRxiv2022

Lack of ITS sequence homogenization in congeneric plant species with different ploidy levels

The internal transcribed spacers (ITS) exhibit concerted evolution by the fast homogenization of these sequences at the intragenomic level. However, the rate and extension of this process are unclear and might be conditioned by the number and divergence of the different ITS copies. In some cases, such as hybrid species and polyploids, ITS sequence homogenization appears incomplete, resulting in multiple haplotypes within the same organism. Here, we studied the dynamics of concerted evolution in 85 individuals of seven plant species of the genus Erysimum (Brassicaceae) with multiple ploidy levels. We estimated the rate of concerted evolution and the degree of sequence homogenization separately for ITS1 and ITS2 and whether these varied with ploidy. Our results showed incomplete sequence homogenization, especially for polyploid samples, indicating a lack of concerted evolution in these taxa. Homogenization was usually higher in ITS2 than in ITS1, suggesting that concerted evolution operates more efficiently on the former. Furthermore, the hybrid origin of several species appears to contribute to the maintenance of high haplotype diversity, regardless of the level of ploidy. These findings indicate that sequence homogenization of ITS is a dynamic and complex process that might result in varying intra- and inter-genomic diversity levels.

evolutionary biology↗

bioRxiv2022

The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS CoV 2 coronavirus

Since the outbreak of the COVID-19 pandemic, the SARS-CoV-2 coronavirus has accumulated an important amount of genetic and genomic variability through mutation and recombination events. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we summarize all this sequence variability by computing the Sequence Compositional Complexity (SCC) in more than 23,000 high-quality coronavirus genome sequences from across the globe, covering the period spanning from the start of the pandemic in December 2019 to March 2022. In early samples, we found no statistical support for any trend in SCC values over time, although the virus as a whole appears to evolve faster than Brownian Motion expectation. However, in samples taken after the first Variant of Concern (VoC) with higher transmissibility (Alpha) emerges, and controlling for phylogenetic and sampling effects, we were able to detect a statistically significant trend for decreased SCC values over time. SARS-CoV-2 evolution towards lower values of genome heterogeneity is further intensified by the emergence of successive, widespread VoCs. Concomitantly to the temporal reduction in SCC, its absolute evolutionary rate kept increasing toward the present, meaning that the SCC decrease itself accelerated over time. As compared to Alpha or Delta variants, the currently dominant VoC, Omicron, shows much stronger trends in both SCC values and rates over time. These results indicate that the increases in fitness of variant genomes associated to a higher transmissibility leads to a reduction of their genome sequence heterogeneity, thus explaining the general slowdown of SCC along with the pandemic course.

genomics↗

bioRxiv2021

Accelerated decline of genome heterogeneity in the SARS-CoV-2 coronavirus

During the spread of the COVID-19 pandemic, the SARS-CoV-2 coronavirus underwent mutation and recombination events that altered its genome compositional structure, thus providing an unprecedented opportunity to search for adaptive evolutionary trends in real-time. The mutation rate in coronavirus is known to be lower than expected for neutral evolution, thus suggesting a role for natural selection. We summarize the compositional heterogeneity of each viral genome by computing its Sequence Compositional Complexity (SCC). To study the full range of SCC diversity, random samples of high-quality coronavirus genomes covering pandemic time span were analyzed. We then search for evolutionary trends that could inform on the adaptive process of the virus to its human host by computing the phylogenetic ridge regression of SCC against time (i.e., the collection date of each viral isolate). In early samples, we find no statistical support for any trend in SCC, although the viral genome appears to evolve faster than Brownian Motion (BM) expectation. However, in samples taken after the emergence of high fitness variants, and despite the brief time span elapsed, a driven decreasing trend for SCC, and an increasing one for its absolute evolutionary rate, are detected, pointing to a role for selection in the evolution of SCC in coronavirus genomes. We conclude that the higher fitness of variant genomes leads to adaptive trends of SCC over pandemic time in the coronavirus.

genomics↗

bioRxiv2021

Hybridization and introgression are prevalent in Southern European Erysimum (Brassicaceae) species

Background and AimsHybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles of sympatry and isolation, creating conditions for extensive hybridization and introgression. Polyploidization is another genome-wide process with a major influence on plant evolution. Both hybridization and polyploidization can have complex effects on plant evolution. However, these effects are often difficult to understand in recently evolved species complexes. MethodsWe combined flow cytometry, transcriptomic and genomic analyses, and pollen-tube growth assays to investigate the consequences of polyploidization, hybridization, and introgression on the recent evolution of several Erysimum (Brassicaceae) species from the South of the Iberian Peninsula, a well-known glacial refugium. This species complex differentiated in the last 2Myr, and its evolution has been hypothesized to be determined mainly by polyploidization, interspecific hybridization, and introgression. Key ResultsOur results support a scenario of widespread hybridization involving both extant and "ghost" taxa. Several taxa studied here, most notably those with purple corollas, are polyploids, likely of allopolyploid origin. Moreover, hybridization in this group might be an ongoing phenomenon, as prezygotic barriers appeared weak in many cases. ConclusionsThe evolution of Erysimum spp. has been determined by hybridization to a large extent. The adaptive value of such genomic exchanges remains unclear, but our results indicate the importance of hybridization for plant diversification across evolutionary scales.

evolutionary biology↗

bioRxiv2021

On the contingent nature of satellite DNA evolution

BackgroundThe full catalogue of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago. ResultsWe found that about one-third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra- and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species. ConclusionsOur analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.

genomics↗

bioRxiv2021

Phenotypic plasticity triggers rapid morphological convergence

Phenotypic convergence, the independent evolution of similar traits, is ubiquitous in nature, happening at all levels of biological organizations and in most kinds of living beings. Uncovering its mechanisms remains a fundamental goal in biology. Evolutionary theory considers that convergence emerges through independent genetic changes selected over long periods of time. We show in this study that convergence can also arise through phenotypic plasticity. We illustrate this idea by investigating how plasticity drives Moricandia arvensis, a mustard species displaying within-individual polyphenism in flowers, across the morphological space of the entire Brassicaceae family. By compiling the multidimensional floral phenotype, the phylogenetic relationships, and the pollination niche of over 3000 Brassicaceae species, we demonstrated that Moricandia arvensis exhibits a plastic-mediated within-individual floral disparity greater than that found not only between species but also between higher taxonomical levels such as genera and tribes. As a consequence of this divergence, M. arvensis moves outside the morphospace region occupied by its ancestors and close relatives, crosses into a new region where it encounters a different pollination niche and converges phenotypically with distant Brassicaceae lineages. Our study suggests that, by inducing phenotypes that explore simultaneously different regions of the morphological space, plasticity triggers rapid phenotypic convergence.

evolutionary biology↗

bioRxiv2019

Rapid and independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a highly resolved phylogeny, revealing that cardenolide diversity increased rapidly rather than gradually over evolutionary time. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on distinct molecular diversification mechanisms. Ancestral and novel chemical defenses in Erysimum thus appear to provide complementary rather than redundant functions.

plant biology↗