Biology subjects

Saadain, S.

Publications and source records attributed to Saadain, S..

4 recordsLinked to original sources

bioRxiv2026

pastForward: a Snakemake pipeline for ancient and historical DNA with eukaryote-wide taxonomic screening and tracking of copy-number variation

Ancient and historical DNA has the potential to resolve many open questions in biology. While pipelines for processing ancient and historical DNA exist, none combine user-friendly, configurable processing with copy number variation tracking and targeted taxonomic profiling. Therefore, we developed pastForward, a fully automated Snakemake pipeline that integrates all analysis steps from raw reads to damage-rescaled BAM files in a single reproducible workflow. It performs ancient and historical DNA processing, including adapter trimming, read merging, deduplication, damage assessment, quality rescaling, and generates interactive reports summarizing the endogenous read content, library complexity, and breadth and depth coverage statistics. These reports allow users to rapidly assess the quality of sequencing data. It handles single- and paired-end NGS libraries. Mapping to multiple reference sequences is supported, facilitating co-analysis of host and endosymbiont sequences and genotyping of marker genes such as COI. pastForward further integrates two novel tools. ECMSD (Efficient Comprehensive Mitochondrial Sequence Detector) screens each library for eukaryotic DNA by aligning reads against a mitochondrial reference database. The presence of bacteria, archaea and viruses is detected in parallel with Centrifuge. REVEAL (Read-based Estimation and visualization of Element Abundance and Loci) quantifies and visualizes copy number variation of genetic features, such as transposable elements (TEs) or gene duplications. Two case studies demonstrate the usage of the pipeline. Using pastForward on dog genomic time series, including Neolithic samples, we confirm that the copy number of AMY2B, which encodes the starch-digesting enzyme amylase, increased during domestication. From historical D. melanogaster genomes, we recover the recent invasion of the transposable element opus. It is absent in specimens from the 1800s and present from 1933 onward. By efficiently processing large numbers of samples, pastForward facilitates longitudinal tracking of genomic features in diverse species.

bioinformatics↗

bioRxiv2025

The ongoing invasion of the endogenous retrovirus Kuruka in natural Drosophila melanogaster populations

Transposable elements are mobile DNA sequences capable of proliferating within host genomes, occasionally capable of crossing species boundaries via horizontal transfer (HT). Here, we report the discovery and characterization of Kuruka, a newly invading endogenous retrovirus in natural D. melanogaster populations. Kuruka encodes an envelope protein and belongs to the gypsy /gypsy superfamily. Analysis of over 1000 D. melanogaster genomes revealed that Kuruka first appeared in sub-Saharan Africa in 2010. By 2017-2019 Kuruka had spread to Asia, Europe and America in 2017-2019, and is still actively invading Europe and Oceania as of 2021. Phylogenomic analyses suggest that Kuruka entered in D. melanogaster via a recent HT from an Afrotropical Drosophila species, most likely D. erecta. This is the first case of a recent HT from an Afrotropical donor species to D. melanogaster. In D. erecta, Kuruka has a single genomic insertion, which is located within flamenco, a master regulator of TE activity. The presence of an active host defense (piRNAs) suggests that Kuruka is silenced in D. erecta. Our findings establish Kuruka as a valuable model for studying the early stages of TE invasions and the dynamics of genome defense in real time.

genomics↗

bioRxiv2024

Closely related facultative and constitutive CAM phenotypes show little transcriptomic overlap in the subgenus Tillandsia

Crassulacean acid metabolism (CAM) is a water-efficient photosynthetic strategy involving a coordinated suite of complex traits including metabolic, anatomical and regulatory aspects that shift across the diel cycle. While CAM has evolved repeatedly in land plants, the evolutionary routes enabling this convergence remain elusive. Whereas the same core CAM (de)carboxylation genes are consistently involved, a key question is whether distinct CAM phenotypes also depend on a shared set of auxiliary genes, reflecting a quantitative continuum of expression, or whether they can instead emerge through divergent or redundant peripheral solutions. The bromeliad subgenus Tillandsia, with diverse photosynthetic strategies, offers an ideal system to explore this question. Using physiological and transcriptomic analyses of well-watered and water-limited accessions of two closely related species, we characterized facultative and constitutive CAM. By comparing orthologous gene expression and orthogroup recruitment, we found that while both species performed CAM upon water-withholding, transcriptional shifts in pathways related to stomatal movement, sugar/malate transport, aquaporins and starch metabolism showed minimal overlap. Core enzymes involved in the CAM (de)carboxylation cycle exhibited broadly shared expression patterns, yet the facultative CAM species uniquely up-regulated PPC2 at night instead of the canonical CAM-related PEPC ortholog PPC1. Our study reveals that, while the expression of certain core CAM enzymes is conserved, the surrounding transcriptional architecture can differ substantially even between closely related species. This supports a model in which CAM evolves through a mosaic recruitment of functionally equivalent, yet non-orthologous genes - underscoring its flexible and modular genetic architecture. These insights advance our understanding of the mechanisms enabling the repeated evolution of CAM and its capacity to facilitate adaptive diversification.

evolutionary biology↗

bioRxiv2023

Short structural variation fuelled CAM evolution within an explosive bromeliad radiation

1.The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, TE dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species, but are no candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.

evolutionary biology↗