Biology subjects

Sloan, D. B.

Publications and source records attributed to Sloan, D. B..

At least 19 recordsLinked to original sources

bioRxiv2026

Mitochondrial dynamics can resolve stoichiometric challenges in plant mtDNA repair

Although mitochondrial DNA (mtDNA) is subject to damage and high mutation rates in many eukaryotes, plants have a variety of mtDNA repair pathways that somehow result in exceptionally low mutation rates. However, the stoichiometry of biomolecules in plant mitochondria raises challenges for the DNA repair process. The protein complexes responsible for repair pathways contain subunits present at low copy numbers per mitochondrion. Mitochondria on average contain less than a full genome, limiting the capacity for templated repair, and raising the risk that repair machinery is localised to a DNA-empty mitochondrion where it cannot be used. Here we build on recent experimental characterisation of the copy numbers and physical processes involved to model the capacity for DNA repair in plant mitochondria. We find that targeted import of protein machinery, biased fusion of mitochondria bearing DNA, and exchange of biomolecules upon fusion can improve repair capacity through different mechanisms. Specifically, our model indicates that base excision repair can keep ~95% of mtDNA intact even without targetting or exchange rules and that targetting protein import to DNA-bearing mitochondria or exchanging protein content drives this to effectively 100%. In contrast, template repair cannot keep a majority of mtDNA intact unless mtDNA is shared across mitochondria through fusion, in which case its efficacy increases. Exchanging of metabolons (repair protein complexes) increases repair efficiency across all circumstances. We discuss the implications of our model for plant development and organelle inheritance.

plant biology↗

bioRxiv2026

Plant MutS Homolog 1 is a mismatch-directed nuclease required for organelle genome maintenance

The exceptionally low mutation rates of plant organellar genomes imply the existence of DNA surveillance mechanisms that counteract replication errors and DNA damage. Genetic evidence implicates MutS HOMOLOG 1 (MSH1) as a central component of this pathway, as loss of MSH1 results in the accumulation of point mutations. MSH1 is a unique protein that combines an N-terminal MutS-like mismatch-recognition module with a Cterminal GIYYIG nuclease domain. Here, we show that Arabidopsis thaliana MSH1 (AtMsh1) recognizes mismatches, insertion/deletion loops, and damaged bases within double-stranded DNA and introduces staggered DNA breaks at positions flanking the mismatch or lesion. Given the presence of an active homologous recombination machinery in plant organelles, we hypothesize that these DNA ends may be processed by exonucleases to remove the mismatched or damaged DNA while generating 3' single-stranded DNA substrates suitable for homologous recombination-mediated repair and gene conversion. Together, our findings support a model in which AtMsh1 functions as a minimal mismatch repair system that couples mismatch recognition to DNA incision, providing a potential mechanism for suppressing mutation accumulation and maintaining the remarkable stability of plant organellar genomes

biochemistry↗

bioRxiv2026

Reshaping Organellar Translation and tRNA Metabolism: The Consequences of Photosynthesis Loss and Massive Horizontal Gene Transfer

The transition to holoparasitism in plants precipitates the loss of photosynthesis, fundamentally altering the selective landscape acting on organellar genomes. These changes raise questions about the mechanisms by which the essential, coevolved machinery of translation responds to extreme genomic erosion and metabolic dependency. Integrating comparative genomics, tRNA sequencing, and subcellular localization assays, we elucidate the extensive rewiring of organellar translation systems and the tRNA-dependent tetrapyrrole biosynthesis pathway in the holoparasitic angiosperm family Balanophoraceae, which exhibits extreme reduction of tRNA content in plastid and mitochondrial genomes. We identified a rare evolutionary event: the putative intracellular transfer of the plastid initiator tRNA (tRNA-iMet) to the nucleus, which compensates for its loss from the plastid genome. We also demonstrate that the unusual UAG-to-Trp reassignment in the Balanophora plastid genetic code is driven by the loss of release factor pRF1 and the recruitment of a mutated nuclear tRNA-Trp. Furthermore, we reveal that the retention of organellar nuclear-encoded aminoacyl-tRNA synthetases is dictated by the presence/absence of cognate organellar tRNAs, which appear to be functional regardless of their foreign (horizontal transfer from the host plant) or native origins. Finally, we uncover a striking evolutionary asymmetry in nuclear-encoded ribosomal proteins: while plastid subunits exhibit elevated substitution rates consistent with relaxed selection and compensatory coevolution, mitochondrial subunits display high sequence conservation, likely maintaining compatibility with the extensive horizontal gene transfer observed in this lineage. Collectively, these findings represent some of the most extreme changes ever identified in the anciently conserved machinery of plant organellar translation.

evolutionary biology↗

bioRxiv2025

Evolutionary rates provide genomic insights into convergent and lineage-specific evolution in carnivorous plants

Carnivorous plants (CPs) are striking examples of convergent evolution across ecological, morphological, and molecular scales, making them ideal systems for investigating genomic adaptation to extreme environments. While genomic studies have shown that gene family expansion and functional recruitment underlie key carnivorous traits, the effects of these transitions on rates of sequence evolution remain incompletely understood. Here, we present a comparative framework to examine evolutionary rate shifts across 30 carnivorous and non-carnivorous eudicots in over 12,000 gene families. Analyzing branch-lengths and evolutionary rate covariation (ERC), we detect both lineage-specific and convergent acceleration in CPs for genes associated with stress response, stimulus signaling, and light perception. Accelerated genes often belong to expanded families and show relaxation of purifying selection pressure. Despite the limited number of specific genes or gene families showing convergent acceleration across CP lineages, we find strong convergence at the functional level. Distinct sets of accelerated genes in each CP lineage are enriched for similar functional pathways, particularly light and hormone responses. ERC network analysis identifies a stress- and stimulus-responsive gene community with lineage-specific acceleration in Sarraceniaceae species and moderate acceleration in other CP lineages. Hub genes in this network are also co-expressed in a distantly related non-CP model system, suggesting repeated co-option of an ancestral regulatory module for carnivorous functions. Together, our results show that convergent genomic rate accelerations in CPs primarily involve functionally equivalent or similar but lineage-distinct genes, shaped by gene duplication, relaxed selection, and co-option of stress-response networks.

evolutionary biology↗

bioRxiv2025

The effects of rapid mitochondrial gene loss on organellar proteomes

Mitochondrial genomes retain only a tiny number of genes from their bacterial progenitors, including key components of protein translation machinery. The set of mitochondrially encoded tRNAs and ribosomal subunits is highly variable across angiosperms, with many examples of mitochondrial gene loss, replacement, and/or transfer to the nucleus. This dynamic history suggests large-scale remodeling of mitochondrial translation machinery in some lineages, but such conclusions are largely inferred from genomic sequence and protein targeting predictions. Here, we use proteomic (LC-MS/MS) analysis of purified mitochondria and chloroplasts from angiosperm species with major differences in mitochondrial gene content (Arabidopsis thaliana and Silene conica). Our analysis largely confirms the current understanding of subcellular localization for nuclear-encoded proteins involved in tRNA metabolism and ribosome function in A. thaliana, although some aminoacyl-tRNA synthetases (aaRSs) may have more specialized subcellular roles than previously thought. In contrast, S. conica has undergone extensive mitochondrial gene loss and numerous associated changes in the composition of its mitochondrial proteome, including apparent retargeting of aaRSs, replacement of ribosomal subunits, and loss of the glutamine amidotransferase (GatCAB) complex. Overall, this analysis illustrates how the complex network of molecular interactions necessary for mitochondrial translation are perturbed by gene loss, transfer, and replacement. Significance StatementPlant mitochondrial genomes exhibit exceptional diversity in gene content across species due to ongoing processes of gene loss, transfer, and functional replacement. However, our understanding of the consequences of these genomic changes on the mitochondrial proteome remain limited. Here, we compare organellar (mitochondrial and chloroplast) proteomes across species of flowering plants, revealing a large-scale rewiring of mitochondrial protein synthesis machinery has coincided with loss of tRNA and ribosomal protein genes from the mitochondrial genome.

molecular biology↗

bioRxiv2025

Plant MutS2 proteins function in plastid ribosome quality control

Tight regulation of chloroplast translation is essential for plant growth, development and environmental response. Active translation can result in stalling and collision of ribosomes, which have negative fitness consequences. However, the ways in which chloroplasts respond to these types of translational stressors remain unknown. Here, we identify two MutS2 proteins that act as critical players in plastid ribosome-associated quality control (RQC) in Arabidopsis. We found that both MutS2A and MutS2B are required to overcome specific antibiotic-induced ribosome stalling and collisions. Further, these proteins appear to be essential for tissue greening during de-etiolation, potentially due to increased translational demand during the transition from etioplast to chloroplast. Although bacterial homologs of MutS2 have been widely recognized for their role in regulating homologous recombination, we found only weak support for this function in Arabidopsis plastids. Therefore, these proteins, which are widely conserved among photosynthetic eukaryotes, appear to be central in the resolution of ribosome collisions and may play a critical role during times of increased translational demand.

plant biology↗

bioRxiv2025

Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities

Mismatches between interacting mitochondrial and nuclear gene products in hybrids have been proposed to disproportionately contribute to early species boundaries. Under this model, genetic incompatibilities emerge when mitochondrial haplotypes are in a cellular context without their coevolved nuclear-encoded mitochondrial (n-mt) proteins. Some case studies have shown that such disruptions in mitonuclear coevolution can contribute to reproductive isolation, but whether mitonuclear incompatibilities generate selection that impacts multiple n-mt loci and/or causes broad, genome-wide contributions to speciation is unclear. Here, we leverage a system with several hybridizing species pairs (Xiphophorus fishes) that have known mitonuclear incompatibilities of large effect. We divided nuclear-encoded genes into three classes based on level of interaction with mitochondrial gene products. We found only inconsistent statistical support for a difference between these classes in the degree of positive covariation in mitonuclear ancestry. We discuss evidence that these analyses are sensitive to the amount of non-synonymous divergence between parent species in interacting n-mt genes or the age of the hybridization event. Overall, our results imply that genome-wide scans focused on enrichment of broad functional gene classes may often be insufficient for detecting a history of mitonuclear coevolution, even when strong selection is acting on mitonuclear incompatibilities at multiple loci.

genomics↗

bioRxiv2025

The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana

In plants, comparative analyses of organellar genomes often depend on draft assemblies, with large-scale investigations into the complex structural rearrangements of mitochondrial genomes remaining scarce. Here, we conducted a comprehensive analysis of the dominant conformations and dynamic heteroplasmic variants of organellar genomes in the model plant Arabidopsis thaliana, utilizing high-quality long-read assemblies validated at read-level resolution from 149 samples. We found that mitochondrial and plastid genomes share common types of structural and small-scale variants driven by similar DNA sequence features. However, rearrangements mediated by repetitive sequences in mitochondrial genomes evolved so rapidly that they often became decoupled from other types of variants. Rare complex events involving elongation and fusion were also observed, contributing to the unalignable regions commonly found at the interspecies level. Additionally, we demonstrated that disrupting and rescuing organellar DNA maintenance could drive the rapid evolution of dominant mitochondrial genome conformations. Our study provides an unprecedentedly detailed view of the dynamics of organellar genomes at pan-genome scale in A. thaliana, paving the way to unlock the full potential of organellar genetic resources. SignificancePlant mitochondrial genomes exhibit rapid rearrangements within species. Large-scale analyses using high-quality assemblies offer detailed insights into their evolutionary dynamics, paving the way for organellar genome engineering and functional research in the future.

evolutionary biology↗

bioRxiv2025

Flipping the switch on some of the slowest mutating genomes: Direct measurements of plant mitochondrial and plastid mutation rates in msh1 mutants

Plant mitochondrial and plastid genomes have exceptionally slow rates of sequence evolution, and recent work has identified an unusual member of the MutS gene family ("plant MSH1") as being instrumental in preventing point mutations in these genomes. However, the eXects of disrupting MSH1-mediated DNA repair on "germline" mutation rates have not been quantified. Here, we used Arabidopsis thaliana mutation accumulation (MA) lines to measure mutation rates in msh1 mutants and matched wild type (WT) controls. We detected 124 single nucleotide variants (SNVs: 49 mitochondrial and 75 plastid) and 668 small insertions and deletions (indels: 258 mitochondrial and 410 plastid) in msh1 MA lines. In striking contrast, we did not find any organelle mutations in the WT MA lines, and reanalysis of data from a much larger WT MA experiment also failed to detect any variants. The observed number of SNVs in the msh1 MA lines corresponds to estimated mutation rates of 6.1{xi}10-7 and 3.2 {xi}10-6 per bp per generation in mitochondrial and plastid genomes, respectively. These rates exceed those of species known to have very high mitochondrial mutation rates (e.g., nematodes and fruit flies) by an order of magnitude or more and are on par with estimated rates in humans despite the generation times of A. thaliana being nearly 100-fold shorter. Therefore, disruption of a single plant-specific genetic factor in A. thaliana is suXicient to erase or even reverse the enormous diXerence in organelle mutation rates between plants and animals.

genetics↗

bioRxiv2024

Fungal-derived tRNAs are expressed and aminoacylated in orchid mitochondria

Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer (HGT), including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom HGT are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that fungal-derived tRNA genes are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal HGT has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for HGT and functional replacement is further illustrated by the diversity of tRNA genes in the C. maculata mitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts.

evolutionary biology↗

bioRxiv2024

The landscape of Arabidopsis tRNA aminoacylation

The function of tRNAs depends on enzymes that cleave primary transcript ends, add a 3' CCA tail, introduce post-transcriptional base modifications, and charge (aminoacylate) mature tRNAs with the correct amino acid. Maintaining an available pool of the resulting aminoacylated tRNAs is essential for protein synthesis. High-throughput sequencing techniques have recently been developed to provide a comprehensive view of aminoacylation state in a tRNA-specific fashion. However, these methods have never been applied to plants. Here, we treated Arabidopsis thaliana RNA samples with periodate and then performed tRNA-seq to distinguish between aminoacylated and uncharged tRNAs. This approach successfully captured every tRNA isodecoder family and detected expression of additional tRNA-like transcripts. We found that estimated aminoacylation rates and CCA tail integrity were significantly higher on average for organellar (mitochondrial and plastid) tRNAs than for nuclear/cytosolic tRNAs. Reanalysis of previously published human cell line data showed a similar pattern. Base modifications result in nucleotide misincorporations and truncations during reverse transcription, which we quantified and used to test for relationships with aminoacylation levels. We also determined that the Arabidopsis tRNA-like sequences (t-elements) that are cleaved from the ends of some mitochondrial mRNAs have post-transcriptionally modified bases and CCA-tail addition. However, these t-elements are not aminoacylated, indicating that they are only recognized by a subset of tRNA-interacting enzymes and do not play a role in translation. Overall, this work provides a characterization of the baseline landscape of plant tRNA aminoacylation rates and demonstrates an approach for investigating environmental and genetic perturbations to plant translation machinery.

molecular biology↗

bioRxiv2024

Correlated evolutionary rates reveal novel components and cross-compartment connectivity in plant proteostasis systems

Plant cells rely on an interconnected network of proteins interacting at many levels (e.g. physical enzyme complexes, gene regulatory modules, and biosynthetic pathways). Pairs of proteins that interact at any of these levels have been shown to exhibit phylogenetic signatures of evolutionary rate covariation (ERC), providing a basis for detecting functional interactions among proteins. Here, we apply ERCnet, a bioinformatic tool for performing genome-scale ERC analyses, to predict a plant protein-protein interactome network. We find a clustered set of proteins that exhibit strong signatures of ERC with the plastid caseinolytic protease (Clp) and other plastid proteostasis components, thus forming a functional module within the network. In addition to including proteins with known or predicted functions in protein import, transcription, translation, and degradation in plastids, the module also includes proteins with previously unknown molecular function, thus providing evidence that these proteins may contribute to plastid proteostasis in novel ways. Perhaps the most surprising members of this module are a set of proteins that are not thought to localize to the plastid at all. These proteins include a mitochondrial-localized pentatricopeptide repeat (PPR) protein with genetic evidence of interaction with the mitochondrial Clp system and two nuclear-localized actin-related proteins involved in chromatin remodeling and epigenetic regulation of nuclear genes. We speculate that these non-plastid-localized proteins act as mediators of organellar crosstalk and retrograde signaling of cellular proteostasis status in plants. In summary, our results highlight the connected nature of plant proteostasis systems and point to a promising set of novel proteostasis protein candidates.

molecular biology↗

bioRxiv2024

Phylogenomic prediction of interaction networks in the presence of gene duplication

Assigning gene function from genome sequences is a rate-limiting step in molecular biology research. A proteins position within an interaction network can potentially provide insights into its molecular mechanisms. Phylogenetic analysis of evolutionary rate covariation (ERC) in protein sequence has been shown to be effective for large-scale prediction of functional relationships and interactions. However, gene duplication, gene loss, and other sources of phylogenetic incongruence are barriers for analyzing ERC on a genome-wide basis. Here, we developed ERCnet, a bioinformatic program designed to overcome these challenges, facilitating efficient all- vs-all ERC analyses for large protein sequence datasets. We simulated proteome datasets and found that ERCnet achieves combined false positive and negative error rates well below 10% and that our novel branch-by-branch length measurements outperforms root-to-tip approaches in most cases, offering a valuable new strategy for performing ERC. We also compiled a sample set of 35 angiosperm genomes to test the performance of ERCnet on empirical data, including its sensitivity to user-defined analysis parameters such as input dataset size and branch-length measurement strategy. We investigated the overlap between ERCnet runs with different species samples to understand how species number and composition affect predicted interactions and to identify the protein sets that consistently exhibit ERC across angiosperms. Our systematic exploration of the performance of ERCnet provides a roadmap for design of future ERC analyses to predict functional interactions in a wide array of genomic datasets. ERCnet code is freely available at https://github.com/EvanForsythe/ERCnet.

genomics↗

bioRxiv2024

Expansion of the MutS gene family in plants

The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics. One-Sentence SummaryPlants are distinguished from other eukaryotes by a functionally diverse complement of MutS proteins gained via a combination of gene duplication, endosymbiotic gene transfer, and horizontal gene transfer.

evolutionary biology↗

bioRxiv2024

Disruption of recombination machinery alters the mutational landscape in plant organellar genomes

Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long- read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.

genetics↗

bioRxiv2024

Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing

Mutations are the source of novel genetic diversity but can also lead to disease and maladaptation. The conventional view is that mutations occur randomly with respect to their environment-specific fitness consequences. However, intragenomic mutation rates can vary dramatically due to transcription coupled repair and based on local epigenomic modifications, which are non-uniformly distributed across genomes. One sequence feature associated with decreased mutation is higher expression level, which can vary depending on environmental cues. To understand whether the association between expression level and mutation rate creates a systematic relationship with environment-specific fitness effects, we perturbed expression through a heat treatment in Arabidopsis thaliana. We quantified gene expression to identify differentially expressed genes, which we then targeted for mutation detection using Duplex Sequencing. This approach provided a highly accurate measurement of the frequency of rare somatic mutations in vegetative plant tissues, which has been a recent source of uncertainty in plant mutation research. We included mutant lines lacking mismatch repair (MMR) and base excision repair (BER) capabilities to understand how repair mechanisms may drive biased mutation accumulation. We found wild type (WT) and BER mutant mutation frequencies to be very low (mean variant frequency 1.8x10-8 and 2.6x10-8, respectively), while MMR mutant frequencies were significantly elevated (1.13x10-6). These results show that somatic variant frequencies are extremely low in WT plants, indicating that larger datasets will be needed to address the fundamental evolutionary question as to whether environmental change leads to gene-specific changes in mutation rate. SIGNIFICANCEAccurately measuring mutations in plants grown under different environments is important for understanding the determinants of mutation rate variation across a genome. Given the low rate of de novo mutation in plant germlines, such measurements can take years to obtain, hindering tests of mutation accumulation under varying environmental conditions. We implemented highly accurate Duplex Sequencing to study somatic mutations in plants grown in two different temperatures. In contrast to plants with deficiencies in DNA mismatch repair machinery, we found extremely low mutation frequencies in wild type plants. These findings help resolve recent uncertainties about the somatic mutation rate in plant tissues and indicate that larger datasets will be necessary to understand the interaction between mutation and environment in plant genomes.

genetics↗

bioRxiv2023

UV damage induces production of mitochondrial DNA fragments with specific length profiles

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). In eukaryotic cells, photodamage and other bulky lesions occurring in nuclear genomes (nucDNAs) can be repaired through nucleotide excision repair (NER), where dual incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current views hold that the only way to eliminate bulky DNA damage in mtDNAs is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with anti-damage antibodies and sequenced (XR-seq) to produce high resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in 2-nt (S. cerevisiae) or 4-nt (A. thaliana) intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. We hypothesize that these fragments may reflect the outcome of a previously uncharacterized mechanism of NER-like repair in mitochondria or a programmed mtDNA degradation pathway.

genetics↗

bioRxiv2023

The Silene latifolia genome and its giant Y chromosome

In some species, the Y is a tiny chromosome but the dioecious plant Silene latifolia has a giant [~]550 Mb Y chromosome, which has remained unsequenced so far. Here we used a hybrid approach to obtain a high-quality male S. latifolia genome. Using mutants for sexual phenotype, we identified candidate sex-determining genes on the Y. Comparative analysis of the sex chromosomes with outgroups showed the Y is surprisingly rearranged and degenerated for a [~]11 MY-old system. Recombination suppression between X and Y extended in a stepwise process, and triggered a massive accumulation of repeats on the Y, as well as in the non-recombining pericentromeric region of the X, leading to giant sex chromosomes. One-Sentence SummaryThis work uncovers the structure, function, and evolution of one of the largest giant Y chromosomes, that of the model plant Silene latifolia, which is almost 10 times larger than the human Y, despite similar genome sizes.

genomics↗