The Spirogyra pratensis genome illuminates the evolution of developmental programs and spiral chloroplast biology

Evolution of multicellularity and reproductive strategies in yellow-green algae (Xanthophyceae, Heterokontophyta)

The evolution of multicellularity has long been linked to reproductive strategies. A long-standing debate concerns whether multicellular organisms are primarily stabilized by small single-cell propagules that minimize genetic heterogeneity or by larger multicellular and multinucleate propagules that may improve developmental success and survival of individuals. the Xanthophyceae provides an excellent model for investigating these questions, exhibiting transitions between unicellular to multicellular filamentous and coenocytic forms together with diverse reproductive modes, including single-cell zoospores and autospores, and multinucleate monospores and akinetes. However, a robust phylogenetic framework and systematic analyses of character evolution have remained lacking in this lineage. Here, we present a phylogenomic framework based on a nuclear dataset of 680 genes from 18 species, including 17 newly generated transcriptomes. Nuclear phylogenies robustly resolve all sampled inter-ordinal and inter-familial relationships with full concordance between concatenation and coalescent analyses, while plastid (141 genes) and mitochondrial (31 genes) datasets from 33 species recover identical topologies. Based on these results, we establish one new order (Pseudopleurochloridales), emend one order (Heterococcales), and propose five new families. Ancestral character reconstruction indicates at least four independent transitions from unicellular ancestors to simple multicellularity. Bayesian analyses of multicellularity and reproductive characters show that these transitions were consistently accompanied by shifts from multiple autospore-type propagules toward single monospore- and akinete-type propagules, whereas reversions to unicellularity were associated with the reappearance of autospore-based reproduction. These results provide a phylogenomic framework for understanding multicellular evolution in Xanthophyceae and shed light on the relationship between reproductive modes and the emergence of simple multicellularity.

Spatiotemporal Profiling of the Marchantia Sporophyte Reveals Ancestral Meristem Module and Dynamic Epigenetic Reprogramming during Early Embryogenesis

Caught in transition: facultative intracellularity and genome evolution of Symbiopectobacterium in Rhodnius species

Findings indicate that Symbiopectobacterium represents an intermediate stage in the transition from environmentally associated bacteria to obligate intracellular mutualists in Triatominae.

CHLOROPLAST GENOME SEQUENCING IN BRASSICACEAE AND ITS PHYLOGENETIC APPLICATIONS: A COMPREHENSIVE REVIEW

New methodologies were examined, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.

Laboratory evolution drives continued genome degradation in the facultative tsetse symbiont Sodalis glossinidius

Bacterial symbionts of insects undergo dramatic genome reduction during their evolutionary transition from free-living to host-dependent lifestyles, but the dynamics of genome degradation remain poorly understood due to the difficulty of observing these processes in real-time. Sodalis glossinidius, a facultative bacterial endosymbiont of tsetse flies, provides an exceptional opportunity to study this transition experimentally: Unlike highly specialised obligate symbionts, S. glossinidius can be cultured in vitro and retains a large genome (4 Mbp) with extensive pseudogene content (49%, vs. ~ 1% in free-living bacteria), suggesting a recent evolutionary transition. Here, we present a comparative genomic analysis of S. glossinidius strains isolated from laboratory colony-derived Glossina morsitans morsitans, comparing one strain after ten years of serial passaging in laboratory culture (SgGmmC1*) to a counterpart isolated at the same time from the same colony (SgGmmB4). Hybrid genome assembly using Oxford Nanopore and Illumina technologies produced a high-quality 4.29 Mbp genome comprising one circular chromosome and four plasmids. Comparative analysis revealed a significant deletion (16,493 bp) containing 31 genes, including thiM (involved in thiamine biosynthesis) and genes encoding sulfur transporters. Additionally, we identified multiple small-scale chromosomal mutations (8 deletions, 39 insertions, 11 SNPs) resulting in frameshifts in genes including a hemolysin precursor (shlA). Our findings demonstrate that, under stable laboratory conditions without the selective pressures of the host environment, S. glossinidius continues to undergo genome degradation. The loss of thiM supports previous hypotheses of complementary metabolic pathways between S. glossinidius and the primary symbiont Wigglesworthia glossinidia for thiamine biosynthesis. This study provides insights into the evolutionary trajectory of facultative symbionts and has implications for studying the patterns of genome evolution in bacterial symbionts adapting to novel ecological niches, as well as paratransgenic approaches using S. glossinidius for trypanosome control.

De Novo Genome Sequence Assembly of the Algal Endosymbiont Micractinium conductrix Derived From Its Host Paramecium bursaria 186b

Abstract Endosymbiosis is a major driver of evolutionary innovation and underpins the function of diverse ecosystems. The origins and evolution of endosymbiosis are challenging to study experimentally due to the short-lived culturability of many microbial strains derived from endosymbiotic interactions. The facultative endosymbiosis between the ciliate, Paramecium bursaria, and the green alga, Micractinium conductrix (Chlorellaceae, Trebouxiophyceae), is ecologically widespread and has emerged as a powerful lab-tractable model system. This endosymbiosis is founded upon a reciprocal nutrient exchange, but each of the species can be cultured independently enabling quantification of symbiotic fitness effects, new partnerships to be generated in the lab, and co-associations to be subject to experimental evolution. To date, evolve-and-resequence approaches have been limited due to a lack of high-quality genome assemblies enabling gene variants to be identified. Here, we report a near telomere-to-telomere genome assembly for M. conductrix 186b, using a range of sequencing technologies. Comparative analysis shows that this is one of the most complete Chlorellaceae algal genome assemblies available to date. To aid accurate gene calling and annotation, we conducted both RNAseq and Iso-Seq transcriptome sequencing experiments. Collectively, these ‘omics datasets will facilitate: (i) comparative genomics studies of endosymbiont evolution, (ii) evolve-and-resequence experiments, (iii) genome-scale metabolic modeling studies, and (iv) identification of targets for genetic modification experiments and biotechnological applications.