National Center for Genome Resources

Speciation is a central process in evolutionary biology that involves the formation of reproductive barriers between diverging populations. This process can occur through multiple ecological, behavioral, and genetic mechanisms that ultimately lead to changes within a population leading to the formation of distinct species. The relatively young adaptive radiation of Cyprinodon pupfishes in the lakes of San Salvador Island provides a powerful system to study the drivers of speciation in species that exist both sympatrically and allopatrically. The three species; C. variegatus , C. desquamator , and C. brontotheroides , can be found in many lakes on the island, exhibit distinct morphological adaptations relating to feeding, and, when in sympatry, the three species have overlapping habitats and breeding grounds. Species boundaries are maintained by asymmetric mate choice by both males and females, which reinforce extreme fitness costs of hybridization. Here we present high-quality annotated reference genomes for these three species generated using PacBio hifi sequencing. The assemblies resulted in a genome size of approximately 1.2 Gb for each species with most sequences scaffolding into 24 chromosomes with BUSCO analysis indicating a >99% level of completion. The annotation of these three genomes generated over 21,500 protein coding genes with BUSCO analysis indicating a >86 completion. These genomes provide a key resource for studying the genomic architecture of ecological specialization, reproductive isolation in sympatry, and rapid speciation and will facilitate future comparative and population genomic studies on adaptive radiations. ### Competing Interest Statement The authors have declared no competing interest. Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health, P20GM103451

Here, we describe a collection of genomic database portals, SoyBase (https://soybase.org), Legume Information System (https://legumeinfo.org), and PeanutBase (https://peanutbase.org), that support breeding and research work in the legume plant family. The legume family includes important crops such as soybean, peanut, common bean, lentils, chickpeas, as well as approximately 20,000 other species that are important in all terrestrial ecosystems. Beyond the value of the portals for species in this large clade (as well as for plant biology more generally), the database and site architecture of these portals will be of interest to developers of similar genomic sites, as the data management and software solutions are generic and should be applicable to a wide variety of organisms. The architecture for these sites has been designed for rapid, modular, flexible development well suited to genomic data and to rapid incorporation of new data. Website content is handled with a static site generator (Jekyll). Interactive applications are developed using javascript encapsulated as Web Components that access back-end data via APIs for stability and flexibility. This architecture allows for both code portability and for customization to serve the unique needs of each research community.

Root nodule symbiosis (RNS) is found in approximately 16–18 widely-separated lineages within the “nitrogen-fixing nodulation clade (NFNC)”. Although modeling of trait gain and loss across approximately 13,000 species within the rosid group indicates multiple gains and losses, there is no consensus about whether RNS had a single or multiple origins; and our understanding is fragmentary regarding the molecular mechanisms underlying those changes. Evolution of a new organ and functions involves many thousands of genes; but the evolutionary histories for many of these genes may be uninformative regarding RNS evolution. A portion of the genes, however, are likely to be derived from prior gene duplications and to have acquired new functions or to have come under new regulatory patterns. Whole genome duplications (WGDs) could conceivably enable the necessary neo- or sub-functionalization for new roles in the nodule. All species that exhibit RNS share a history of several ancient WGDs; but the last such common WGD for these species was the “gamma” paleohexaploidy that occurred early in the core eudicot lineage, ~120 Mya. This presents a puzzle: If legume RNS within the NFNC only arose in the Late Cretaceous, several tens of millions of years after the gamma event, what explains the long, seemingly quiescent interval and the many eudicot lineages without RNS? This study focuses on a collection of gene superfamilies with additional independent WGDs that appear to have occurred in the interim period, after the gamma triplication and prior to the evolution of RNS, identifying several that are both essential for RNS and that show evidence of critical roles of both ancient WGDs and more recent local duplications.

The Green Lineage (Viridiplantae) represents one of the most successful evolutionary radiations on Earth, with remarkable morphological diversity from unicellular algae to complex multicellular land plants. Recent advances in single-cell genomics have transformed our understanding of plant cell-type diversity and evolution, revealing fundamental principles underlying cellular organization and specification. This review synthesizes current knowledge of plant cell-type identity and evolution through the lens of single-cell approaches. We examine how plant cell types are specified through combinatorial transcription factor networks analogous to animal terminal selector systems yet operate within a fundamentally different developmental framework characterized by positional determination, extensive plasticity, and environmental responsiveness. We highlight unique features of plant cells, including plastids, large vacuoles, cell walls, and plasmodesmata, that profoundly influence cellular identity and present distinct challenges for single-cell profiling. Comparative analysis across the Green Lineage reveals that new cell types arise through subfunctionalization following gene and genome duplications, co-option of ancestral gene regulatory networks, and cis-regulatory evolution driven by transposable elements. We address major analytical challenges, including orthology assignment in polyploid genomes, cross-species dataset integration, gene regulatory network reconstruction, and functional validation in diverse plant systems. Despite these challenges, plant single-cell genomics offers unprecedented opportunities to understand cellular evolution, with implications extending from fundamental biology to agricultural innovation.

In this work, we investigate whether motif subsequence features can predict accessible chromatin regions (ACR) in a genome, i.e. regions that are accessible to regulatory proteins, thus enabling transcription of associated genes. We focus on plants, whose agricultural and ecological importance make them interesting and important organisms to study, and whose complex genomes provide important stress tests for our algorithm. We show that regulatory motif sequence similarity can be found efficiently using co-linear chaining. The similarity scores found are then used as features in machine learning models to explore the feasibility of effectively predicting ACRs in genome assemblies.