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1. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants

   https://doi.org/10.1093/gbe/evab042  

   Geng, Yuan ; Cai, Chao ; McAdam, Scott A.M ; Banks, Jo Ann ; Wisecaver, Jennifer H ; Zhou, Yun ( March 2021 , Genome Biology and Evolution)

   Gaut, Brandon (Ed.)

   Abstract As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, wemore »uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.« less
2. Genome-enabled insights into the biology of thrips as crop pests

   https://doi.org/10.1186/s12915-020-00862-9  

   Rotenberg, Dorith ; Baumann, Aaron A. ; Ben-Mahmoud, Sulley ; Christiaens, Olivier ; Dermauw, Wannes ; Ioannidis, Panagiotis ; Jacobs, Chris G. ; Vargas Jentzsch, Iris M. ; Oliver, Jonathan E. ; Poelchau, Monica F. ; et al ( December 2020 , BMC Biology)

   Abstract Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) amore »comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.« less
3. Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

   https://doi.org/10.1093/g3journal/jkab189  

   Williams, Alissa M ; Itgen, Michael W ; Broz, Amanda K ; Carter, Olivia G ; Sloan, Daniel B ( January 2021 , G3 Genes|Genomes|Genetics)

   Abstract The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious species Silene latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 14,126 S. noctiflora genes and 25,317 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Furthermore, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and threefold larger than the 0.9-Gb genome of Silene conica, another species in the same subgenus. Karyotyping confirmed that S. noctiflora is a diploid, indicating that its largemore »genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.« less
4. The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa

   https://doi.org/10.1128/mBio.02148-15  

   Wang, Zheng ; Li, Ning ; Li, Jigang ; Dunlap, Jay C. ; Trail, Frances ; Townsend, Jeffrey P. ( March 2016 , mBio)

   ABSTRACT Rapid responses to changes in incident light are critical to the guidance of behavior and development in most species. Phytochrome light receptors in particular play key roles in bacterial physiology and plant development, but their functions and regulation are less well understood in fungi. Nevertheless, genome-wide expression measurements provide key information that can guide experiments that reveal how genes respond to environmental signals and clarify their role in development. We performed functional genomic and phenotypic analyses of the two phytochromes in Neurospora crassa , a fungal model adapted to a postfire environment that experiences dramatically variable light conditions. Expression of phy-1 and phy-2 was low in early sexual development and in the case of phy-2 increased in late sexual development. Under light stimulation, strains with the phytochromes deleted exhibited increased expression of sexual development-related genes. Moreover, under red light, the phy-2 knockout strain commenced sexual development early. In the evolution of phytochromes within ascomycetes, at least two duplications have occurred, and the faster-evolving phy-2 gene has frequently been lost. Additionally, the three key cysteine sites that are critical for bacterial and plant phytochrome function are not conserved within fungal phy-2 homologs. Through the action of phytochromes, transitions between asexualmore »and sexual reproduction are modulated by light level and light quality, presumably as an adaptation for fast asexual growth and initiation of sexual reproduction of N. crassa in exposed postfire ecosystems. IMPORTANCE Environmental signals, including light, play critical roles in regulating fungal growth and pathogenicity, and balance of asexual and sexual reproduction is critical in fungal pathogens’ incidence, virulence, and distribution. Red light sensing by phytochromes is well known to play critical roles in bacterial physiology and plant development. Homologs of phytochromes were first discovered in the fungal model Neurospora crassa and then subsequently in diverse other fungi, including many plant pathogens. Our study investigated the evolution of red light sensors in ascomycetes and confirmed—using the model fungus Neurospora crassa —their roles in modulating the asexual-sexual reproduction balance in fungi. Our findings also provide a key insight into one of the most poorly understood aspects of fungal biology, suggesting that further study of the function of phytochromes in fungi is critical to reveal the genetic basis of the asexual-sexual switch responsible for fungal growth and distribution, including diverse and destructive plant pathogens.« less
5. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

   https://doi.org/10.1038/s41598-019-53968-8  

   Marchant, D. Blaine ; Sessa, Emily B. ; Wolf, Paul G. ; Heo, Kweon ; Barbazuk, W. Brad ; Soltis, Pamela S. ; Soltis, Douglas E. ( December 2019 , Scientific Reports)

   Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern speciesCeratopteris richardiito address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies ofCeratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history ofCeratopterisbased on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying themore »formation of these massive genomes.

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