More Like this

1. Expression analyses in Ginkgo biloba provide new insights into the evolution and development of the seed

   https://doi.org/10.1038/s41598-021-01483-0  

   Zumajo-Cardona, Cecilia; Little, Damon P.; Stevenson, Dennis; Ambrose, Barbara A. (December 2021, Scientific Reports)

   Abstract Although the seed is a key morphological innovation, its origin remains unknown and molecular data outside angiosperms is still limited. Ginkgo biloba, with a unique place in plant evolution, being one of the first extant gymnosperms where seeds evolved, can testify to the evolution and development of the seed. Initially, to better understand the development of the ovules in Ginkgo biloba ovules, we performed spatio-temporal expression analyses in seeds at early developing stages, of six candidate gene homologues known in angiosperms: WUSCHEL, AINTEGUMENTA, BELL1, KANADI, UNICORN, and C3HDZip . Surprisingly, the expression patterns of most these ovule homologues indicate that they are not wholly conserved between angiosperms and Ginkgo biloba . Consistent with previous studies on early diverging seedless plant lineages, ferns, lycophytes, and bryophytes, many of these candidate genes are mainly expressed in mega- and micro-sporangia. Through in-depth comparative transcriptome analyses of Ginkgo biloba developing ovules, pollen cones, and megagametophytes we have been able to identify novel genes, likely involved in ovule development. Finally, our expression analyses support the synangial or neo-synangial hypotheses for the origin of the seed, where the sporangium developmental network was likely co-opted and restricted during integument evolution. 

   more » « less
2. cis -Regulatory Elements in Plant Development, Adaptation, and Evolution

   https://doi.org/10.1146/annurev-arplant-070122-030236  

   Marand, Alexandre P.; Eveland, Andrea L.; Kaufmann, Kerstin; Springer, Nathan M. (May 2023, Annual Review of Plant Biology)

   cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment. Accumulating evidence implicates changes to gene expression as a major source of phenotypic novelty in eukaryotes, including acute phenotypes such as disease and cancer in mammals. Moreover, genetic and epigenetic variation affecting cis-regulatory sequences over longer evolutionary timescales has become a recurring theme in studies of morphological divergence and local adaptation. Here, we discuss the functions of and methods used to identify various classes of cis-regulatory elements, as well as their role in plant development and response to the environment. We highlight opportunities to exploit cis-regulatory variants underlying plant development and environmental responses for crop improvement efforts. Although a comprehensive understanding of cis-regulatory mechanisms in plants has lagged behind that in animals, we showcase several breakthrough findings that have profoundly influenced plant biology and shaped the overall understanding of transcriptional regulation in eukaryotes. 

   more » « less
3. Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation

   https://doi.org/10.1073/pnas.2002357117  

   Dowle, Edwina J.; Powell, Thomas H.; Doellman, Meredith M.; Meyers, Peter J.; Calvert, McCall B.; Walden, Kimberly K.; Robertson, Hugh M.; Berlocher, Stewart H.; Feder, Jeffrey L.; Hahn, Daniel A.; et al (September 2020, Proceedings of the National Academy of Sciences)

   Many organisms enter a dormant state in their life cycle to deal with predictable changes in environments over the course of a year. The timing of dormancy is therefore a key seasonal adaptation, and it evolves rapidly with changing environments. We tested the hypothesis that differences in the timing of seasonal activity are driven by differences in the rate of development during diapause in Rhagoletis pomonella , a fly specialized to feed on fruits of seasonally limited host plants. Transcriptomes from the central nervous system across a time series during diapause show consistent and progressive changes in transcripts participating in diverse developmental processes, despite a lack of gross morphological change. Moreover, population genomic analyses suggested that many genes of small effect enriched in developmental functional categories underlie variation in dormancy timing and overlap with gene sets associated with development rate in Drosophila melanogaster . Our transcriptional data also suggested that a recent evolutionary shift from a seasonally late to a seasonally early host plant drove more rapid development during diapause in the early fly population. Moreover, genetic variants that diverged during the evolutionary shift were also enriched in putative cis regulatory regions of genes differentially expressed during diapause development. Overall, our data suggest polygenic variation in the rate of developmental progression during diapause contributes to the evolution of seasonality in R. pomonella . We further discuss patterns that suggest hourglass-like developmental divergence early and late in diapause development and an important role for hub genes in the evolution of transcriptional divergence. 

   more » « less
4. Dynamic genome evolution in a model fern

   https://doi.org/10.1038/s41477-022-01226-7  

   Marchant, D. Blaine; Chen, Guang; Cai, Shengguan; Chen, Fei; Schafran, Peter; Jenkins, Jerry; Shu, Shengqiang; Plott, Chris; Webber, Jenell; Lovell, John T.; et al (September 2022, Nature Plants)

   Abstract The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii . The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology. 

   more » « less
5. Water lily ( Nymphaea thermarum ) genome reveals variable genomic signatures of ancient vascular cambium losses

   https://doi.org/10.1073/pnas.1922873117  

   Povilus, Rebecca A.; DaCosta, Jeffrey M.; Grassa, Christopher; Satyaki, Prasad R. V.; Moeglein, Morgan; Jaenisch, Johan; Xi, Zhenxiang; Mathews, Sarah; Gehring, Mary; Davis, Charles C.; et al (March 2020, Proceedings of the National Academy of Sciences)

   For more than 225 million y, all seed plants were woody trees, shrubs, or vines. Shortly after the origin of angiosperms ∼140 million y ago (MYA), the Nymphaeales (water lilies) became one of the first lineages to deviate from their ancestral, woody habit by losing the vascular cambium, the meristematic population of cells that produces secondary xylem (wood) and phloem. Many of the genes and gene families that regulate differentiation of secondary tissues also regulate the differentiation of primary xylem and phloem, which are produced by apical meristems and retained in nearly all seed plants. Here, we sequenced and assembled a draft genome of the water lilyNymphaea thermarum, an emerging system for the study of early flowering plant evolution, and compared it to genomes from other cambium-bearing and cambium-less lineages (e.g., monocots andNelumbo). This revealed lineage-specific patterns of gene loss and divergence.Nymphaeais characterized by a significant contraction of the HD-ZIP III transcription factors, specifically loss ofREVOLUTA, which influences cambial activity in other angiosperms. We also found theNymphaeaand monocot copies of cambium-associated CLE signaling peptides display unique substitutions at otherwise highly conserved amino acids.Nelumbodisplays no obvious divergence in cambium-associated genes. The divergent genomic signatures of convergent loss of vascular cambium reveals that even pleiotropic genes can exhibit unique divergence patterns in association with independent events of trait loss. Our results shed light on the evolution of herbaceousness—one of the key biological innovations associated with the earliest phases of angiosperm evolution. 

   more » « less