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1. 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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2. Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

   https://doi.org/10.1093/gbe/evy157  

   Perry, Blair W ; Card, Daren C ; McGlothlin, Joel W ; Pasquesi, Giulia I ; Adams, Richard H ; Schield, Drew R ; Hales, Nicole R ; Corbin, Andrew B ; Demuth, Jeffery P ; Hoffmann, Federico G ; et al ( July 2018 , Genome Biology and Evolution)
3. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies

   https://doi.org/10.1371/journal.pcbi.1007981  

   Zimin, Aleksey V. ; Salzberg, Steven L. ( June 2020 , PLOS Computational Biology)
4. Application of Cas12a and nCas9-activation-induced cytidine deaminase for genome editing and as a non-sexual strategy to generate homozygous/multiplex edited plants in the allotetraploid genome of tobacco

   https://doi.org/10.1007/s11103-019-00907-w  

   Hsu, Chen-Tran ; Cheng, Yu-Jung ; Yuan, Yu-Hsua ; Hung, Wei-Fon ; Cheng, Qiao-Wei ; Wu, Fu-Hui ; Lee, Lan-Ying ; Gelvin, Stanton B. ; Lin, Choun-Sea ( November 2019 , Plant Molecular Biology)
5. Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database

   https://doi.org/10.1038/s41438-021-00476-4  

   Liu, Tianjia ; Li, Muzi ; Liu, Zhongchi ; Ai, Xiaoyan ; Li, Yongping ( December 2021 , Horticulture Research)

   Abstract Cultivated strawberry ( Fragaria × ananassa ) is an important fruit crop species whose fruits are enjoyed by many worldwide. An octoploid of hybrid origin, the complex genome of this species was recently sequenced, serving as a key reference genome for cultivated strawberry and related species of the Rosaceae family. The current annotation of the F. ananassa genome mainly relies on ab initio predictions and, to a lesser extent, transcriptome data. Here, we present the structure and functional reannotation of the F. ananassa genome based on one PacBio full-length RNA library and ninety-two Illumina RNA-Seq libraries. This improved annotation of the F. ananassa genome, v1.0.a2, comprises a total of 108,447 gene models, with 97.85% complete BUSCOs. The models of 19,174 genes were modified, 360 new genes were identified, and 11,044 genes were found to have alternatively spliced isoforms. Additionally, we constructed a strawberry genome database (SGD) for strawberry gene homolog searching and annotation downloading. Finally, the transcriptome of the receptacles and achenes of F. ananassa at four developmental stages were reanalyzed and qualified, and the expression profiles of all the genes in this annotation are also provided. Together, this study provides an updated annotation of the F. ananassa genome,more »which will facilitate genomic analyses across the Rosaceae family and gene functional studies in cultivated strawberry.« less