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1. A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.)

   https://doi.org/10.1371/journal.pone.0265096  

   Davik, Jahn; Røen, Dag; Lysøe, Erik; Buti, Matteo; Rossman, Simeon; Alsheikh, Muath; Aiden, Erez Lieberman; Dudchenko, Olga; Sargent, Daniel James (March 2022, PLOS ONE)

   Sharakhov, Igor V. (Ed.)

   Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar ‘Anitra’ are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R . idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders. 

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2. 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)

   null (Ed.)

   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, which will facilitate genomic analyses across the Rosaceae family and gene functional studies in cultivated strawberry. 

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3. Diversity in olfactory receptor repertoires is associated with dietary specialization in a genus of frugivorous bat

   https://doi.org/10.1093/g3journal/jkab260  

   Yohe, Laurel R; Leiser-Miller, Leith B; Kaliszewska, Zofia A; Donat, Paul; Santana, Sharlene E; Dávalos, Liliana M (July 2021, G3 Genes|Genomes|Genetics)

   null (Ed.)

   Abstract Mammalian olfactory receptor genes (ORs) are a diverse family of genes encoding proteins that directly interact with environmental chemical cues. ORs evolve via gene duplication in a birth-death fashion, neofunctionalizing and pseudogenizing over time. Olfaction is a primary sense used for food detection in plant-visiting bats, but the relationship between dietary specialization and OR repertoire diversity is unclear. Within neotropical Leaf-nosed bats (Phyllostomidae), many lineages are plant specialists, and some have a distinct OR repertoire compared to insectivorous species. Yet, whether specialization on particular plant genera is associated with the evolution of specialized, less diverse OR repertoires has never been tested. Using targeted sequence capture, we sequenced the OR repertoires of three sympatric species of short-tailed fruit bats (Carollia), which vary in their degree of specialization on the fruits of Piper plants. We characterized orthologous vs duplicated receptors among Carollia species, and explored the diversity and redundancy of the receptor gene repertoire. At the species level, the most dedicated Piper specialist, Carollia castanea, had lower OR diversity compared to the two generalists (C. sowelli and C. perspicillata), but we discovered a few unique sets of ORs within C. castanea with high redundancy of similar gene duplicates. These unique receptors potentially enable C. castanea to detect Piper fruit odorants better than its two congeners. Carollia perspicillata, the species with the most generalist diet, had a higher diversity of intact receptors, suggesting the ability to detect a wider range of odorant molecules. Variation among ORs may be a factor in the coexistence of these sympatric species, facilitating the exploitation of different plant resources. Our study sheds light on how gene duplication and changes in OR diversity may play a role in dietary adaptations and underlie ecological interactions between bats and plants. 

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4. Engineering the future of Physalis grisea : A focus on agricultural challenges, model species status, and applied improvements

   https://doi.org/10.1002/ppp3.10536  

   Dale, Savanah Marie; Tomaszewski, Elise; Lippman, Zachary; Van_Eck, Joyce (July 2024, PLANTS, PEOPLE, PLANET)

   Societal Impact StatementGroundcherry (Physalis grisea) is a plant species grown for its flavorful fruit. The fruit drops from the plant, hence the common name groundcherry. This makes harvest cumbersome and puts the fruit at risk for carrying soil‐borne pathogens, therefore making them unsellable. Furthermore, insects often damage the plants, reducing yield. Advances in gene editing offer promise for addressing these issues and aiding home gardeners and farmers. Improvement will expand access to this nutritious fruit, rich in potassium, vitamin C, and antioxidants. Additionally, studies of its biology could serve as a model for improving other fruiting plants, particularly underutilized species. SummaryP. griseais an underutilized, semidomesticated fruit crop with rising agronomic value. Several resources have been developed for its use in fundamental biological research, including a plant transformation system and a high‐quality reference genome. Already,P. griseahas been used as a model to investigate biological phenomena including inflated calyx syndrome and gene compensation.P. griseahas also been used to demonstrate the potential of fast‐tracking domestication trait improvement through approaches such as CRISPR/Cas9 gene editing. This work has led to thePhysalisImprovement Project, which relies on reverse genetics to understand the mechanisms that underlie fruit abscission and plant–herbivore interactions to guide approaches for improvement of undesirable characteristics. CRISPR/Cas9 gene editing has been used to targetP. griseagenes that are suspected to act in fruit abscission, particularly orthologs of those that are reported in tomato abscission zone development. A similar approach is being taken to targetP. griseagenes involved in the withanolide biosynthetic pathway to determine the impact of withanolides on plant–herbivore interactions. Results from these research projects will lead to a greater understanding of important biological processes and will also generate knowledge needed to develop cultivars with reduced fruit drop and increased resistance to insect herbivory. 

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5. Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids?

   Gaynor, Michelle L; Ng, Julienne; Laport, Robert G. (April 2018, Frontiers in ecology and evolution)

   Polyploidy is widely acknowledged to have played an important role in the evolution and diversification of vascular plants. However, the influence of genome duplication on population-level dynamics and its cascading effects at the community level remain unclear. In part, this is due to persistent uncertainties over the extent of polyploid phenotypic variation, and the interactions between polyploids and co-occurring species, and highlights the need to integrate polyploid research at the population and community level. Here, we investigate how community-level patterns of phylogenetic relatedness might influence escape from minority cytotype exclusion, a classic population genetics hypothesis about polyploid establishment, and population-level species interactions. Focusing on two plant families in which polyploidy has evolved multiple times, Brassicaceae and Rosaceae, we build upon the hypothesis that the greater allelic and phenotypic diversity of polyploids allow them to successfully inhabit a different geographic range compared to their diploid progenitor and close relatives. Using a phylogenetic framework, we specifically test (1) whether polyploid species are more distantly related to diploids within the same community than co-occurring diploids are to one another, and (2) if polyploid species tend to exhibit greater ecological success than diploids, using species abundance in communities as an indicator of successful establishment. Overall, our results suggest that the effects of genome duplication on community structure are not clear-cut. We find that polyploid species tend to be more distantly related to co-occurring diploids than diploids are to each other. However, we do not find a consistent pattern of polyploid species being more abundant than diploid species, suggesting polyploids are not uniformly more ecologically successful than diploids. While polyploidy appears to have some important influences on species co-occurrence in Brassicaceae and Rosaceae communities, our study highlights the paucity of available geographically explicit data on intraspecific ploidal variation. The increased use of high-throughput methods to identify ploidal variation, such as flow cytometry and whole genome sequencing, will greatly aid our understanding of how such a widespread, radical genomic mutation influences the evolution of species and those around them. 

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