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1. 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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2. A graph-based genome and pan-genome variation of the model plant Setaria

   https://doi.org/10.1038/s41588-023-01423-w  

   He, Qiang; Tang, Sha; Zhi, Hui; Chen, Jinfeng; Zhang, Jun; Liang, Hongkai; Alam, Ornob; Li, Hongbo; Zhang, Hui; Xing, Lihe; et al (July 2023, Nature Genetics)

   Abstract Setaria italica(foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established theSetariapan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield geneSiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions. 

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3. De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)

   https://doi.org/10.1186/s12864-022-09000-x  

   Linscott, T. Mason; González-González, Andrea; Hirano, Takahiro; Parent, Christine E. (December 2022, BMC Genomics)

   Abstract Background Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO 3 ), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species. Results Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2–3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome . Conclusions Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO 3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs. 

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4. Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome

   https://doi.org/10.1016/j.jsb.2017.08.005  

   Johnson, Matthew C.; Sena-Velez, Marta; Washburn, Brian K.; Platt, Georgia N.; Lu, Stephen; Brewer, Tess E.; Lynn, Jason S.; Stroupe, M. Elizabeth; Jones, Kathryn M. (December 2017, Journal of Structural Biology)
5. GenAx: A Genome Sequencing Accelerator

   https://doi.org/10.1109/ISCA.2018.00017  

   Fujiki, Daichi; Subramaniyan, Arun; Zhang, Tianjun; Zeng, Yu; Das, Reetuparna; Blaauw, David; Narayanasamy, Satish (June 2018, 2018 ACM/IEEE 45th Annual International Symposium on Computer Architecture (ISCA))