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1. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

   https://doi.org/10.1186/s12864-021-07967-7  

   Hong, Zhou; Liao, Xuezhu; Ye, Yuanjun; Zhang, Ningnan; Yang, Zengjiang; Zhu, Weidong; Gao, Wei; Sharbrough, Joel; Tembrock, Luke R.; Xu, Daping; et al (December 2021, BMC Genomics)

   Abstract Background Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera . Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera , the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. Results We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera . The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. Conclusion For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes. 

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2. Draft genome sequence of Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts

   https://doi.org/10.1128/mra.00882-24  

   Darden, Brynne; Johnson, Gabriel; Busch, Grace; Sharma, Indu (May 2025, Microbiology Resource Announcements)

   Thrash, J Cameron (Ed.)

   We report a draft genome sequence for Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. The whole-genome sequence will help understand the ecology and evolution of various ecotypes that are physiologically distinct from the surrounding environments. 

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3. Liftoff: an accurate gene annotation mapping tool

   https://doi.org/10.1101/2020.06.24.169680  

   Shumate, A.; Salzberg, S.L. (June 2020, bioRxiv)

   Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however for most species, only the reference genome is well-annotated. One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously-annotated reference genome. Here we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely-related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript, and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.4% of human protein-coding genes to a chimpanzee genome assembly with 98.7% sequence identity. Availability The source code for Liftoff is available at https://github.com/agshumate/Liftoff 

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4. Complete Genome Sequence of a Non-Carbapenemase-Producing Carbapenem-Resistant Providencia rettgeri Strain Isolated from a Clinical Urine Sample in Arkansas

   https://doi.org/10.1128/mra.00474-22  

   Udaondo, Zulema; Abram, Kaleb Z.; Gulley, Trent; Garner, Kelley; Shray, Jennifer; Whisnant, Mary; Harris-Spotts, Ashley; Crawford, Maui; Kothari, Atul; Wongsurawat, Thidathip; et al (August 2022, Microbiology Resource Announcements)

   Dunning Hotopp, Julie C. (Ed.)

   ABSTRACT Here, we report the complete genome sequence of Providencia rettgeri isolate PROV_UAMS_01, which was recovered in 2021 from a urine sample from a hospitalized patient in Arkansas, USA. The genome sequence of P. rettgeri isolate PROV_UAMS_01 comprises a single chromosomal replicon with a G+C content of 40.51% and a total of 3,887 genes. 

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5. A Reference Genome Sequence for Giant Sequoia

   https://doi.org/10.1534/g3.120.401612  

   Scott, Alison D; Zimin, Aleksey V; Puiu, Daniela; Workman, Rachael; Britton, Monica; Zaman, Sumaira; Caballero, Madison; Read, Andrew C; Bogdanove, Adam J; Burns, Emily; et al (November 2020, G3 Genes|Genomes|Genetics)

   Abstract The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management. 

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