RT Journal Article SR Electronic T1 First whole genome assembly of Vaccinium floribundum Kunth, an emblematic Andean species JF bioRxiv FD Cold Spring Harbor Laboratory SP 2024.04.26.591377 DO 10.1101/2024.04.26.591377 A1 Albuja-Quintana, Martina A1 Pozo, Gabriela A1 Gordillo-Romero, Milton A1 Armijos, Carolina E. A1 Torres, María de Lourdes YR 2024 UL http://biorxiv.org/content/early/2024/04/29/2024.04.26.591377.abstract AB Background Vaccinium floribundum Kunth, known as "mortiño," is an endemic shrub species of the Andean region adapted to harsh conditions in high-altitude ecosystems. It plays an important ecological role as a pioneer species in the aftermath of deforestation and human-induced fires within paramo ecosystems, emphasizing its conservation value. While previous studies have offered insights into the genetic diversity of mortiño, comprehensive genomic studies are still missing to fully understand the unique adaptations of this species and its population status, highlighting the importance of generating a reference genome for this plant.Results ONT and Illumina sequencing were used to establish a reference genome for this species. Three different de novo genome assemblies were generated and compared for quality, continuity and completeness. The Flye assembly was selected as the best and refined by filtering out short ONT reads, screening for contaminants and genome scaffolding. The final assembly has a genome size of 529 MB, containing 1,317 contigs and 97% complete BUSCOs, indicating a high level of integrity of the genome. Additionally, the LAI Index of 12.93, further categorizes this assembly as a reference genome.Conclusions The genome of V. floribundum reported in this study is the first reference genome generated for this species, providing a valuable tool for further studies. This high-quality genome, based on the quality and completeness parameters obtained, will not only help uncover the genetic mechanisms responsible for its unique traits and adaptations to high-altitude ecosystems, but will also contribute to conservation strategies for a species endemic to the Andes.Competing Interest StatementThe authors have declared no competing interest.The genome assembly and all sequencing data have been deposited in the GenBank database under the BioProject PRJNA1071645 (SAMN39706721). The script used for the assembly and annotation of this genome is described in protocol.io (dx.doi.org/10.17504/protocols.io.n92ldmo4nl5b/v1). All supporting data and material is available in the GigaScience GigaDB database.m.a.s.lmeters above sea levelUVultraviolet lightBUSCOBenchmarking Universal Single-Copy OrthologsLAILong Terminal Repeat Assembly IndexQUSFUSFQ herbariumHMW-DNAHigh Molecular DNACTABCetyltrimethylammonium bromideSREshort-read eliminatorONTOxford Nanopore TechnologiesMaSuRCAMaryland Super-Read Celera AssemblerQUASTQuality Assessment Tool for Genome AssembliesLTRlong terminal repeatBWABurrows-Wheeler AlignerNCBINational Center for Biotechnology InformationESTExpressed sequence tagHMMhidden Markov modelgffgeneral feature formatAGATAnother Gff Analysis ToolkitGbgigabaseKbkilobasebpbase pairMbmegabaseAEDAnnotation Edit DistanceCDScoding sequence