An unusually large genome from an unusually large stonefly: a chromosome-length genome assembly for the giant salmonfly, Pteronarcys californica (Plecoptera: Pteronarcyidae).

Autor:	Eichert A; Division of Invertebrate Zoology, American Museum of Natural History; 200 Central Park West, New York, NY 10024-5192, USA.; Richard Gilder Graduate School, American Museum of Natural History, 200 Central Park West,; New York, NY 10024-5192, USA., Sproul J; Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT, 84604, USA., Tolman ER; Division of Invertebrate Zoology, American Museum of Natural History; 200 Central Park West, New York, NY 10024-5192, USA.; Department of Biological Sciences, Virginia Tech University, Blacksburg, VA, 24061, USA., Birrell J; The Salmonfly Project, 123 W. Central Ave, Missoula, MT, 59801, USA., Meek J; Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA., Heckenhauer J; Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Hesse, 60325, Germany.; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse, 60325, Germany., Nelson CR; Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT, 84604, USA., Dudchenko O; DNAZoo, The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Jeong J; DNAZoo, The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Weisz D; DNAZoo, The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Aiden EL; DNAZoo, The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Hotaling S; Department of Watershed Sciences, Utah State University, Logan, UT, 84321, USA., Ware JL; Division of Invertebrate Zoology, American Museum of Natural History; 200 Central Park West, New York, NY 10024-5192, USA., Frandsen PB; Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, 84604, USA.
Jazyk:	angličtina
Zdroj:	The Journal of heredity [J Hered] 2024 Aug 22. Date of Electronic Publication: 2024 Aug 22.
DOI:	10.1093/jhered/esae044
Abstrakt:	Pteronarcys californica (Newport 1848) is commonly referred to as the giant salmonfly and is the largest species of stonefly (Insecta: Plecoptera) in the western United States. Historically, it was widespread and abundant in western rivers, but populations have experienced a substantial decline in the past few decades, becoming locally extirpated in numerous rivers in Utah, Colorado, and Montana. Although previous research has explored the ecological variables conducive to the survivability of populations of the giant salmonfly, a lack of genomic resources hampers exploration of how genetic variation is spread across extant populations. To accelerate research on this imperiled species, we present a de novo chromosomal-length genome assembly of P. californica generated from PacBio HiFi sequencing and Hi-C chromosome conformation capture. Our assembly includes 14 predicted pseudo chromosomes and 98.8% of Insecta universal core orthologs. At 2.40 gigabases, the P. californica assembly is the largest of available stonefly assemblies, highlighting at least 9.5-fold variation in assembly size across the order. Repetitive elements (REs) account for much of the genome size increase in P. californica relative to other stonefly species, with the content of Class I retroelements alone exceeding the entire assembly size of all but two other species studied. We also observed preliminary suborder-specific trends in genome size that merit testing with more robust taxon sampling. (© The American Genetic Association. 2024.)
Databáze:	MEDLINE
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