Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor).

Autor:	Tsuchiya MTN; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA.; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA., Dikow RB; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA., Koepfli KP; Smithsonian-Mason School of Conservation, George Mason Univeristy, Front Royal, VA, USA.; Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA., Frandsen PB; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA.; Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT, USA., Rockwood LL; Department of Biology, George Mason University, Fairfax, VA, USA., Maldonado JE; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.; Department of Biology, George Mason University, Fairfax, VA, USA.
Jazyk:	angličtina
Zdroj:	Genome biology and evolution [Genome Biol Evol] 2021 Jan 07; Vol. 13 (1).
DOI:	10.1093/gbe/evaa255
Abstrakt:	Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes. We discovered significant variation in contig and scaffold N50 and L50 statistics and genome completeness depending on the de novo assembler used. We compared the performance of these three assembly algorithms in hopes that this study will aid others looking to improve the quality of existing draft genome assemblies even without additional sequence data. We also estimate the demographic histories of raccoons and kinkajous using the Pairwise Sequentially Markovian Coalescent and discuss the variation in population sizes with respect to climatic change during the Pleistocene, as well as aspects of their ecology and taxonomy. Our goal is to achieve a better understanding of the evolutionary history of procyonids and to create robust genomic resources for future studies regarding adaptive divergence and selection. (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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