气候变化领域集成服务门户(CCPortal): Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

CCPortal

DOI	10.1073/pnas.2016274118
	Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes
	Halo J.V.; Pendleton A.L.; Shen F.; Doucet A.J.; Derrien T.; Hitte C.; Kirby L.E.; Myers B.; Sliwerska E.; Emery S.; Moran J.V.; Boyko A.R.; Kidd J.M.
发表日期	2021
ISSN	00278424
卷号	118 期号:11
英文摘要	Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the Can- Fam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1-Cfs). Analysis of sequences flanking the 3′ end of LINE-1-Cfs (i.e., LINE-1-Cf 3′-transductions) suggests multiple retrotransposition-competent LINE-1-Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1-Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC-Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Canis familiaris; Long-read assembly; Mobile elements; Structural variation
语种	英语
scopus关键词	long untranslated RNA; 3' flanking region; Article; boxer (dog); DNA base composition; DNA structure; dog; female; GC rich sequence; gene deletion; gene insertion; gene structure; genetic polymorphism; genetic recombination; genetic variation; genome; great Dane (dog); human; human cell; long interspersed nuclear element 1; mobile element; nonhuman; nucleotide sequence; open reading frame; priority journal; retroposon; sequence alignment; short interspersed nuclear element; transcription initiation site
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/180295
作者单位	Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, United States; Universite Cote d'Azur, CNRS, INSERM, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Nice, F-06100, France; Universite de Rennes 1, CNRS, Institut de Genetique et Developpement de Rennes-UMR 6290, Rennes, F-35000, France; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States; Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, United States; Department Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
推荐引用方式 GB/T 7714	Halo J.V.,Pendleton A.L.,Shen F.,et al. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes[J],2021,118(11).
APA	Halo J.V..,Pendleton A.L..,Shen F..,Doucet A.J..,Derrien T..,...&Kidd J.M..(2021).Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes.Proceedings of the National Academy of Sciences of the United States of America,118(11).
MLA	Halo J.V.,et al."Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes".Proceedings of the National Academy of Sciences of the United States of America 118.11(2021).