干旱区生态环境知识资源中心(Arid): Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

Arid

DOI	10.1093/gbe/evaa016
	Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds
	Dolby, Greer A.1,2; Morales, Matheo 1; Webster, Timothy H.1,3; DeNardo, Dale F.1; Wilson, Melissa A.1,4; Kusumi, Kenro 1
通讯作者	Dolby, Greer A. ; Kusumi, Kenro
来源期刊	GENOME BIOLOGY AND EVOLUTION
ISSN	1759-6653
出版年	2020
卷号	12 期号:2 页码:3917-3925
英文摘要	Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.
英文关键词	immune system orthology reptile reference genome synteny testudines
类型	Article
语种	英语
国家	USA
开放获取类型	gold, Green Published
收录类别	SCI-E
WOS记录号	WOS:000522862200014
WOS关键词	TOLL-LIKE RECEPTORS ; IMMUNE-SYSTEM ; PREDICTION ; EVOLUTION ; RECOGNITION ; SEQUENCE ; INSIGHTS ; TURTLE ; RNA
WOS类目	Evolutionary Biology ; Genetics & Heredity
WOS研究方向	Evolutionary Biology ; Genetics & Heredity
来源机构	Arizona State University
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/314573
作者单位	1.Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA; 2.Arizona State Univ, Ctr Mech Evolut, Tempe, AZ 85287 USA; 3.Univ Utah, Dept Anthropol, Salt Lake City, UT 84112 USA; 4.Arizona State Univ, Ctr Evolut & Med, Tempe, AZ 85287 USA
推荐引用方式 GB/T 7714	Dolby, Greer A.,Morales, Matheo,Webster, Timothy H.,et al. Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds[J]. Arizona State University,2020,12(2):3917-3925.
APA	Dolby, Greer A.,Morales, Matheo,Webster, Timothy H.,DeNardo, Dale F.,Wilson, Melissa A.,&Kusumi, Kenro.(2020).Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds.GENOME BIOLOGY AND EVOLUTION,12(2),3917-3925.
MLA	Dolby, Greer A.,et al."Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds".GENOME BIOLOGY AND EVOLUTION 12.2(2020):3917-3925.