A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

	A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
	Toh, H; Yang, CT; Formenti, G; Raja, K; Yan, L; Tracey, A; Chow, W; Howe, K; Bergeron, LA; Zhang, GJ; Haase, B; Mountcastle, J; Fedrigo, O; Fogg, J; Kirilenko, B; Munegowda, C; Hiller, M; Jain, A; Kihara, D; Rhie, A; Phillippy, AM; Swanson, SA; Jiang, P; Clegg, DO; Jarvis, ED; Thomson, JA; Stewart, R; Chaisson, MJP; Bukhman, YV
	2022
发表期刊	BMC BIOLOGY
卷号	20 期号:1
摘要	Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. Conclusions Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/13456
专题	科研部门_遗传多样性基因组学研究组（张国捷）
推荐引用方式 GB/T 7714	Toh, H,Yang, CT,Formenti, G,et al. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes[J]. BMC BIOLOGY,2022,20(1).
APA	Toh, H.,Yang, CT.,Formenti, G.,Raja, K.,Yan, L.,...&Bukhman, YV.(2022).A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.BMC BIOLOGY,20(1).
MLA	Toh, H,et al."A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes".BMC BIOLOGY 20.1(2022).

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