Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes

Author:

Li Ruidong12,Qu Han1,Chen Jinfeng1,Wang Shibo1,Chater John M1,Zhang Le2,Wei Julong13,Zhang Yuan-Ming4,Xu Chenwu5,Zhong Wei-De6,Zhu Jianguo7,Lu Jianming16,Feng Yuanfa16,Chen Weiming7,Ma Renyuan18,Ferrante Sergio Pietro1,Roose Mikeal L12,Jia Zhenyu12

Affiliation:

1. Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA

2. Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, Riverside, CA

3. Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI

4. Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China

5. Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China

6. Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China

7. Department of Urology, Guizhou Provincial People’s Hospital, Guizhou, China

8. Department of Mathematics, Bowdoin College, Brunswick, ME

Abstract

Abstract Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

Funder

University of California

UC Academic Senate Regents Faculty Fellowship and Faculty Development Award

UCR Hellman Fellowship

National Institute of Food and Agriculture

National Key Basic Research Program of China

National Natural Science Foundation of China

Guangzhou Municipal Science and Technology Project

Science and Technology Project of Guizhou Province

Publisher

Oxford University Press (OUP)

Subject

Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics

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