Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses

Most genomic studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias have gained limited attention. This study compared population genomic analyses using four different reference genomes of mango (<i>Mangifera indica</i>), including the two haploid assemblies of haplotype-resolved telomere-to-telomere (T2T) genome assembly, a pangenome, and an older version of the reference genome available on NCBI. The choice of reference genome dramatically impacted the mapping efficiency and resulted in notable differences in calling the genetic variants, particularly structural variations (SVs). Phylogenetic analysis was more sensitive to the reference genome compared to genetic differentiation. Population genomic analyses of artificial selection in domestication and SV hotspot regions varied across reference genomes. Notably, the gene enrichment analyses showed significant differences in the top enriched biological processes depending on the reference genome used. Overall, the mango pangenome outperformed the other reference genomes across various metrics, followed by T2T reference genomes, as they captured greater diversity and effectively reduced reference bias. Our findings highlight the role of the mango pangenome in reducing reference bias and underscore the critical role of reference genome selection, suggesting that it is one of the most important factors in population genomic studies.

Authors

Institutions

Publication Details

Journal
Horticulture Research
Published
2025-07-01
DOI
https://doi.org/10.1093/hr/uhaf166
Citations
5
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
4.03

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses

R. Arshad, Zhongxin Jin, Yeyuan Chen, Yanling Peng et al.
5 citations
Horticulture Research
Genomics and Phylogenetic Studies
4.03
article

Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses

R. Arshad, Zhongxin Jin, Yeyuan Chen, Yanling Peng, Zhenzhou Chu, Xiaodong Xu, Qi Xu, Ting Hou, Q. Wang, Yi Zhang, Yu Zhang, Xingyi Wang, Sheikh Bilal Ahmad, Yingchun Zhang, Xuanwen Yang, Jianfeng Huang, Hua Xiao, Chaochao Li, Chengjie Chen, Xinmin Tian, Guiqi Bi, Yongfeng Zhou, Xiangnian Su, C Li, Guizhou Huang, Yani Hao, Tayyaba Razzaq, Ying Su
article en
5 citations

Abstract

Most genomic studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias have gained limited attention. This study compared population genomic analyses using four different reference genomes of mango (<i>Mangifera indica</i>), including the two haploid assemblies of haplotype-resolved telomere-to-telomere (T2T) genome assembly, a pangenome, and an older version of the reference genome available on NCBI. The choice of reference genome dramatically impacted the mapping efficiency and resulted in notable differences in calling the genetic variants, particularly structural variations (SVs). Phylogenetic analysis was more sensitive to the reference genome compared to genetic differentiation. Population genomic analyses of artificial selection in domestication and SV hotspot regions varied across reference genomes. Notably, the gene enrichment analyses showed significant differences in the top enriched biological processes depending on the reference genome used. Overall, the mango pangenome outperformed the other reference genomes across various metrics, followed by T2T reference genomes, as they captured greater diversity and effectively reduced reference bias. Our findings highlight the role of the mango pangenome in reducing reference bias and underscore the critical role of reference genome selection, suggesting that it is one of the most important factors in population genomic studies.

Horticulture ResearchVol. 12(9)
Chinese Academy of Tropical Agricultural Sciences (CN), Guangxi University (CN), Guangxi Normal University (CN), Beijing Forestry University (CN), Soochow University (CN), Agricultural Genomics Institute at Shenzhen (CN), Tropical Crops Genetic Resources Institute (CN), Guangxi Academy of Agricultural Science (CN), Chinese Academy of Agricultural Sciences (CN), Sanya University (CN), Ministry of Agriculture and Rural Affairs (CN), Xinjiang University (CN)
National Natural Science Foundation of China, National Key Research and Development Program of China
Life in Land
Openalex Percentile: Top 6%
Genomics and Phylogenetic Studies
4.03
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.