Evidence map›Paper›PMID 42255470›Full record

ArticleaBIOTECH2026

Alleleauto: a pipeline for allele identification and analysis of allele-specific gene expression with haplotype-resolved diploid genome assemblies.

Tian-Le Shi, Shuai Nie, Yu-Tao Bao, Zhi-Chao Li, Zhao-Yang Chen, Shi-Wei Zhao, Xue-Mei Yan, Hai-Yao Ma, Xue-Chan Tian, Kai-Hua Jia and 3 more

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Article in aBIOTECH, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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4 · The record

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5 · Who and what money

Authors and funding

13 authors.

Tian-Le ShiKey Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China.
Shuai NieRice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Rice Science and Technology; Guangdong Rice Engineering Laboratory; Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China.
Yu-Tao BaoState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
Zhi-Chao LiState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
Zhao-Yang ChenDepartment of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, 90187, Sweden.
Shi-Wei ZhaoDepartment of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, 90187, Sweden.
Xue-Mei YanState Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Hai-Yao MaState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
Xue-Chan TianSchool of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
Kai-Hua JiaKey Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China.
Jing-Fang GuoGuangdong Eco-Engineering Polytechnic, Guangzhou, 510520, China.
Jun-Ke ZhangKey Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China.
Jian-Feng MaoState Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Advanced sequencing now enables haplotype resolution of genomes from non-model diploid plant species, facilitating allele identification and the use of allele-specific expression (ASE) analysis to uncover the relationships between genes and phenotypes in heterozygous genomes. However, identification of true allelic pairs remains challenging due to the presence of paralogous genes from ancient genome duplications, and existing methods lack systematic, reproducible filtering criteria. In this study, we developed Alleleauto, a workflow integrating the parametric 3σ rule and the non-parametric Tukey's method as two complementary outlier detection methods to precisely identify alleles and perform ASE analysis from haplotype-resolved assemblies. Alleleauto first searches for homologous genes across homologous chromosomes, then applies statistical filtering criteria based on synonymous substitution rates (

Indexed as

Allele identificationAllele-specific expressionHaplotype-resolvedNon-model diploid plant genomeSequence similarity

Identifiers

PMID42255470
PMCPMC13240741

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