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Mar 08, 2024;11 (1): 278.

A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.).

Liqun Han, Xiang Luo, Yu Zhao, Ning Li, Yuhui Xu, Kai Ma
Author Information
  1. Liqun Han: Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.
  2. Xiang Luo: College of Agriculture, Henan University, Zhengzhou, China.
  3. Yu Zhao: Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.
  4. Ning Li: Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China.
  5. Yuhui Xu: Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China. genetics_2010@163.com. ORCID
  6. Kai Ma: Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, the State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China. sunshine002mk@163.com.
PMID: 38459062 DOI: 10.1038/s41597-024-03096-4

Abstract

Wild germplasm resources are crucial for gene mining and molecular breeding because of their special trait performance. Haplotype-resolved genome is an ideal solution for fully understanding the biology of subgenomes in highly heterozygous species. Here, we surveyed the genome of a wild walnut tree from Gongliu County, Xinjiang, China, and generated a haplotype-resolved reference genome of 562.99 Mb (contig N50 = 34.10 Mb) for one haplotype (hap1) and 561.07 Mb (contig N50 = 33.91 Mb) for another haplotype (hap2) using PacBio high-fidelity (HiFi) reads and Hi-C technology. Approximately 527.20 Mb (93.64%) of hap1 and 526.40 Mb (93.82%) of hap2 were assigned to 16 pseudochromosomes. A total of 41039 and 39744 protein-coding gene models were predicted for hap1 and hap2, respectively. Moreover, 123 structural variations (SVs) were identified between the two haplotype genomes. Allele-specific expression genes (ASEGs) that respond to cold stress were ultimately identified. These datasets can be used to study subgenome evolution, for functional elite gene mining and to discover the transcriptional basis of specific traits related to environmental adaptation in wild walnut.

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MeSH Term

Alleles
China
Haplotypes
Juglans
Phenotype
Genome, Plant
Dataset Journal Article

Word Cloud

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