期刊
MOLECULAR ECOLOGY RESOURCES
卷 21, 期 6, 页码 2063-2076出版社
WILEY
DOI: 10.1111/1755-0998.13394
关键词
gene family evolution; genome assembly and annotation; lesion nematode; Manchurian walnut; Nanopore sequencing; PR gene family
资金
- Natural Science Foundation of Shaanxi Province of China [2019JM-008]
- Shaanxi Academy of Science Research Funding Project [2019K-06]
- Opening Foundation of Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education [ZSK2018009]
- National Natural Science Foundation of China [32070372, 41471038, 31200500]
The study presented an improved assembly of the J. mandshurica genome, revealing its common ancestor relationship with J. regia and the two whole genome duplication events that both species have undergone. J. mandshurica lacks certain genes found in J. regia but also includes unique genes not present in the J. regia genome, with significant changes observed in gene families related to disease resistance.
Manchurian walnut (Juglans mandshurica Maxim.) is a synonym of J. cathayensis, a diploid, vulnerable, temperate deciduous tree valued for its wood and nut. It is also valued as a rootstock for Juglans regia because of its reported tolerance of lesion nematode. Reference genomes are available for several Juglans species, our goal was to produce a de novo, chromosome-level assembly of the J. mandshurica genome. Here, we reported an improved assembly of J. mandshurica with a contig N50 size of 6.49 Mb and a scaffold N50 size of 36.1 Mb. The total genome size was 548 Mb encoding 29,032 protein coding genes which were annotated. The collinearity analysis showed that J. mandshurica and J. regia originated from a common ancestor, with both species undergoing two WGD events. A genomic comparison showed that J. mandshurica was missing 1657 genes found in J. regia, and J. mandshurica includes 2827 genes not found in of the J. regia genome. The J. mandshurica contained 1440 unique paralogues that were highly enriched for flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction. Four gene families related to disease resistance notable contraction (rapidly evolving; LEA, WAK, PPR, and PR) in J. mandshurica compared to eight species. JmaPR10 and JmaPR8 contained three orthologous gene pairs with J. regia that were highly expressed in root bark. JmaPR10 is a strong candidate gene for lesion nematodes resistance in J. mandshurica. The J. mandshurica genome should be a useful resource for study of the evolution, breeding, and genetic variation in walnuts (Juglans).
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