文献类型：期刊文献

英文题名：Improved de novo chromosome-level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode

作者：Yan, Feng[1] Xi, Rui-Min[1] She, Rui-Xue[1] Chen, Peng-Peng[1] Yan, Yu-Jie[1] Yang, Ge[1] Dang, Meng[1] Yue, Ming[2] Pei, Dong[3] Woeste, Keith[4] Zhao, Peng[1]

第一作者：Yan, Feng

通信作者：Zhao, P[1]

机构：[1]Northwest Univ, Coll Life Sci, Key Lab Resource Biol & Biotechnol Western China, Minist Educ, Xian, Peoples R China;[2]Xian Bot Garden Shaanxi Prov, Xian, Peoples R China;[3]Chinese Acad Forestry, Res Inst Forestry, State Forestry & Grassland Adm, State Key Lab Tree Genet & Breeding,Key Lab Tree, Beijing, Peoples R China;[4]Purdue Univ, Dept Forestry & Nat Resources, USDA, US Forest Serv,Hardwood Tree Improvement & Regene, W Lafayette, IN 47907 USA

年份：2021

卷号：21

期号：6

起止页码：2063-2076

外文期刊名：MOLECULAR ECOLOGY RESOURCES

收录：;Scopus(收录号：2-s2.0-85104462555);WOS:【SCI-EXPANDED(收录号:WOS:000640785900001)】；

基金：Natural Science Foundation of Shaanxi Province of China, Grant/Award Number: 2019JM-008; Shaanxi Academy of Science Research Funding Project, Grant/Award Number: 2019K-06; Opening Foundation of Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Grant/Award Number: ZSK2018009; National Natural Science Foundation of China, Grant/Award Number: 32070372, 41471038 and 31200500

语种：英文

外文关键词：gene family evolution; genome assembly and annotation; lesion nematode; Manchurian walnut; Nanopore sequencing; PR gene family

摘要：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).