Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan

Xiao, Li; Yu, Mengjun; Zhang, Ying; Hu, Jie; Zhang, Rui; Wang, Jianhua; Guo, Hao; Zhang, He; Guo, Xinyu; Deng, Tianquan; Lv, Saibin; Li, Xuan; Huang, Jianqin; Fan, Guangyi

doi:10.1016/j.xplc.2021.100247

Cited by 12 publications

(13 citation statements)

References 96 publications

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“…14b–c ), consistent with the result of Xiao et al 6 who, using sequence similarity as a criterion, found that one subgenome of pecan showed higher average identity with Myrica rubra . Reassuringly, a disproportionate loss of duplicated genes between the two subgenomes (i.e., biased fractionation) has been detected in prior studies of Juglans and Carya genomes 3 , 5 , 6 and in our study (Fig. 6 and Supplementary Fig.…”

Section: Discussionsupporting

confidence: 90%

“…Because of their economic importance, several genomes have been assembled to study fungal resistance genes and genes related to fruit quality, and their analysis has revealed an ancient whole-genome duplication (WGD) in the family 1 – 5 , termed juglandoid WGD 1 . In addition, comparisons of the genomes of Juglans regia and Carya illinoinensis show biased fractionation and asymmetric loss of duplicated genes between two parental subgenomes that persist in these species 3 , 5 , 6 , pointing to an allotetraploid origin of the family. This was also suggested in cytogenetic studies that explained the predominant Juglandaceae chromosome numbers of 2 n = 32 or 64 by assuming an ancestor shared with, or embedded in, Myricaceae, which have a basic number of x = 8 7 , 8 .…”

Section: Introductionmentioning

confidence: 99%

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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

et al. 2023

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In lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that differ in gene content and syntenic structure. Presence or absence of genes and microsynteny along chromosomal blocks can serve to differentiate subgenomes and to infer phylogenies. We here apply genome-structural data to infer relationships in an ancient allopolyploid lineage, the walnut family (Juglandaceae), by using seven chromosome-level genomes, two of them newly assembled. Microsynteny and gene-content analyses yield identical topologies that place Platycarya with Engelhardia as did a 1980s morphological-cladistic study. DNA-alignment-based topologies here and in numerous earlier studies instead group Platycarya with Carya and Juglans, perhaps misled by past hybridization. All available data support a hybrid origin of Juglandaceae from extinct or unsampled progenitors nested within, or sister to, Myricaceae. Rhoiptelea chiliantha, sister to all other Juglandaceae, contains proportionally more DNA repair genes and appears to evolve at a rate 2.6- to 3.5-times slower than the remaining species.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

et al. 2023

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“…Genus Carya , as the second largest genus in the Juglandiodeae subfamily of Fagales, contains typical temperate-subtropical forest trees for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA) ( Zhang et al., 2013 ; Huang et al., 2019 ). Carya is comprised of up to 20 extant species disjunctively distributed in EA and NA, and most species of the genera are also economically important for their valuable timbers and/or edible nut kernels (e.g., the pecan, Chinese hickory and Dabieshan hickory) ( Grauke, 2003 ; Kozlowski et al., 2018 ; Huang et al., 2019 ; Xiao. et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…Owing to the richness in health factors of its nut kernels, C. illinoinensis became the most commercially valuable species of Carya . Commercial production of C. illinoinensis has persisted for about a century and a half, and it has been widely planted across six continents with more than 400 cultivars released so far, including some varieties promoted and planted in large areas ( Grauke et al., 2016 ; Xiao. et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…Among the cultivars of C. illinoinensis , many were formed by both natural and artificial hybridization ( ). For example, the varieties ‘Pawnee’, ‘Lakota’ and ‘Elliott’ mentioned above, belong to intraspecies hybrids with interspecies introgression in history, based on whole genome sequencing data ( Thompson et al., 2008 ; Huang et al., 2019 ; Lovell et al., 2021 ; Xiao et al., 2021 ; ). However, the maternal relationships of the varieties are still unclear, the investigation of plastome variations inherited from the female parent may provide important clues for tracking both ancient and recent gene flows among different varieties caused by inter- and intraspecies hybridization.…”

Section: Introductionmentioning

confidence: 99%

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Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus

Zhang

et al. 2022

Front. Plant Sci.

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Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.

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Epistatic interaction effect between chromosome 1BL (Yr29) and a novel locus on 2AL facilitating resistance to stripe rust in Chinese wheat Changwu 357-9

et al. 2022

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Stripe rust (yellow rust) is a serious disease of bread wheat ( Triticum aestivum L.) worldwide. Genetic resistance is considered the most economical, effective and environmentally friendly method to control the disease. The current study focused on characterizing the components of stripe rust resistance and understanding the interactions in Changwu 357-9 (CW357-9)/Avocet S RIL population. A genetic linkage map constructed using a new GenoBaits Wheat 16K Panel and the 660K SNP array had 5,104 polymorphic SNP markers spanning 3,533.11 cM. Four stable QTL were detected on chromosome arms 1BL, 2AL, 3DS, and 6BS across all environments in Chngwu357-9. The most effective QTL Q YrCW357-1BL was Yr29 and the 6BS QTL was identi ed as Yr78 . The novel QTL on 2AL with moderate effect showed signi cant epistatic interaction with Yr29 . The QTL on 3DL should be same as QYrsn.nwafu-3DL and enriches the overall stripe rust resistance gene pool for breeding. Polymorphisms of anking AQP markers AX-110020417 (for QYrCW357-1BL ), AX-110020417 (for QYrCW357 -2AL ), AX-109466386 (for QYrCW357 -3DL ), and AX-109995005 (for QYrCW357 -6BS ), were evaluated in a diversity panel including 225 wheat cultivars and breeding lines. The results suggested that these high-throughput markers could be used to introduce QYrCW357-1BL ( Yr29 ), QYrCW357-2AL , QYrCW357 -3DL , and QYrCW357 -6BS into commercial wheat cultivars. Combinations of these genes with other APR QTL should lead to higher levels of stripe rust resistance along with the bene cial effects of multi-disease resistance gene Yr29 on improving resistance to other diseases. Key MessageFour stable QTLfor adult plant resistancewere identi ed in wheat line Changwu 357-9, including a new QTL on 2AL showing signi cant interaction with Yr29 to reduce stripe rust severity.

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Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan

Cited by 12 publications

References 96 publications

Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus

Epistatic interaction effect between chromosome 1BL (Yr29) and a novel locus on 2AL facilitating resistance to stripe rust in Chinese wheat Changwu 357-9

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