Whole-genome duplication reshaped adaptive evolution in a relict plant species, <i>Cyclocarya paliurus</i>

Qu, Yinquan; Shang, Xianwen; Ziyan, Zeng; Yu, Yanhao; Bian, Guoliang; Wang, Wenling; Li, Liu; Tian, Li; Zhang, Shengcheng; Wang, Qian; Xie, Deti; Xuequn, Chen; Liao, Zhenyang; Wang, Yibin; Qin, Jian; Yang, Wanxia; Sun, Caowen; Fu, Xiangxiang; Zhang, Xingtan; Fang, Shengzuo

doi:10.1101/2022.09.04.506500

Cited by 2 publications

(2 citation statements)

References 99 publications

(108 reference statements)

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“…. (Qu et al 2023). Bottomleft) Heterozygosity in 500bp windows for 13 Pterocarya stenoptera individuals across the region syntenic with the Juglans G-locus.…”

Section: Ggmentioning

confidence: 99%

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Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

Groh,

Vik,

Stevens

et al. 2023

Preprint

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The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). We show that two distinct genetic systems control heterodichogamous mating systems in these genera. In each genus, we find ancient (>50Mya) structural variants that segregate as trans-species polymorphisms. TheJuglanslocus maps to a ca. 20kb structural variant adjacent to gene with likely function in the trehalose-6-phosphate signaling pathway, which is known to regulate flowering time in Arabidopsis and inflorescence architecture in maize. Notably, an insertion in the dominant (protogynous) haplotype contains 8-12 complex tandem duplicates of the 3’ UTR of the gene, and transpecies polymorphism within the gene is restricted to the 3’ UTR. In contrast, theCaryaheterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in floral primordia. The dominant (protogynous) haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows reduced genetic diversity and is over twice as long as its recessive counterpart due to proliferation of multiple transposable element families. We did not detect either genetic system in another heterodichogamous genus within the Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.

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“…. (Qu et al 2023). Bottomleft) Heterozygosity in 500bp windows for 13 Pterocarya stenoptera individuals across the region syntenic with the Juglans G-locus.…”

Section: Ggmentioning

confidence: 99%

“…Topright) Heterozygosity in 500bp windows for 12 diploid Cyclocarya paliurus individuals across the region syntenic with the Juglans G-locus. Two of these individuals represent each dichogamy type(Qu et al 2023). Bottomleft) Heterozygosity in 500bp windows for 13 Pterocarya stenoptera individuals across the region syntenic with the Juglans G-locus.…”

mentioning

confidence: 99%

Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

Groh,

Vik,

Stevens

et al. 2023

Preprint

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Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes

Shang

Fang

et al. 2023

Sci Data

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Cyclocarya paliurus, an endemic species in the genus Juglandaceae with the character of heterodichogamy, is one of triterpene-rich medicinal plants in China. To uncover the genetic mechanisms behind the special characteristics, we sequenced the genomes of two diploid (protandry, PA-dip and protogyny, PG-dip) and one auto-tetraploid (PA-tetra) C. paliurus genomes. Based on 134.9 (~225x), 75.5 (~125x) and 271.8 Gb (~226x) subreads of PacBio platform sequencing data, we assembled 586.62 Mb (contig N50 = 1.9 Mb), 583.45 Mb (contig N50 = 1.4 Mb), and 2.38 Gb (contig N50 = 430.9 kb) for PA-dip, PG-dip and PA-tetra genome, respectively. Furthermore, 543.53, 553.87, and 2168.65 Mb in PA-dip, PG-dip, and PA-tetra, were respectively anchored to 16, 16, and 64 pseudo-chromosomes using over 65.4 Gb (~109x), 68 Gb (~113x), and 264 (~220x) Hi-C sequencing data. Annotation of PA-dip, PG-dip, and PA-tetra genome assembly identified 34,699, 35,221, and 34,633 protein-coding genes (90,752 gene models) or allele-defined genes, respectively. In addition, 45 accessions from nine locations were re-sequenced, and more than 10 × coverage reads were generated.

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Whole-genome duplication reshaped adaptive evolution in a relict plant species, Cyclocarya paliurus

Cited by 2 publications

References 99 publications

Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes

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