The chromosome‐scale genome assembly, annotation and evolution of <i>Rhododendron henanense</i> subsp. <i>lingbaoense</i>

Zhou, Xiaojun; Li, Jiantao; Wang, Hailiang; Han, Jun-Wang; Zhang, Kai; Dong, Shuaiwei; Zhang, Yanzhao; Ya, Huiyuan; Cheng, Yanwei; Sun, Shan‐Shan

doi:10.1111/1755-0998.13529

Cited by 16 publications

(16 citation statements)

References 91 publications

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“…Based on comparisons with 11 related plant species, our gene family results identified 2713 G. pentaphyllum -specific genes ( Figure 1h , Supplementary Data Table S10 ), where 3247 gene families expanded and 4598 gene families contracted ( Figure 1g ). The expansion and contraction of gene families are regarded as key drivers of adaptive evolution and stress tolerance in various species [ 40 – 42 ]. Further analyses could focus on the associated molecular evolutionary mechanisms and functional analyses of these genes families.…”

Section: Discussionmentioning

confidence: 99%

“…WGD events are of great significance for species diversification, morphological diversity, and the acquisition of new functions during evolution [ 42 , 43 ]. Previous studies have demonstrated that Cucurbitaceae plants underwent four WGD events, where an early large-scale cucurbit-common tetraploidization (CCT) occurred shortly after the ancient WGTγ event (approximately 130–150 Mya) shared by all core eudicots, and three recent WGDs within some genera in the tribe Cucurbitaeae, tribe Sicyoeae, and tribe Gomphogyneae 23 [ 33 , 35 , 39 , 44 , 45 ],.…”

Section: Discussionmentioning

confidence: 99%

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Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae)

Zhang

Zhao

Kou

et al. 2022

Horticulture Research

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Gynostemma pentaphyllum (Thunb.) Makino is a perennial creeping herbaceous plant in the family Cucurbitaceae, which has great medicinal value and commercial potential, but urgent conservation efforts are needed due to the gradual decreases and fragmented distribution of its wild populations. Here, we report the high-quality diploid chromosome-level genome of G. pentaphyllum obtained using a combination of next-generation sequencing short reads, Nanopore long reads, and Hi-C sequencing technologies. The genome is anchored to 11 pseudo-chromosomes with a total size of 608.95 Mb and 26,588 predicted genes. Comparative genomic analyses indicate that G. pentaphyllum is estimated to have diverged from Momordica charantia 60.7 million years ago, with no recent whole-genome duplication event. Genomic population analyses based on genotyping-by-sequencing and ecological niche analyses indicated low genetic diversity but a strong population structure within the species, which could classify 32 G. pentaphyllum populations into three geographical groups shaped jointly by geographic and climate factors. Furthermore, comparative transcriptome analyses showed that the genes encoding enzyme involved in gypenoside biosynthesis had higher expression levels in the leaves and tendrils. Overall, the findings obtained in this study provide an effective molecular basis for further studies of demographic genetics, ecological adaption, and systematic evolution in Cucurbitaceae species, as well as contributing to molecular breeding, and the biosynthesis and biotransformation of gypenoside.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae)

Zhang

Zhao

Kou

et al. 2022

Horticulture Research

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“…The genomes used herein were taken from recently published articles on Rhododendron species. Assembly of R. griersonianum, R. simsii, R. henanense, R. williamsianum, and R. ovatum was derived from Ma et al (2021), Yang et al (2020), Zhou et al (2022), Soza et al (2019), and (Wang et al 2021a), respectively, and those of R. mucronatum and R. kiyosumense were taken from Shirasawa et al (2021).…”

Section: Rhododendron Species and Their Genome Sequencesmentioning

confidence: 99%

Identification and characterization of genome‐wide long terminal repeat retrotransposons provide an insight into elucidating the trait evolution of five Rhododendron species

et al. 2023

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Rhododendron is well‐known for its beauty and colourful corolla. Although some high‐quality whole‐genome sequencing of it has been completed, there are few studies on long terminal repeat (LTR) retrotransposons in Rhododendron, which limits our ability to elucidate the causes of genetic variations in Rhododendron species. Properties of the intact Rhododendron LTR retrotransposons were investigated at a genome‐wide level. Based on available data, the high‐quality genomes from five species, i.e. R. griersonianum, R. simsii, R. henanense subsp. lingbaoense, R. mucronatum var. ripense and R. ovatum, were selected as targets with good assembly continuity. A total of 17,936 intact LTR retrotransposons were identified; these belong to superfamilies Copia and Gypsy, with 17 clades. The insertion time of these transposons was later than 120 million years ago (Mya), and the outbreak period was concentrated more recently than 30 Mya. Phylogenetic analysis revealed that many LTR retrotransposons might originate from intraspecific duplication. Current evidence also suggests that most LTR retrotransposons were inserted in the interstitial part of genes in R. griersonianum, R. simsii, R. henanense, and R. ovatum, and the functions of the inserted genes mainly involve starch metabolism, proteolysis, etc. The effect of the LTR retrotransposon on gene expression depends on its insertion site and activation. Highly expressed LTR retrotransposons tend to be younger. The results herein improve our knowledge of LTR retrotransposons in Rhododendron genomes and facilitate further study of genetic variation and trait evolution in Rhododendron.

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“…The fact that the H. difformis chromosome number is not a multiple of 16 indicates that its genome may be a result of chromosome fusion need to be further investigated. By using PacBio Sequel platform (Zhou et al, 2021), the genome of H. difformis was sequenced, separated and assembled to the haploid genome. This initial genome assembly comprised 2,752 contigs covering 871.90 Mb, with a contig N50 of 0.68 Mb.…”

Section: Genome Sequencing Assembly and Annotationmentioning

confidence: 99%

Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

Zhao

Yang

et al. 2022

Preprint

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The phenomenon by which a single plant dramatically changes its leaf shape in response to the surrounding environment is called heterophylly, an ideal model for the study of plant phenotypic adaptation to environment. Hygrophila difformis (Acanthaceae), also known as Water-Wisteria, has recently merged as a model to study heterophylly due to its typical phenotypic plasticity to various ecological factors. Here, we generated a chromosome-level genome of H. difformis (scaffold N50: 57.63Mb, and genome size: 831.53 Mb) and predicted 36,099 protein-coding genes mainly on 15 pseudochromosomes. H. difformis evolved a gene expansion for its acclimation to the amphibious environment. RNA-seq analysis revealed that genes relative to environmental stimuli, leaf development and other processes are elaborated, regulating its morphological and physiological acclimations to the changing environments. Finally, we identified candidate genes under different ecological factors, and illuminated the roles of LATE MERISTEM IDENTITY 1 (LMI1) on the regulation of heterophylly in H. difformis. Our study contributes the first genome and transcriptome for Hygrophila, establishing H. difformis as a model for the relationships of ecological factors and plant morphological features. We provide new insights into the adaptability of plants in evolution, along with potential resources for trait improvement in crops.

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The chromosome‐scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense

Cited by 16 publications

References 91 publications

Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae)

Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae)

Identification and characterization of genome‐wide long terminal repeat retrotransposons provide an insight into elucidating the trait evolution of five Rhododendron species

Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

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