asymbiotic-germination-leaf-explant-based-regeneration-endangered

Asymbiotic Germination and Leaf Explant-Based Regeneration of the Endangered Medicinal Orchid <em>Hemipilia cucullata</em> from Mature Seeds

Hemipilia cucullata (Orchidaceae) is a terrestrial orchid widely valued for its medicinal properties and ornamental appeal, yet its wild populations are ...

Zhejiang University

Warm-temperate evergreen (WTE) forest represents the typical vegetation type of subtropical China, but how its component species responded to past environmental change remains largely unknown. Here, we reconstruct the evolutionary history of Tetrastigma hemsleyanum, an herbaceous climber restricted to the WTE forest. Twenty populations were genotyped using chloroplast DNA sequences and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and ecological niche modeling (ENM) of the species distributions during the Last Glacial Maximum (LGM) and at present. Lineages in Southwest vs Central-South-East China diverged through climate/tectonic-induced vicariance of an ancestral southern range during the early Pliocene. Long-term stability in the Southwest contrasts with latitudinal range shifts in the Central-South-East region during the early-to-mid-Pleistocene. Genetic and ENM data strongly suggest refugial persistence in situ at the LGM. Pre-Quaternary environmental changes appear to have had a persistent influence on the population genetic structure of this subtropical WTE forest species. Our findings suggest relative demographic stability of this biome in China over the last glacial-interglacial cycle, in contrast with palaeobiome reconstructions showing that this forest biome retreated to areas of today's tropical South China during the LGM.

Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio-Pleistocene range dynamics of evergreen forest in subtropical China.

Tetrastigma hemsleyanum is of great medicinal importance and used as a model system to address the evolutionary history of warm-temperate evergreen (WTE) forest biomes in East Asia over Neogene time scales. However, further studies on the neutral and adaptive divergence processes of T. hemsleyanum are currently impeded by a lack of genomic resources. In this study, we de novo assembled and annotated a reference transcriptome for two cpDNA lineages (Central-South-East vs. Southwest) of T. hemsleyanum. We further used comparative genomic and multilocus coalescent approaches to investigate the tempo and mode of lineage diversification in T. hemsleyanum.

Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum.

Here, we present a high-quality chromosome-scale genome assembly (2.19 Gb) and annotation of Tetrastigma hemsleyanum, a perennial herbaceous liana native to subtropical China with diverse medicinal applications. Approximately 73% of the genome was comprised of transposable elements (TEs), of which long terminal repeat retrotransposons (LTR-RTs) were a predominant group (69% of the genome). The genome size increase of T. hemsleyanum (relative to Vitis species) was mostly due to the proliferation of LTR-RTs. Of the different modes of gene duplication identified, transposed duplication (TRD) and dispersed duplication (DSD) were the predominant ones. Genes, particularly those involved in the phenylpropanoid-flavonoid (PF) pathway and those associated with therapeutic properties and environmental stress resistance, were significantly amplified through recent tandem duplications. We dated the divergence of two intraspecific lineages in Southwest (SW) versus Central-South-East (CSE) China to the late Miocene (approximately 5.2 million years ago). Of those, the former showed more upregulated genes and metabolites. Based on resequencing data of 38 individuals representing both lineages, we identified various candidate genes related to 'response to stimulus' and 'biosynthetic process', including ThFLS11, which is putatively involved in flavonoid accumulation. Overall, this study provides abundant genomic resources for future evolutionary, ecological, and functional genomics studies in T. hemsleyanum and related species.

Chromosome-level reference genome of Tetrastigma hemsleyanum (Vitaceae) provides insights into genomic evolution and the biosynthesis of phenylpropanoids and flavonoids.

The mobility of transposable elements (TEs) partly drives genome evolution, potentially leading to either adaptive or deleterious effects. However, it remains far from clear whether and how TEs contribute to adaptation to changing environments, especially in plants. We analyzed whole-genome sequencing data from 29 ecologically diverse Tetrastigma hemsleyanum populations to infer the species' demographic history and its impact on TE polymorphisms. Integrated selective sweep and genome-environment association (GEA) approaches were employed to examine the contribution of TEs to environmental adaptation. The ancestor of T. hemsleyanum diverged during the late Miocene/Pliocene, forming two lineages that further split into four sublineages. These (sub)lineages underwent periodic population declines and recoveries during the late-Pleistocene climatic oscillations, with most polymorphic TEs transposing during the last glacial period. A small fraction of these TEs (0.033-0.40%) showed signatures of positive selection, while a broader subset (0.081-0.76%) correlated significantly with climatic variables. Notably, these selected or climate-linked TE polymorphisms were preferentially retained in gene-poor regions and frequently linked to genes involved in organ development and stress/defense response. Our findings demonstrate that TEs played a key regulatory and adaptive role in T. hemsleyanum's response to environmental change, underscoring their importance in better understanding the genomic mechanisms underlying adaptation.

Genome-wide patterns of local adaptation associated with transposable elements in Tetrastigma hemsleyanum (Vitaceae).

The demographic histories of temperate plants in Northeast Asia in response to Quaternary climate oscillations have long been the focus of evolutionary biologists, but have rarely been studied in herbaceous plants. Here, we investigated the phylogeographic patterns of Mukdenia and Oresitrophe.

Article	Year
Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio-Pleistocene range dynamics of evergreen for... The New phytologist\| PubMed ID: 25639152	2015
Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum. BMC plant biology\| PubMed ID: 30249188	2018
Chromosome-level reference genome of Tetrastigma hemsleyanum (Vitaceae) provides insights into genomic evolution and the biosynthesis of phenylpropanoids and flavonoids. The Plant journal : for cell and molecular biology\| PubMed ID: 36864731	2023
Genome-wide patterns of local adaptation associated with transposable elements in Tetrastigma hemsleyanum (Vitaceae). The New phytologist\| PubMed ID: 40448394	2025
Refugial isolation and ecological niche differentiation promote genetic divergence of Oresitrophe and Mukdenia in Northeast Asia. American journal of botany\| PubMed ID: 40904271	2025

Weimei Jiang

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