The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP)

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled size of was 1.84 Gb, contig N50 ca. 45 Mb scaffold 92 Mb. Identified repeats constituted approximately 57% genome, 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that magnolias form sister clade eudicots order Ceratophyllales, while monocots are other core angiosperms. our total 21 individuals 5 remnant populations as well 22 specimens belonging 8 related Magnoliaceae species, resequenced. results showed had higher genetic diversity (θw = 0.01126 θπ 0.01158) than species in Magnoliaceae. However, population structure suggested differentiation among very low. Analyses demographic history using different models consistently revealed 2 bottleneck events occurred. contemporary effective estimated be 10.9. patterns loads (inbreeding numbers deleterious mutations) constructive strategies conservation these sinica. Overall, will valuable genomic resource

Language: Английский

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Chromosome-scale genomes of Quercus sichourensis and Quercus rex provide insights into the evolution and adaptation of Fagaceae

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: April 1, 2024

Language: Английский

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Chromosome-level genome assembly of the threatened resource plant Cinnamomum chago

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: May 3, 2024

Abstract Cinnamomum chago is a tree species endemic to Yunnan province, China, with potential economic value, phylogenetic importance, and conservation priority. We assembled the genome of C. using multiple sequencing technologies, resulting in high-quality, chromosomal-level annotation information. The size approximately 1.06 Gb, contig N50 length 92.10 Mb. About 99.92% sequences could be anchored 12 pseudo-chromosomes, only one gap, 63.73% consists repeat sequences. In total, 30,497 genes were recognized according annotation, including 28,681 protein-coding genes. This high-quality chromosome-level assembly will assist us utilization this valuable resource, while also providing crucial data for studying evolutionary relationships within genus, offering opportunities further research exploration its diverse applications.

Language: Английский

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Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis

Genes, Journal Year: 2024, Volume and Issue: 15(6), P. 787 - 787

Published: June 14, 2024

Magnolia lotungensis is an extremely endangered endemic tree in China. To elucidate the genetic basis of M. lotungensis, we performed a comprehensive transcriptome analysis using sample integrating plant’s bark, leaves, and flowers. De novo assembly yielded 177,046 transcripts 42,518 coding sequences. Notably, identified 796 species-specific genes enriched organelle gene regulation defense responses. A codon usage bias revealed that mutation appears to be primary driver selection shaping species’ architecture. An evolutionary based on dN/dS values paralogous orthologous pairs indicated predominance purifying selection, suggesting strong constraints most genes. comparative transcriptomic with sinica approximately 1000 ultra-conserved genes, essential cellular processes such as transcriptional regulation, protein synthesis, genome stability. Interestingly, only limited number 511 rapidly evolving under positive were detected compared kuangsiensis. These metabolic associated adaptation specific environments, potentially limiting ability expand its range. Our findings contribute understanding architecture suggest insufficient adaptive status.

Language: Английский

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Characterization and functional reconstruction of a highly productive germacrene A synthase from Liriodendron chinense

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Summary Plants produce a large array of natural products which play important roles in flavours, fragrances and medicines. However, some high‐value plant intermediate metabolites cannot be directly extracted from plants. The tulip tree ( Liriodendron chinense ) the Magnoliaceae family is rich sesquiterpenes. Upon characterizing functions 11 terpene synthases, we discovered that LcTPS3 could high yields (+)‐germacrene A, was shown to central scaffold sesquiterpene biosynthesis. This compound can completely transformed into β‐elemene at temperature, broad‐spectrum antitumor drug widely used clinical treatment. By expressing precursor‐providing Saccharomyces cerevisiae chassis with aid metabolic engineering, fermentation yield A has been achieved 14.71 g/L. Site‐directed mutagenesis experiments molecular dynamics simulations revealed A280V suppresses cyclization substrate by influencing conformation enzyme‐substrate. Y282L facilitates secondary α‐guaiene shortening distance between catalytic residue Y531 substrate. These insights underscore plasticity suggest its targeted engineering unlock synthesis wider valuable

Language: Английский

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Phylogeography and genetic diversity of Ulmus elongata (Ulmaceae), a Tertiary relict tree with extremely small populations (PSESP)

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 16, 2025

Assessing the current status and identifying mechanisms threatening endangered plants are significant challenges fundamental to biodiversity conservation, particularly for protecting Tertiary relict trees plant species with extremely small populations (PSESP). Ulmus elongata (Ulmus, Ulmaceae) high values ornamental application, is a tree one of members from PSESP in China. Currently, wild U. have been threatened by excessive deforestation urbanization, but limited knowledges its genetic diversity seriously hinder conservation efforts. Therefore, further study on drivers pattern crucial preserving resources can serve as reference other under climate change. Here, total 12 70 individuals were collected covering geographical distribution Utilizing chloroplast genome datasets, we found that exhibited remarkably low nucleotide gene flow (π = 0.00013, Nm 0.03). Analysis molecular variance (AMOVA) showed variation occurs mainly between eight clades (60.95%). The Mantel tests indicated correlation differentiation distances (r 0.3777, p < 0.05) populations. A notable phylogeographic structure was identified elongata, comprising distinct haplogroups (NST 0.917, GST 0.876, 0.05), which attributed global cooling East Asia Quaternary oscillations. Overall, our using representative supported hypothesis belonging simultaneously exhibits significantly lower compared those either or individually. Furthermore, be primarily ascribed combination factors, including habitat fragmentation resulting human activities, contraction during LGM population sizes. This provides foundation guiding efforts implementing management strategies PSESP. Our findings also provide evidence important roles Asian monsoon system oscillations shaping subtropical broad-leaved forests.

Language: Английский

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Conservation genomics of a threatened subtropical Rhododendron species highlights the distinct conservation actions required in marginal and admixed populations

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(2)

Published: April 1, 2025

SUMMARY With the impact of climate change and anthropogenic activities, underlying threats facing populations with different evolutionary histories distributions, associated conservation strategies necessary to ensure their survival, may vary within a species. This is particularly true for marginal and/or those showing admixture. Here, we re‐sequence genomes 102 individuals from 21 locations Rhododendron vialii , threatened species distributed in subtropical forests southwestern China that has suffered habitat fragmentation due deforestation. Population structure results revealed R . can be divided into five genetic lineages using neutral single‐nucleotide polymorphisms (SNPs), whereas selected SNPs divide six lineages. Guigu (GG) population, which identified as admixed SNPs, but assigned distinct cluster non‐neutral loci. experienced multiple bottlenecks, demographic have been suggested among populations. Ecological niche modeling combined genomic offset analysis suggests population (Northeast, NE) harboring highest diversity likely risk maladaptation future. The therefore needs urgent ex situ areas where influence future predicted well buffered. Alternatively, GG potential local adaptation, will need conservation. Puer carries heaviest load, rescue. Our findings highlight how genomics, analysis, ecological integrated inform targeted

Language: Английский

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Conservation and threatened status of plant species with extremely small populations in the karst region of southeastern Yunnan, China

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 24, 2024

The southeastern Yunnan is one of the most typical areas in China with karst landforms. rich variety vegetation types and plant diversity means that threatened status are also synchronized. Over past 20 years, comprehensive conservation team for species extremely small populations (PSESP) has conducted in-depth field surveys region, combining relevant literature projects to compile a list PSESP which including endangered status, actions, scientific research. Among all 116 PSESP, relatively abundant families include Cycadaceae (12 species), Magnoliaceae (17species) Orchidaceae (18 species). Hekou Malipo counties highest number, 44 43 respectively. A total 81 included List National Key Protected Wild Plants . For 24 critically (CR) 41 (EN) represent levels severe threat. Up now, 96 have taken at least protective measure from situ conservation, ex breeding or reintroduction/reinforcement. But there still not any measures. Additionally, research been on 86 species, but 30 had initiated. threat human interference mainly overcollection habitat destruction, threats limitations imposed itself natural disasters cannot be ignored. Our findings underscore importance integrated strategies, addition reintroduction/reinforcement, we should pay attention research, germplasm environmental education ethnic culture. We propose consider establishing professional botanical garden Yunnan, hope this study can offer valuable insights biodiversity Yunnan.

Language: Английский

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Current conservation status and potential distribution under climate change of Michelia lacei, a Plant Species with Extremely Small Populations in Yunnan, China

Oryx, Journal Year: 2024, Volume and Issue: 58(5), P. 631 - 640

Published: Sept. 1, 2024

Abstract Michelia lacei W.W. Smith, a magnolia species categorized as Endangered on the IUCN Red List, is subject to severe disturbance. We carried out field surveys and review of literature records present detailed description current status M. . then predicted potential distribution under different climatic scenarios based 60 occurrence (53 recorded during our 7 earlier records) 19 bioclimatic variables from WorldClim database. selected 18 locations four for model training. Temperature seasonality annual temperature range were most influential predicting species. used MaxEnt climate conditions Shared Socioeconomic Pathway in future time periods determine effects change habitat suitable predict areas moderately highly will gradually decrease over time. recommend increased situ ex conservation efforts mitigate this decline protect populations

Language: Английский

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