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

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

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

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

BACKGROUND

Assessing the current status and identifying the mechanisms threatening endangered plants are significant challenges and fundamental to biodiversity conservation, particularly for protecting Tertiary relict trees and plant species with extremely small populations (PSESP). Ulmus elongata (Ulmus, Ulmaceae) with high values for the ornamental application, is a Tertiary relict tree species and one of the members from PSESP in China. Currently, the wild populations of U. elongata have been threatened by excessive deforestation and urbanization, but limited knowledges of its genetic diversity seriously hinder conservation efforts. Therefore, a further study on the genetic diversity and drivers of genetic pattern in U. elongata is crucial for preserving genetic resources and can serve as a reference for other Tertiary relict plants and PSESP under climate change.

RESULTS

Here, a total of 12 populations from 70 individuals of U. elongata were collected covering its geographical distribution in China. Utilizing chloroplast genome datasets, we found that U. elongata exhibited remarkably low nucleotide diversity and gene flow (π = 0.00013, Nm = 0.03). Analysis of molecular variance (AMOVA) showed that genetic variation in U. elongata occurs mainly between eight clades (60.95%). The Mantel tests indicated a significant correlation between genetic differentiation and geographical distances (r = 0.3777, p < 0.05) in U. elongata populations. A notable phylogeographic structure was identified in U. elongata, comprising eight distinct haplogroups (NST = 0.917, GST = 0.876, p < 0.05), which was attributed to the global cooling in the East Asia and Quaternary climate oscillations.

CONCLUSIONS

Overall, our study using Ulmus elongata as a representative supported the hypothesis that plants belonging to Tertiary relict species and PSESP simultaneously exhibits significantly lower genetic diversity compared to those are either Tertiary relict species or PSESP individually. Furthermore, the low genetic diversity and significant genetic differentiation in U. elongata populations can be primarily ascribed to a combination of factors, including habitat fragmentation resulting from human activities, populations contraction during LGM and small population sizes. This provides a crucial foundation for guiding conservation efforts and implementing management strategies for other Tertiary relict tree species and PSESP. Our findings also provide evidence for the important roles of East Asian monsoon system and climate oscillations in shaping the phylogeographic pattern in subtropical broad-leaved forests.

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

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

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

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

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

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

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

The Fagaceae, a plant family with a wide distribution and diverse adaptability, has garnered significant interest as a subject of study in plant speciation and adaptation. Meanwhile, certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood. In this study, we present two high-quality, chromosome-scale genome sequences for Quercus sichourensis (848.75 Mb) and Quercus rex (883.46 Mb). Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio (Ka/Ks) of protein-coding genes among Fagaceae species are related to different environmental adaptations. Interestingly, most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome, as compared to the outgroup species, Fagus sylvatica. Furthermore, resequencing and population analysis of Q. sichourensis and Q. rex reveal that Q. sichourensis has lower genetic diversity and higher deleterious mutations compared to Q. rex. The high-quality, chromosome-level genomes and the population genomic analysis of the critically endangered Q. sichourensis and Q. rex will provide an invaluable resource as well as insights for future study in these two species, even the genus Quercus, to facilitate their conservation.