Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense

Shen, Yu-Fang; Cheng, Yanli; Li, Kangqin; Li, Huogen

doi:10.3390/f10070565

Cited by 18 publications

(18 citation statements)

References 85 publications

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“…Although C. camphora is widely distributed in southern China, its origin is limited to East Asia and the Indochina Peninsula. The limited geographical distribution inhibits the gene exchange among populations and enhances genetic diversity within the population [33]. In addition, this study, together with the findings from Wu et al, showed lower genetic diversity of C. camphora in China than that of the Japanese population, which was not consistent with the results of Kameyama et al [2].…”

Section: Genetic Diversity Of C Camphoracontrasting

confidence: 93%

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Gong

Yang

et al. 2021

Forests

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Cinnamomum camphora (L.) J.Presl is a representative tree species of evergreen broad-leafed forests in East Asia and has exceptionally high economic, ornamental, and ecological value. However, the excessive exploitation and utilization of C. camphora trees have resulted in the shrinking of wild population sizes and rare germplasm resources. In this study, we characterized 171 C. camphora trees from 39 natural populations distributed throughout the whole of China and one Japanese population. We investigated genetic diversity and population structure using genome-wide single-nucleotide polymorphism (SNP) identified by genotyping by sequencing (GBS) technology. The results showed the genetic diversity of the C. camphora populations from western China > central China > eastern China. Moreover, the Japanese population showed the highest diversity among all populations. The molecular variance analysis showed 92.03% of the genetic variation within populations. The average pairwise FST was 0.099, and gene flow Nm was 2.718, suggesting a low genetic differentiation among populations. Based on the genetic clustering analysis, the 40 C. camphora populations clustered into three major groups: Western China, Central China, and Eastern China + Japan. Eastern China’s population had the closest genetic relationship with the Japanese population, suggesting possible gene exchange between the two adjacent areas. This study furthers our understanding of the genetic diversity and genetic structure of C. camphora in East Asia and provides genetic tools for developing strategies of C. camphora germplasm utilization.

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Section: Genetic Diversity Of C Camphoracontrasting

confidence: 93%

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Gong

Yang

et al. 2021

Forests

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“…4A-C), which is consistent with the pattern of their natural geographical distribution [40,42,68]. This result is consistent with our previous research showing that there are shared haplotypes between the XN population and CW based on cpDNA and adaptive gene sequences [67]. This may be related to the geographical location of the XN population, which is closer to CE between CE and CW and may have experienced recent historical gene ow with CW.…”

Section: Discussionsupporting

confidence: 90%

“…For L. chinense, the long-term in situ refugia pattern may have caused genetic differentiation among the isolated populations [67]. In this study, the population structure analysis showed an obvious genetic divergence between CE and CW, but not the XN population (Figs.…”

Section: Discussionmentioning

confidence: 50%

Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics

Shen¹,

Xia²,

Tu³

et al. 2020

Preprint

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Background: Adaptive genetic differentiation is a hotspot in the research of speciation mechanisms in evolutionary biology. Genomic resources are important for detecting ecological adaptive evolution of non-model plants. Using RNA-seq for non-model plants is a good approach to obtain their genomic resources. The combination of population transcriptome resources and environmental data can provide insights into the genetic mechanism of adaptive genetic differentiation.Results: Based on the population transcriptome data, we investigated the spatial distribution of genetic variations in Liriodendron to detect relationships between ecological factors and genetic differentiation. Environmental data and genetic variations from 17 populations were integrated to detect the population structure, adaptive genes and key environmental factors that shape the population genetic structure by landscape genetic approach. Here, we identified 16592 high-quality single nucleotide polymorphisms (SNPs). The population structure analysis results showed that 17 populations were divided into three groups: L. tulipifera, eastern group and western group of L. chinense. Redundancy analysis and latent factor mixed model analysis suggested that precipitation seasonality, precipitation in the driest quarter, diurnal temperature, and solar radiation in May were closely associated with the adaptive genetic differentiation of Liriodendron. Ecological niche differentiation analysis implied significant ecological niche divergence between L. chinense and L. tulipifera habitats. In total, 858 environment-related loci were identified, which were associated with 464 genes. Pathway enrichment analysis revealed that these genes were significantly enriched in multiple biological pathways. Related studies confirmed that these biological pathways play vital roles in plant growth, development, stress, immune response and photosynthesis.Conclusions: Our research provided empirical evidence that environmental factors may play a key role in driving adaptive genetic differentiation of species. Furthermore, the combination of population transcriptome resources and environmental datasets provides new insights into the study of adaptive genetic differentiation of species.

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“…Generally, the genetic diversity of species with a widespread distribution is higher than that of species with a narrow or endemic distribution [47,48]. Considering that the native habitant of C. camphora is widespread in the whole region of South China, it is not surprising that the genetic diversity in this study (Ho = 0.45 and He = 0.40) is much higher than that of other narrow or endemic species, such as Dalbergia odorifera (Ho = 0.28 and He = 0.37) [21], Gastrodia elata (Ho = 0.05 and He = 0.46) [24], and Ottelia acuminata (Ho = 0.28 and He = 0.37) [49].…”

Section: Genetic Diversity Of C Camphoramentioning

confidence: 99%

Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Zhong

Yang

et al. 2019

Forests

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Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

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Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense

Cited by 18 publications

References 85 publications

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics

Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

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