Genetic diversity variation during the natural regeneration of Vatica guangxiensis, an endangered tree species with extremely small populations

Zhu, Xianliang; Zhou, Rong; Tang, Jialei; Deng, Lili; Xiao, Wei

doi:10.1016/j.gecco.2023.e02400

Cited by 5 publications

(3 citation statements)

References 37 publications

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“…Next, we will further improve VCF2PCACluster by adopting additional input formats, such as PLINK2, and implementing more clustering algorithm for users to choose from. Since its initial release one year ago, four studies have used VCF2PCACluster (previously known as MingPCACluster) [ 19 , 20 ] to conduct their analyses and visualize the results.…”

Section: Discussionmentioning

confidence: 99%

VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs

He,

Xu,

Wang

et al. 2024

BMC Bioinformatics

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Principal component analysis (PCA) is an important and widely used unsupervised learning method that determines population structure based on genetic variation. Genome sequencing of thousands of individuals usually generate tens of millions of SNPs, making it challenging for PCA analysis and interpretation. Here we present VCF2PCACluster, a simple, fast and memory-efficient tool for Kinship estimation, PCA and clustering analysis, and visualization based on VCF formatted SNPs. We implemented five Kinship estimation methods and three clustering methods for its users to choose from. Moreover, unlike other PCA tools, VCF2PCACluster possesses a clustering function based on PCA result, which enabling users to automatically and clearly know about population structure. We demonstrated the same accuracy but a higher performance of this tool in performing PCA analysis on tens of millions of SNPs compared to another popular PLINK2 software, especially in peak memory usage that is independent of the number of SNPs in VCF2PCACluster.

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Section: Discussionmentioning

confidence: 99%

VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs

He,

Xu,

Wang

et al. 2024

BMC Bioinformatics

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show abstract

“…PCA and phylogenetic analyses were carried out using MingPCACluster v1.38, a simple and efficient piece of software for working with population VCF files [28].…”

Section: Population Genetics Population Structure and Genetic Relatio...mentioning

confidence: 99%

“…After filtering, a total of 4884 high quality SNP loci were identified and were found to be evenly distributed across 19 chromosomes (Figure 2). PCA and phylogenetic analyses were carried out using MingPCACluster v1.38, simple and efficient piece of software for working with population VCF files [28].…”

Section: Snp Calling Based On the Reference Genomementioning

confidence: 99%

Evidence for the Use of Karst Tiankengs as Shelters: The Effect of Karst Tiankengs on Genetic Diversity and Population Differentiation in Manglietia aromatica

Yang,

Tang,

Zhu

et al. 2024

Forests

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Karst tiankengs in China are globally significant locations for studying ecological environments and plant diversity. However, there are few reports on how the unique geographical environment of tiankengs affects plant genetic diversity and genetic structure. This study used Hyper-seq gene sequencing technology to develop large-scale genomic SNPs of Manglietia aromatica, both within and outside the tiankengs. Its aim was to investigate the impact of tiankengs on the genetic diversity and genetic structure of the M. aromatica population. The analysis results indicate that the genetic diversity of the populations within the tiankeng (π = 0.2044) is higher than that of the populations outside of it (π = 0.1671), indicating that the tiankengs have a positive impact on species diversity. The genetic differentiation coefficient (FST) between the populations inside and outside the tiankeng was 0.0534 and the FST values of populations within the tiankeng were 0.077, 0.082, and 0.141, meaning that the genetic variation in the tiankengs is very high. The genetic similarity outside the tiankengs is also very high, indicating that the tiankengs are effectively preserving the genetic diversity of M. aromatica. Furthermore, the gene introgression analysis results gave no proof of gene flow between the three tiankeng populations. This suggests that the tiankengs not only protect species diversity, but also hinder gene flow between populations to some extent. However, this hindrance may gradually subside with the evolution of the tiankengs. The genetic structure analysis revealed that the M. aromatica population in Guangxi, China, can be classified into three subpopulations. The first is the tiankeng subpopulation, including all the populations in tiankengs. The second subpopulation consists of populations surrounding the tiankengs. These two subpopulations are distributed in Leye County in northwestern Guangxi, China, and are very close to each other. The third is the Huanjiang subpopulation, which is located far away from the tiankengs. Considering the direction of gene flow and genetic structure, it is speculated that the populations in the tiankengs evolved from the populations near the pit mouth. This study confirms that the tiankengs are shelters and provide a suitable habitat for the endangered plant M. aromatica, because its genetic diversity is well conserved and the species is well adapted to the habitat within the tiankengs.

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Genetic potential and breeding strategies in Psidium cattleianum Sabine: a bibliometric analysis

da Silva Santos,

Gallo,

Silva

et al. 2024

Journal of Crop Improvement

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Genetic diversity variation during the natural regeneration of Vatica guangxiensis, an endangered tree species with extremely small populations

Cited by 5 publications

References 37 publications

VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs

VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs

Evidence for the Use of Karst Tiankengs as Shelters: The Effect of Karst Tiankengs on Genetic Diversity and Population Differentiation in Manglietia aromatica

Genetic potential and breeding strategies in Psidium cattleianum Sabine: a bibliometric analysis

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