HollyGTD: an integrated database for holly (Aquifoliaceae) genome and taxonomy

Guo, Zhonglong; Wei, Jun-Rong; Xu, Zhen; Ye, Peng; Wang, Qi; Wang, Dong; Yang, Xiaozeng; Xu, Ke‐Wang

doi:10.3389/fpls.2023.1220925

Cited by 3 publications

(2 citation statements)

References 23 publications

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“…Annotations of Gene Ontology (GO) terms were obtained from HollyGTD (https://hollygdb.com/, accessed on 22 January 2024) [31]. The associations of the predicted target genes of SS-miRNAs and conserved miRNAs with the GO terms were analyzed using custom scripts.…”

Section: Go Analysismentioning

confidence: 99%

“…The dominant species in holly are broad-leaved species, which are an important component of the tropical and subtropical forest ecosystems and are commonly used as ornamental plants in parks and gardens [ 27 , 28 , 29 ]. Recently, genome and transcriptome sequencing in holly have been conducted for unraveling the genetic structure and understanding the biological principles of the diverse traits [ 30 , 31 , 32 , 33 ]. However, the systematic identification and annotation of miRNAs in holly are only sketchy.…”

Section: Introductionmentioning

confidence: 99%

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Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species in Ilex

Guo,

Xu,

et al. 2024

Plants

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MicroRNAs (miRNAs) are pivotal regulators of gene expression, playing crucial roles in plant developmental processes and environmental responses. However, the function of miRNAs in influencing deciduous traits has been little explored. Here, we utilized sRNA-seq on two deciduous species, Ilex polyneura (Hand.-Mazz.) S. Y. Hu and Ilex asprella Champ. ex Benth., along with an evergreen species, Ilex latifolia Thunb., to identify and annotate miRNAs within these species. Our analysis revealed 162 species-specific miRNAs (termed SS-miRNAs) from 120 families, underscoring the fundamental roles and potential influence of SS-miRNAs on plant phenotypic diversity and adaptation. Notably, three SS-miRNAs in I. latifolia were found to target crucial genes within the abscission signaling pathway. Analysis of cis-regulatory elements suggested a novel regulatory relationship that may contribute to the evergreen phenotype of I. latifolia by modulating the abscission process in a light-independent manner. These findings propose a potential mechanism by which SS-miRNAs can influence the conserved abscission pathway, contributing to the phenotypic divergence between deciduous and evergreen species within the genus Ilex.

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Section: Go Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species in Ilex

Guo,

Xu,

et al. 2024

Plants

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ANAgdb: a multi-omics and taxonomy database for ANA-grade

Guo,

Luo,

Wang

et al. 2024

BMC Plant Biol

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Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity of Ilex Species

Xu,

Wei,

et al. 2024

Plants

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The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex latifolia Thunb., Ilex polyneura (Hand.-Mazz.) S. Y. Hu, and Ilex asprella Champ. ex Benth., indicated a recent fusion event contributing to the reduction of chromosomes in I. asprella. Comparative genome analyses showed slight differences in gene annotation among the three species, implying a minimal disruption of genes following chromosomal fusion in I. asprella. Comprehensive annotation of transposable elements (TEs) revealed that TEs constitute a significant portion of the Ilex genomes, with LTR transposons being predominant. TEs exhibited an inverse relationship with gene density, potentially influencing gene regulation and chromosomal architecture. TE insertions were shown to affect the conformation and binding sites of key genes such as 7-deoxyloganetin glucosyltransferase and transmembrane kinase (TMK) genes, highlighting potential functional impacts. The structural variations caused by TE insertions suggest significant roles in the evolutionary dynamics, leading to either loss or gain of gene function. This study underscores the importance of TEs in shaping the genomic landscape and evolutionary trajectories of Ilex species.

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HollyGTD: an integrated database for holly (Aquifoliaceae) genome and taxonomy

Cited by 3 publications

References 23 publications

Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species in Ilex

Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species in Ilex

ANAgdb: a multi-omics and taxonomy database for ANA-grade

Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity of Ilex Species

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