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Guo Z, Xu Z, Li L, Xu KW. Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species in Ilex. PLANTS (BASEL, SWITZERLAND) 2024; 13:1429. [PMID: 38891238 PMCID: PMC11174832 DOI: 10.3390/plants13111429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
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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Affiliation(s)
- Zhonglong Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.G.); (Z.X.)
| | - Zhenxiu Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.G.); (Z.X.)
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Ke-Wang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.G.); (Z.X.)
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Zhou P, Zhang Q, Li F, Huang J, Zhang M. Assembly and comparative analysis of the complete mitochondrial genome of Ilex metabaptista (Aquifoliaceae), a Chinese endemic species with a narrow distribution. BMC PLANT BIOLOGY 2023; 23:393. [PMID: 37580695 PMCID: PMC10424370 DOI: 10.1186/s12870-023-04377-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/12/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Ilex metabaptista is a woody tree species with strong waterlogging tolerance and is also admired as a landscape plant with high development prospects and scientific research value. Unfortunately, populations of this species have declined due to habitat loss. Thus, it is a great challenge for us to efficiently protect I. metabaptista resources from extinction. Molecular biology research can provide the scientific basis for the conservation of species. However, the study of I. metabaptista genetics is still in its infancy. To date, no mitochondrial genome (mitogenome) in the genus Ilex has been analysed in detail. RESULTS The mitogenome of I. metabaptista was assembled based on the reads from Illumina and Nanopore sequencing platforms; it was a typical circular DNA molecule of 529,560 bp with a GC content of 45.61% and contained 67 genes, including 42 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 286 dispersed repeats, 140 simple repeats, 18 tandem repeats, and 543 RNA editing sites. Analysis of codon usage showed that codons ending in A/T were preferred. Gene migration was observed to occur between the mitogenome and chloroplast genome via the detection of homologous fragments. In addition, Ka/Ks analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB gene had undergone potential positive selection in most asterids. Nucleotide polymorphism analysis revealed the variation in each gene, with atp9 being the most notable. Furthermore, comparative analysis showed that the GC contents were conserved, but the sizes and structure of mitogenomes varied greatly among asterids. Phylogenetic analysis based on the mitogenomes reflected the exact evolutionary and taxonomic status of I. metabaptista. CONCLUSION In this study, we sequenced and annotated the mitogenome of I. metabaptista and compared it with the mitogenomes of other asterids, which provided essential background information for further understanding of the genetics of this plant and helped lay the foundation for future studies on molecular breeding of I. metabaptista.
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Affiliation(s)
- Peng Zhou
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Qiang Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 210037, Nanjing, China.
| | - Fei Li
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Jing Huang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Min Zhang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China.
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Guo Z, Wei J, Xu Z, Lin C, Peng Y, Wang Q, Wang D, Yang X, Xu KW. HollyGTD: an integrated database for holly (Aquifoliaceae) genome and taxonomy. FRONTIERS IN PLANT SCIENCE 2023; 14:1220925. [PMID: 37469783 PMCID: PMC10352911 DOI: 10.3389/fpls.2023.1220925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Affiliation(s)
- Zhonglong Guo
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Junrong Wei
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Zhenxiu Xu
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Chenxue Lin
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ye Peng
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Qi Wang
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Dong Wang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- WeiRan Biotech, Beijing, China
| | - Xiaozeng Yang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ke-Wang Xu
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Zhou P, Zhang Q, Li J, Li F, Huang J, Zhang M. A first insight into the genomic background of Ilex pubescens (Aquifoliaceae) by flow cytometry and genome survey sequencing. BMC Genomics 2023; 24:270. [PMID: 37208610 DOI: 10.1186/s12864-023-09359-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 05/05/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Ilex pubescens is an important traditional Chinese medicinal plant with many naturally occurring compounds and multiple pharmacological effects. However, the lack of reference genomic information has led to tardiness in molecular biology research and breeding programs of this plant. RESULTS To obtain knowledge on the genomic information of I. pubescens, a genome survey was performed for the first time by next generation sequencing (NGS) together with genome size estimation using flow cytometry. The whole genome survey of I. pubescens generated 46.472 Gb of sequence data with approximately 82.2 × coverage. K-mer analysis indicated that I. pubescens has a small genome of approximately 553 Mb with 1.93% heterozygosity rate and 39.1% repeat rate. Meanwhile, the genome size was estimated to be 722 Mb using flow cytometry, which was possibly more precise for assessment of genome size than k-mer analysis. A total of 45.842 Gb clean reads were assembled into 808,938 scaffolds with a relatively short N50 of 760 bp. The average guanine and cytosine (GC) content was 37.52%. In total, 197,429 microsatellite motifs were detected with a frequency of 2.8 kb, among which mononucleotide motifs were the most abundant (up to 62.47% of the total microsatellite motifs), followed by dinucleotide and trinucleotide motifs. CONCLUSION In summary, the genome of I. pubescens is small but complex with a high level of heterozygosity. Even though not successfully applied for estimation of genome size due to its complex genome, the survey sequences will help to design whole genome sequencing strategies and provide genetic information support for resource protection, genetic diversity analysis, genetic improvement and artificial breeding of I. pubescens.
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Affiliation(s)
- Peng Zhou
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Qiang Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
| | - Jiao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Fei Li
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Jing Huang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China
| | - Min Zhang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing, 211153, China.
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Gao L, Xu W, Xin T, Song J. Application of third-generation sequencing to herbal genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1124536. [PMID: 36959935 PMCID: PMC10027759 DOI: 10.3389/fpls.2023.1124536] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants.
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Zhou P, Li J, Huang J, Li F, Zhang Q, Zhang M. Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:3322. [PMID: 36501361 PMCID: PMC9740704 DOI: 10.3390/plants11233322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Ilex chinensis Sims. is an evergreen arbor species with high ornamental and medicinal value that is widely distributed in China. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. To obtain the whole reference genome, we first conducted a genome survey of I. chinensis by next-generation sequencing (NGS) to perform de novo whole-genome sequencing. As a result, our estimates using k-mer and flow cytometric analysis suggested the genome size of I. chinensis to be around 618-655 Mb, with the GC content, heterozygous rate, and repeat sequence rate of 37.52%, 1.1%, and 38%, respectively. A total of 334,649 microsatellite motifs were detected from the I. chinensis genome data, which will provide basic molecular markers for germplasm characterization, genetic diversity, and QTL mapping studies for I. chinensis. In summary, the I. chinensis genome is complex with high heterozygosity and few repeated sequences. Overall, this is the first report on the genome features of I. chinensis, and the information may lay a strong groundwork for future whole-genome sequencing and molecular breeding studies of this species.
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Affiliation(s)
- Peng Zhou
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
| | - Jiao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jing Huang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
| | - Fei Li
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
| | - Qiang Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Jiangsu Academy of Forestry, 109 Danyang Road, Dongshanqiao, Nanjing 211153, China
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