Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251–269. https://doi.org/10.1023/A:1006344508454
Article PubMed CAS Google Scholar
Bennetzen JL, Wang H (2014) The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes. Annu Rev Plant Biol 65:505–530
Article PubMed CAS Google Scholar
Bürkner P-C (2017) brms: An R Package for Bayesian Multilevel Models Using Stan. J Stat Soft 80:1–28. https://doi.org/10.18637/jss.v080.i01
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Article PubMed CAS PubMed Central Google Scholar
Catlin NS, Josephs EB (2022) The important contribution of transposable elements to phenotypic variation and evolution. Curr Opin Plant Biol 65:102140. https://doi.org/10.1016/j.pbi.2021.102140
Article PubMed CAS Google Scholar
Cheng Q-Q, Ouyang Y, Tang Z-Y et al (2021) Review on the Development and Applications of Medicinal Plant Genomes. Front Plant Sci Volume. https://doi.org/10.3389/fpls.2021.791219. 12-2021
Cheng L-T, Wang Z-L, Zhu Q-H et al (2025) A long road ahead to reliable and complete medicinal plant genomes. Nat Commun 16:2150. https://doi.org/10.1038/s41467-025-57448-8
Article PubMed CAS PubMed Central Google Scholar
Chinese Pharmacopoeia Commission (2020) Pharmacopoeia of the People’s Republic of China. China Medical Science Press, Beijing
Cock PJA, Antao T, Chang JT et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422–1423. https://doi.org/10.1093/bioinformatics/btp163
Article PubMed CAS PubMed Central Google Scholar
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Article PubMed CAS PubMed Central Google Scholar
Ferrari S, Cribari-Neto F (2004) Beta Regression for Modelling Rates and Proportions. J Applied Statistics 31:799–815. https://doi.org/10.1080/0266476042000214501
Fu L, Niu B, Zhu Z et al (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150–3152. https://doi.org/10.1093/bioinformatics/bts565
Article PubMed CAS PubMed Central Google Scholar
Galindo-González L, Mhiri C, Deyholos MK, Grandbastien M-A (2017) LTR-retrotransposons in plants: engines of evolution. Gene 626:14–25. https://doi.org/10.1016/j.gene.2017.04.051
Article PubMed CAS Google Scholar
Hassan AH, Mokhtar MM, El Allali A (2023) Transposable elements: multifunctional players in the plant genome. Front Plant Sci 14:1330127. https://doi.org/10.3389/fpls.2023.1330127
Article PubMed CAS Google Scholar
Huang Y, Sahu SK, Liu X (2025) Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies. Plant Biotechnol J 23:1121–1132. https://doi.org/10.1111/pbi.14570
Article PubMed CAS PubMed Central Google Scholar
Katoh K, Standley DM (2013) MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010
Article PubMed CAS PubMed Central Google Scholar
Kautsar SA, Suarez Duran HG, Blin K et al (2017) plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res 45:W55–W63. https://doi.org/10.1093/nar/gkx305
Article PubMed CAS PubMed Central Google Scholar
Lee S-I, Kim N-S (2014) Transposable elements and genome size variations in plants. Genomics Inf 12:87–97. https://doi.org/10.5808/GI.2014.12.3.87
Legendre P, Gallagher ED (2001) Ecologically Meaningful Transformations for Ordination of Species Data. Oecologia 129:271–280. https://doi.org/10.1007/s004420100716
Li S-F, She H-B, Yang L-L et al (2022) Impact of LTR-retrotransposons on genome structure, evolution, and function in curcurbitaceae species. Int J Mol Sci 23:10158. https://doi.org/10.3390/ijms231710158
Article PubMed CAS PubMed Central Google Scholar
Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14:49–61. https://doi.org/10.1038/nrg3374
Article PubMed CAS Google Scholar
Liu D (2026) EDTA-Audit-Tool: a post-processing quality-control tool for EDTA transposable element annotations
Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101:12404–12410. https://doi.org/10.1073/pnas.0403715101
Article PubMed CAS PubMed Central Google Scholar
Manni M, Berkeley MR, Seppey M et al (2021) BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol 38:4647–4654. https://doi.org/10.1093/molbev/msab199
Article PubMed CAS PubMed Central Google Scholar
Mhiri C, Borges F, Grandbastien M-A (2022) Specificities and Dynamics of Transposable Elements in Land Plants. Biology 11:488. https://doi.org/10.3390/biology11040488
Article PubMed CAS PubMed Central Google Scholar
Minh BQ, Schmidt HA, Chernomor O et al (2020) IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol 37:1530–1534. https://doi.org/10.1093/molbev/msaa015
Article PubMed CAS PubMed Central Google Scholar
Neumann P, Novák P, Hoštáková N, Macas J (2019) Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mob DNA 10:1. https://doi.org/10.1186/s13100-018-0144-1
Article PubMed PubMed Central Google Scholar
Nützmann H-W, Huang A, Osbourn A (2016) Plant metabolic clusters – from genetics to genomics. New Phytol 211:771–789. https://doi.org/10.1111/nph.13981
Article PubMed PubMed Central Google Scholar
Ou S, Su W, Liao Y et al (2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol 20:275. https://doi.org/10.1186/s13059-019-1905-y
Article PubMed CAS PubMed Central Google Scholar
Paradis E, Schliep K (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526–528. https://doi.org/10.1093/bioinformatics/bty633
Comments (0)