Assembly and characterization of the first mitochondrial genome of Phyllanthaceae: a case study of the ornamental aquatic plant

Ala KG, Zhao Z, Ni L, Wang Z (2023) Comparative analysis of mitochondrial genomes of two alpine medicinal plants of Gentiana (Gentianaceae). PLoS ONE 18:e0281134. https://doi.org/10.1371/journal.pone.0281134

Article  CAS  PubMed  PubMed Central  Google Scholar 

Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580. https://doi.org/10.1093/nar/27.2.573

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bi C, Paterson AH, Wang X et al (2016) Analysis of the complete mitochondrial genome sequence of the diploid cotton Gossypium raimondii by comparative genomics approaches. Biomed Res Int 2016:5040598. https://doi.org/10.1155/2016/5040598

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bi C, Qu Y, Hou J et al (2022) Deciphering the multi-chromosomal mitochondrial genome of Populus simonii. Front Plant Sci 13:1–14. https://doi.org/10.3389/fpls.2022.914635

Article  Google Scholar 

Bouman RW, Keßler PJA, Telford IRH et al (2021) Molecular phylogenetics of Phyllanthus sensu lato (Phyllanthaceae): towards coherent monophyletic taxa. Taxon 70:72–98. https://doi.org/10.1002/tax.12424

Article  Google Scholar 

Cadorna CAE, Pahayo DG, Rey JD (2024) The first mitochondrial genome of Calophyllum soulattri Burm.f. Sci Rep 14:1–12. https://doi.org/10.1038/s41598-024-55016-6

Article  CAS  Google Scholar 

Christenhusz MJM, Byng JW (2016) The number of known plants species in the world and its annual increase. Phytotaxa 261:201–217. https://doi.org/10.11646/phytotaxa.261.3.1

Article  Google Scholar 

Cui H, Ding Z, Zhu Q et al (2021) Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer. Sci Rep 11:1595. https://doi.org/10.1038/s41598-020-80149-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong S, Zhao C, Zhang S et al (2019) Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination. BMC Genomics 20:953. https://doi.org/10.1186/s12864-019-6365-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doyle JJ, Doyle JL (1987) Genomic plant DNA preparation from fresh tissue-CTAB method. Phytochem Bull 19:11–15

Google Scholar 

Govaerts RH., Frodin D., Radcliffe-Smith A (2000) World checklist and bibliography of Euphorbiaceae, 4 vols, Richmond,. Royal Botanic Gardens, Kew

Gray MW (2012) Mitochondrial evolution. Cold Spring Harb Perspect Biol 4:a011403–a011403. https://doi.org/10.1101/cshperspect.a011403

Article  CAS  PubMed  PubMed Central  Google Scholar 

Han F, Qu Y, Chen Y et al (2022) Assembly and comparative analysis of the complete mitochondrial genome of Salix wilsonii using PacBio HiFi sequencing. Front Plant Sci 13:1–12. https://doi.org/10.3389/fpls.2022.1031769

Article  Google Scholar 

Hao W, Liu G, Wang W et al (2021) RNA editing and its roles in plant organelles. Front Genet. https://doi.org/10.3389/fgene.2021.757109

Article  PubMed  PubMed Central  Google Scholar 

He T, Ding X, Zhang H et al (2021) Comparative analysis of mitochondrial genomes of soybean cytoplasmic male-sterile lines and their maintainer lines. Funct Integr Genom 21:43–57. https://doi.org/10.1007/s10142-020-00760-x

Article  CAS  Google Scholar 

Hidalgo BF, Bazan SF, Iturralde RB, Borsch T (2020) Phylogenetic relationships and character evolution in neotropical Phyllanthus (Phyllanthaceae), with a focus on the cuban and caribbean taxa. Int J Plant Sci 181:284–305. https://doi.org/10.1086/706454

Article  Google Scholar 

Ibanez A, Flores R (2021) Phyllanthus fluitans (Phyllanthaceae): a new record of an aquatic plant for the flora of Panama. Acta Bot Mex. https://doi.org/10.21289/abm128.2021.1767

Article  Google Scholar 

Ichinose M, Sugita M (2016) RNA editing and its molecular mechanism in plant organelles. Genes (Basel) 8:5. https://doi.org/10.3390/genes8010005

Article  CAS  PubMed  Google Scholar 

Jang W, Lee HO, Kim J-U et al (2020) Complete mitochondrial genome and a set of 10 novel Kompetitive Allele-specific PCR markers in Ginseng (Panax ginseng C. A. Mey.). Agronomy 10:1868. https://doi.org/10.3390/agronomy10121868

Article  CAS  Google Scholar 

Jo YD, Park J, Kim J et al (2011) Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep 30:217–229. https://doi.org/10.1007/s00299-010-0929-2

Article  CAS  PubMed  Google Scholar 

Kan S-L, Shen T-T, Gong P et al (2020) The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome. BMC Evol Biol 20:10. https://doi.org/10.1186/s12862-020-1582-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kathriarachchi H, Samuel R, Hoffmann P et al (2006) Phylogenetics of tribe Phyllantheae (Phyllanthaceae; Euphorbiaceae sensu lato) based on nrITS and plastid matK DNA sequence data. Am J Bot 93:637–655. https://doi.org/10.3732/ajb.93.4.637

Article  CAS  PubMed  Google Scholar 

Kawakita A (2010) Evolution of obligate pollination mutualism in the tribe Phyllantheae (Phyllanthaceae). Plant Species Biol 25:3–19. https://doi.org/10.1111/j.1442-1984.2009.00266.x

Article  Google Scholar 

Kawakita A, Kato M (2017) Diversity of phyllanthaceae plants. Obligate pollination mutualism. Springer, Tokyo, pp 81–115

Google Scholar 

Koren S, Walenz BP, Berlin K et al (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. https://doi.org/10.1101/gr.215087.116

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kozik A, Rowan BA, Lavelle D et al (2019) The alternative reality of plant mitochondrial DNA: one ring does not rule them all. PLOS Genet 15:e1008373. https://doi.org/10.1371/journal.pgen.1008373

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kurtz S (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29:4633–4642. https://doi.org/10.1093/nar/29.22.4633

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. https://doi.org/10.1093/bioinformatics/bty191

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li Q, Wei R (2025) Complete plastome and mitogenome assembly of endangered tree Karpatiosorbus bristoliensis reveals phylogenetic architecture for Sorbus sensu lato (Rosaceae). Front Plant Sci 16:1619267. https://doi.org/10.3389/fpls.2025.1619267

Article  Google Scholar 

Li B, Qiu H, Ma J et al (2008) Euphorbiaceae. Flora of China. Science Press, Beijing, pp 163–314

Google Scholar 

Li H-T, Luo Y, Gan L et al (2021) Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol 19:232. https://doi.org/10.1186/s12915-021-01166-2

Article  PubMed  PubMed Central  Google Scholar 

Li C, Zhou L, Nie J et al (2023) Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae). Physiol Mol Biol Plants 29:239–251. https://doi.org/10.1007/s12298-023-01289-6

Article 

Comments (0)

No login
gif