Comparative mitochondrial genomics of Terniopsis yongtaiensis in Malpighiales: structural, sequential, and phylogenetic perspectives.
Terniopsis yongtaiensis
Evolution
Genome size variation
Mitochondrial genome
Phylogenetic
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
12 Sep 2024
12 Sep 2024
Historique:
received:
19
04
2024
accepted:
03
09
2024
medline:
13
9
2024
pubmed:
13
9
2024
entrez:
12
9
2024
Statut:
epublish
Résumé
Terniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported. In current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes. This study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.
Sections du résumé
BACKGROUND
BACKGROUND
Terniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported.
RESULTS
RESULTS
In current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes.
CONCLUSIONS
CONCLUSIONS
This study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.
Identifiants
pubmed: 39267005
doi: 10.1186/s12864-024-10765-6
pii: 10.1186/s12864-024-10765-6
doi:
Substances chimiques
RNA, Transfer
9014-25-9
Types de publication
Journal Article
Comparative Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
853Subventions
Organisme : Special Project of Orchid Survey of National Forestry and Grassland Administration
ID : 2020-070705
Organisme : Special Project of Orchid Survey of National Forestry and Grassland Administration
ID : 2020-070705
Organisme : Special Project of Orchid Survey of National Forestry and Grassland Administration
ID : 2020-070705
Organisme : Special Project of Orchid Survey of National Forestry and Grassland Administration
ID : 2020-070705
Organisme : Special Project of Orchid Survey of National Forestry and Grassland Administration
ID : 2020-070705
Organisme : National Special Fund for Chinese medicine resources Research in the Public Interest of China
ID : Grant No.2019-39
Organisme : National Special Fund for Chinese medicine resources Research in the Public Interest of China
ID : Grant No.2019-39
Organisme : National Special Fund for Chinese medicine resources Research in the Public Interest of China
ID : Grant No.2019-39
Organisme : National Special Fund for Chinese medicine resources Research in the Public Interest of China
ID : Grant No.2019-39
Organisme : National Special Fund for Chinese medicine resources Research in the Public Interest of China
ID : Grant No.2019-39
Organisme : Natural Science Foundation of Fujian Province
ID : 2020J05037
Organisme : Foundation of Fujian Educational Committee
ID : JAT190089
Organisme : the National Natural Science Foundation of China (NSFC)
ID : #32470215
Informations de copyright
© 2024. The Author(s).
Références
Tǎng HT, Kato M. Culture of river-weed Terniopsis chanthaburiensis (Podostemaceae). Aquat Bot. 2020;166:103–255. https://doi.org/10.1016/j.aquabot.2020.103255 .
doi: 10.1016/j.aquabot.2020.103255
Fujinami R, Imaichi R. Developmental anatomy of Terniopsis malayana (Podostemaceae, subfamily Tristichoideae), with implications for body plan evolution. J Plant Res. 2009;122:551–8. https://doi.org/10.1007/s10265-009-0243-7 .
doi: 10.1007/s10265-009-0243-7
pubmed: 19533269
Rutishauser R. Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification. Ann Bot. 2016;117:811–32. https://doi.org/10.1093/aob/mcv172 .
doi: 10.1093/aob/mcv172
pubmed: 26589968
Taiz L, Zeiger E, Møller IM. Murphy, AS. Plant physiology and development. Sunderland, MA: Sinauer Associates; 2015.
Møller IM, Rasmusson AG, Aken OV. Plant mitochondria – past, present and future. Plant J. 2021;108:912–59. https://doi.org/10.1111/tpj.15495 .
doi: 10.1111/tpj.15495
pubmed: 34528296
Mower JP, Sloan DB, Alverson AJ. Plant mitochondrial genome diversity: the genomics revolution. In: Wendel JF, Greilhuber J, Dolezel J, Leitch AR, editors. Plant genome diversity: plant genomes, their residents, and their evolutionary dynamics. Vienna: Springer; 2012. pp. 123–44.
doi: 10.1007/978-3-7091-1130-7_9
Fox TD, Leaver CJ. The Zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons. Cell. 1981;26:315–23. https://doi.org/10.1016/0092-8674(81)9020-2 .
doi: 10.1016/0092-8674(81)9020-2
pubmed: 6276012
Maréchal A, Brisson N. Recombination and the maintenance of plant organelle genome stability. New Phytol. 2010;186:299–317. https://doi.org/10.1111/j.1469-8137.2010.03195.x .
doi: 10.1111/j.1469-8137.2010.03195.x
pubmed: 20180912
Adams KL, Qiu YL, Stoutemyer M, Palmer JD. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. PNAS. 2002;99(15):9905–12. https://doi.org/10.1073/pnas.042694899 .
doi: 10.1073/pnas.042694899
pubmed: 12119382
pmcid: 126597
Zubaer A, Wai A, Hausner G. The mitochondrial genome of Endoconidiophora resinifera is intron rich. Sci Rep. 2018;8:17591. https://doi.org/10.1038/s41598-018-35926-y .
doi: 10.1038/s41598-018-35926-y
pubmed: 30514960
pmcid: 6279837
Bedoya AM, Ruhfel BR, Philbrick CT, Madriñán S, Bove CP, Mesterházy A, Olmstead RG. Plastid genomes of five species of riverweeds (Podostemaceae): structural organization and comparative analysis in Malpighiales. Front Plant Sci. 2019;10:1035. https://doi.org/10.3389/fpls.2019.01035 .
doi: 10.3389/fpls.2019.01035
pubmed: 31481967
pmcid: 6710714
Jin DM, Jin JJ, Yi TS. Plastome structural conservation and evolution in the clusioid clade of Malpighiales. Sci Rep. 2020;10(1):9091. https://doi.org/10.1038/s41598-020-66024-7 .
doi: 10.1038/s41598-020-66024-7
pubmed: 32499506
pmcid: 7272398
Zhang M, Zhang XH, Ge CL, Chen BH. Terniopsis Yongtaiensis (Podostemaceae), a new species from South East China based on morphological and genomic data. PhytoKeys. 2022;194:105–22. https://doi.org/10.3897/phytokeys.194.83080 .
doi: 10.3897/phytokeys.194.83080
pubmed: 35586323
pmcid: 9038898
Chen BH, Zhang M, Zhao K, Zhang XH, Ge CL. Polypleurum chinense (Podostemaceae), a new species from Fujian, China, based on morphological and genomic evidence. PhytoKeys. 2022;199:167–86. https://doi.org/10.3897/phytokeys.199.85679 .
doi: 10.3897/phytokeys.199.85679
pubmed: 36761873
pmcid: 9848973
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–100. https://doi.org/10.1093/bioinformatics/bty191 .
doi: 10.1093/bioinformatics/bty191
pubmed: 29750242
pmcid: 6137996
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722–36. https://doi.org/10.1101/gr.215087.116 . http://www.genome.org/cgi/doi/ .
doi: 10.1101/gr.215087.116
pubmed: 28298431
pmcid: 5411767
Langdon WB. Which is faster: bowtie2GP bowtie > bowtie2 > BWA. Proceedings of the 15th annual conference companion on Genetic and evolutionary computation. 2013: 1741–1742. https://doi.org/10.1145/2464576.2480772
Wick RR, Judd LM, Gorrie CL, Holt KF. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. https://doi.org/10.1371/journal.pcbi.1005595 .
doi: 10.1371/journal.pcbi.1005595
pubmed: 28594827
pmcid: 5481147
Beier S, Thiel T, Münch T, Mascher M. MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017;33(16):2583–5. https://doi.org/10.1093/bioinformatics/btx198 .
doi: 10.1093/bioinformatics/btx198
pubmed: 28398459
pmcid: 5870701
Benson G. Tandem repeats finder: a program to analyze DNA sequences. NAR. 1999;27(2):573–80. https://doi.org/10.1093/nar/27.2.573 .
doi: 10.1093/nar/27.2.573
pubmed: 9862982
pmcid: 148217
Chen Y, Ye WC, Zhang YD, Xu YS. High speed BLASTN: an accelerated MegaBLAST search tool. NAR. 2015;43(16):7762–8. https://doi.org/10.1093/nar/gkv784 .
doi: 10.1093/nar/gkv784
pubmed: 26250111
pmcid: 4652774
Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, Frank MH, He YH, Xia R. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–202. https://doi.org/10.1016/j.molp.2020.06.009 .
doi: 10.1016/j.molp.2020.06.009
pubmed: 32585190
Song Y, Du XR, Li AX, Fan AM, He LJ, Sun Z, Niu YB, Qiao YG. Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa. (Thunb) Vahl BMC Genomics. 2023;1:708–708. https://doi.org/10.1186/s12864-023-09821-4 .
doi: 10.1186/s12864-023-09821-4
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. https://doi.org/10.1093/molbev/mst010 .
doi: 10.1093/molbev/mst010
pubmed: 23329690
pmcid: 3603318
Zhang D, Gao FL, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. Mol Ecol Resour. 2020;20(1):348–55. https://doi.org/10.1111/1755-0998.13096 . PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.
Kalyaanamoorthy S, Minh BQ, Wong TKF, Haeseler AV, Jermiin L. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9. https://doi.org/10.1038/nmeth.4285 .
doi: 10.1038/nmeth.4285
pubmed: 28481363
pmcid: 5453245
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. https://doi.org/10.1093/molbev/msu300 .
doi: 10.1093/molbev/msu300
pubmed: 25371430
Minh BQ, Nguyen MAT, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 2013;30:1188–95. https://doi.org/10.1093/molbev/mst024 .
doi: 10.1093/molbev/mst024
pubmed: 23418397
pmcid: 3670741
Ronquist F, Teslenko M, Van Der Mark P, Aryes DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539–42. https://doi.org/10.1093/sysbio/sys029 .
doi: 10.1093/sysbio/sys029
pubmed: 22357727
pmcid: 3329765
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. NAR. 2021; 49(W1): W293–W296. https://doi.org/10.1093/nar/gkab301
Xu B, Yang ZH. PAMLX: a graphical user interface for PAML. Mol Biol Evol. 2013;30(12):2723–4. https://doi.org/10.1093/molbev/mst179 .
doi: 10.1093/molbev/mst179
pubmed: 24105918
Mower JP. Variation in protein gene and intron content among land plant mitogenomes. Mitochondrion. 2020;53:203–13. https://doi.org/10.1016/j.mito.2020.06.002 .
doi: 10.1016/j.mito.2020.06.002
pubmed: 32535166
Archibald JM. Origin of eukaryotic cells: 40 years on. Symniosis. 2011;54:69–86. https://doi.org/10.1007/s13199-011-0129-z .
doi: 10.1007/s13199-011-0129-z
Powell W, Machray GG, Provan J. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1996;1:215–22. https://doi.org/10.1016/1360-1385(96)86898-1 .
doi: 10.1016/1360-1385(96)86898-1
Qiu LJ, Yang C, Tian B, Yang JB, Liu AZ. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L). BMC Plant Biol. 2010;10:278. https://doi.org/10.1186/1471-2229-10-278 .
doi: 10.1186/1471-2229-10-278
pubmed: 21162723
pmcid: 3017068
Smyth DR. Dispersed repeats in plant genomes. Chromosoma. 1991;100(6):355–9. https://doi.org/10.1007/BF00337513 .
Lukeš J, Kaur B, Speijer D. RNA editing in mitochondria and plastids: weird and widespread. Trends Genet. 2021;37(2):99–102. https://doi.org/10.1016/j.tig.2020.10.004 .
doi: 10.1016/j.tig.2020.10.004
pubmed: 33203574
Ichinose M, Sugita M. RNA editing and its molecular mechanism in plant organelles. Genes. 2017;8(1):5. https://doi.org/10.3390/genes8010005 .
doi: 10.3390/genes8010005
Parvathy ST, Udayasuriyan V, Bhadana V. Codon usage bias. Mol Biol Rep. 2022;49:539–65. https://doi.org/10.1007/s11033-021-06749-4 .
doi: 10.1007/s11033-021-06749-4
pubmed: 34822069
Wright F. The ‘effective number of codons’ used in a gene. Gene. 1990; 87(1): 23–29. https://doi.org/10.1016/0378-1119(90)90491-9
Choi IS, Schwarz EN, Ruhlman TA, Khiyami MA, Sabir JSM, Hajarah NH, Sabir MJ, Rabah SO, Jansen RK. Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent. BMC Plant Biol. 2019;19:448. https://doi.org/10.1186/s12870-019-2064-8 .
doi: 10.1186/s12870-019-2064-8
pubmed: 31653201
pmcid: 6814987
Wang J, Kan SL, Liao XZ, Zhou JW, Tembrock LR, Daniell H, Jin SX, Wu ZQ. Plant organellar genomes: much done, much more to do. Trends Plant Sci. 2024. https://doi.org/10.1016/j.tplants.2023.12.014 .
doi: 10.1016/j.tplants.2023.12.014
pubmed: 39232945
Cheng Y, He XX, Priyadarshani SVGN, Wang Y, Ye L, Shi C, Ye KZ, Zhou Q, Luo ZQ, Deng F, Cao L, Zheng P, Aslam M, Qin Y. Assembly and comparative analysis of the complete mitochondrial genome of Suaeda Glauca. BMC Genomics. 2021;22:167. https://doi.org/10.1186/s12864-021-07490-9 .
doi: 10.1186/s12864-021-07490-9
pubmed: 33750312
pmcid: 7941912
Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 2012;10:e1001241. https://doi.org/10.1371/journal.pbio.1001241 .
doi: 10.1371/journal.pbio.1001241
pubmed: 22272183
pmcid: 3260318
Hikosaka K, Watanabe Y, Tsuji N, Kita K, Kishine H, Arisue N, Palacpac NM, Kawazu S, Sawai H, Horii T, Igarashi I, Tanabe K. Divergence of the mitochondrial genome structure in the apicomplexan parasites, Babesia and Theileria. Mol Biol Evol. 2010;27:1107–16. https://doi.org/10.1093/molbev/msp320 .
doi: 10.1093/molbev/msp320
pubmed: 20034997
Sloan DB, Wu ZQ. History of plastid DNA insertions reveals weak deletion and AT mutation biases in Angiosperm mitochondrial genomes. Genome Biol Evol. 2014;6:3210–21. https://doi.org/10.1093/gbe/evu253 .
doi: 10.1093/gbe/evu253
pubmed: 25416619
pmcid: 4986453
Hu SQ, Li GJ, Yang JJ, Hou HW. Aquatic plant genomics: advances, applications, and prospects. Int J Genomics. 2017;27:6347874. https://doi.org/10.1155/2017/6347874 .
doi: 10.1155/2017/6347874
Ni Y, Li JL, Chen HM, Yue JW, Chen PH, Liu C. Comparative analysis of the chloroplast and mitochondrial genomes of Saposhnikovia divaricata revealed the possible transfer of plastome repeat regions into the mitogenome. BMC Genomics. 2022;23:570. https://doi.org/10.1186/s12864-022-08821-0 .
doi: 10.1186/s12864-022-08821-0
pubmed: 35945507
pmcid: 9364500
Li J, Tang H, Luo H, Tang J, Zhong N, Xiao LZ. Complete mitochondrial genome assembly and comparison of Camellia sinensis var. Assamica Cv. Duntsa. Front Plant Sci. 2023;14:1117002. https://doi.org/10.3389/fpls.2023.1117002 .
doi: 10.3389/fpls.2023.1117002
pubmed: 36743486
pmcid: 9893290
Xue T, Zheng XH, Chen D, Liang LM, Chen N, Huang Z, Fan WF, Chen JN, Cen W, Chen S, Zhu JM, Chen BH, Zhang XT, Chen YQ. A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae). Hortic Res. 2020;7(1):46. https://doi.org/10.1038/s41438-020-0269-5 .
doi: 10.1038/s41438-020-0269-5
pubmed: 32257232
pmcid: 7109043
Wischmann C, Schuster W. Transfer of rps10 from the mitochondrion to the nucleus in Arabidopsis thaliana: evidence for RNA-mediated transfer and exon shuffling at the integration site. FEBS lett. 1995;374:152–6. https://doi.org/10.1016/0014-5793(95)01100-S .
doi: 10.1016/0014-5793(95)01100-S
pubmed: 7589523
Sánchez H, Fester T, Kloska S, Schröder W, Schuster W. Transfer of rps19 to the nucleus involves the gain of an RNP-binding motif which may functionally replace RPS13 in Arabidopsis mitochondria. EMBO J. 1996;15:2138–49. https://doi.org/10.1002/j.1460-2075.1996.tb00567.x .
doi: 10.1002/j.1460-2075.1996.tb00567.x
pubmed: 8641279
pmcid: 450136
Adams KL, Ong HC, Palmer JD. Mitochondrial gene transfer in pieces: fission of the ribosomal protein gene rpl2 and partial or complete gene transfer to the nucleus. Mol Biol Evol. 2001;18:2289–97. https://doi.org/10.1093/oxfordjournals.molbev.a003775 .
doi: 10.1093/oxfordjournals.molbev.a003775
pubmed: 11719578
Steinhauser S, Beckert S, Capesius I, Malek O, Knoop V. Plant mitochondrial RNA editing. J Mol Evol. 1999;48:303–12. https://doi.org/10.1007/pl00006473 .
doi: 10.1007/pl00006473
pubmed: 10093219
Rosenthal JJC. The emerging role of RNA editing in plasticity. J Exp Biol. 2015;218:1812–21. https://doi.org/10.1242/jeb.119065 .
doi: 10.1242/jeb.119065
pubmed: 26085659
pmcid: 4487009
Takenaka M, Zehrmann A, Brennicke A, Graichen K. Improved computational target site prediction for pentatricopeptide repeat RNA editing factors. PLoS ONE. 2013;8:e65343. https://doi.org/10.1371/journal.pone.0065343 .
doi: 10.1371/journal.pone.0065343
pubmed: 23762347
pmcid: 3675099
Brenner WG, Mader M, Müller NA, Hoenicka H, Schroeder H, Zorn I, Fladung M, Kerste B. High level of conservation of mitochondrial RNA editing sites among four Populus species. G3-Genes Genom. Genet. 2019;9:709–17. https://doi.org/10.1534/g3.118.200763 .
doi: 10.1534/g3.118.200763
Edera AA, Gandini CL, Sanchez-Puerta MV. Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria. Plant Mol Biol. 2018;97:215–31. https://doi.org/10.1007/s11103-018-0734-9 .
doi: 10.1007/s11103-018-0734-9
pubmed: 29761268
Okuda K, Hammani K, Tanz SK, Peng L, Fukao Y, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T. The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J. 2010;61:339–49. https://doi.org/10.1111/j.1365-313X.2009.04059.x .
doi: 10.1111/j.1365-313X.2009.04059.x
pubmed: 19845878
Bi CW, Paterson AH, Wang XL, Xu YQ, Wu DY, Qu YS, Jiang A, Ye QL, Ye N. Corrigendum to Analysis of the complete mitochondrial genome sequence of the diploid cotton Gossypium raimondii by comparative genomics approaches. BioMed. Res. Int. 2019; 2019: 9691253. https://doi.org/10.1155/2019/9691253
Zhou DG, Liu Y, Yao JZ, Yin Z, Wang XW, Xu LP, Que YX, Mo P, Liu XL. Characterization and phylogenetic analyses of the complete mitochondrial genome of sugarcane (Saccharum Spp. Hybrids) line A1. Diversity. 2022;14:333. https://doi.org/10.3390/d14050333 .
doi: 10.3390/d14050333
Niu Y, Zhang T, Chen MX, Chen GJ, Liu ZH, Yu RB, Han X, Chen KH, Huang AZ, Chen CM, Yang Y. Analysis of the complete mitochondrial genome of the bitter gourd (Momordica charantia). Plants. 2023;12:1686. https://doi.org/10.3390/plants12081686 .
doi: 10.3390/plants12081686
pubmed: 37111909
pmcid: 10143269
Thöny-Meyer L, Fischer F, Künzler P, Ritz D, Hennecke H. Escherichia coli genes required for cytochrome c maturation. J Bacteriol. 1995;177(15):4321–6. https://doi.org/10.1128/jb.177.15.4321-4326.1995 .
doi: 10.1128/jb.177.15.4321-4326.1995
pubmed: 7635817
pmcid: 177179
Kory N, uit de Bos J, van der Rijt S, Jankovic N, Güra M, Arp N, Pena IA, Prakash G, Chan SH, Kunchok T, Lewis CA, Sabatini ADM. MCART1/SLC25A51 is required for mitochondrial NAD transport. Sci. Adv. 2020;6(43):eabe5310. https://doi.org/10.1126/sciadv.abe5310 .
doi: 10.1126/sciadv.abe5310
Kubo T, Nishizawa S, Sugawara A, Itchoda N, Estiati A, Mikami T. The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA
doi: 10.1093/nar/28.13.2571
pubmed: 10871408
pmcid: 102699
Cui HN, Ding Z, Zhu QL, Wu Y, Qiu BY, Gao P. Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer. Sci Rep. 2021;11:1595. https://doi.org/10.1038/s41598-020-80149-9 .
doi: 10.1038/s41598-020-80149-9
pubmed: 33452307
pmcid: 7811005
Cummings MP, Nugent JM, Olmstead RG, Palmer JD. Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Curr Genet. 2003;43:131–8. https://doi.org/10.1007/s00294-003-0378-3 .
doi: 10.1007/s00294-003-0378-3
pubmed: 12695853
Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics. 2002;268:434–45. https://doi.org/10.1007/s00438-002-0767-1 .
doi: 10.1007/s00438-002-0767-1
pubmed: 12471441
Yue JP, Hu XY, Sun H, Yang YP, Huang JL. Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun. 2012;3:1152. https://doi.org/10.1038/ncomms2148 .
doi: 10.1038/ncomms2148
pubmed: 23093189