Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales.
psbC
Phylogeny
Plastome
Pseudogenization
Selection signal
Simarouba
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
12 Sep 2024
12 Sep 2024
Historique:
received:
01
04
2024
accepted:
02
09
2024
medline:
13
9
2024
pubmed:
13
9
2024
entrez:
12
9
2024
Statut:
epublish
Résumé
Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions.
Identifiants
pubmed: 39266625
doi: 10.1038/s41598-024-71956-5
pii: 10.1038/s41598-024-71956-5
doi:
Types de publication
Journal Article
Comparative Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
21358Subventions
Organisme : MCTIC/CNPq
ID : #28/2018
Organisme : MCTIC/CNPq
ID : 435477/2018-8
Organisme : Conselho Nacional de Desenvolvimento Científico e Tecnológico
ID : 441114/2023-7
Organisme : TWRA/FAPEG
ID : 202210267000536
Informations de copyright
© 2024. The Author(s).
Références
Herrmann, R. G. & Possingham, J. V. Plastid DNA-the plastome. In: Results and Problems in Cell Differentiation: Chloroplasts. 10, (Springer-Verlag, Berlin, 1980).
Ravi, V., Khurana, J. P., Tyagi, A. K. & Khurana, P. An update on chloroplast genomes. Plant Syst. Evol. 271, 101–122. https://doi.org/10.1007/s00606-007-0608-0 (2008).
doi: 10.1007/s00606-007-0608-0
Mower J. P & Vickrey T. L. Structural diversity among plastid genomes of land plants. In: Plastid genome evolution. In Advances in Botanical Research. Ed. Chaw Shu-Miaw, Jansen Robert) 106p (Elsevier, Cambridge, MA, USA: Academic Press, 2018).
Sobreiro, M. B. et al. Chloroplast genome assembly of Handroanthus impetiginosus: Comparative analysis and molecular evolution in Bignoniaceae. Planta 252, 1–16 (2020).
doi: 10.1007/s00425-020-03498-9
Carvalho, L. R. et al. The complete chloroplast genome sequence of Eugenia klotzschiana O. Berg unveils the evolutionary dynamics in plastomes of Myrteae DC. Tribe (Myrtaceae). Gene 876, 147488 (2023).
pubmed: 37196890
doi: 10.1016/j.gene.2023.147488
Li, C., Liu, Y., Lin, F., Zheng, Y. & Huang, P. Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). PeerJ 10, e13570 (2022).
pubmed: 35795179
pmcid: 9252178
doi: 10.7717/peerj.13570
Xi, Z. et al. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proc. Natl. Acad. Sci. U.S.A. 109, 17519–17524 (2012).
pubmed: 23045684
pmcid: 3491498
doi: 10.1073/pnas.1205818109
Kuo, W. H. et al. Plastome phylogenomics of Allaeanthus, Broussonetia and Malaisia (Dorstenieae, Moraceae) and the origin of B. × kazinoki. J. Plant Resour. 135, 203–220 (2022).
doi: 10.1007/s10265-022-01369-w
Iv, A. P. G. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016).
doi: 10.1111/boj.12385
WFO. World Flora Online. https://wfoplantlist.org/ (2023).
Clayton, J. W. Simaroubaceae. In The Families and Genera of Vascular Plants. Springer. 11, (Springer, Hamburg-Germany, 2011).
Thomas, W. W. The American genera of Simaroubaceae and their distribution. Acta Bot. Bras. 4, 11–18 (1990).
doi: 10.1590/S0102-33061990000100002
Wang, T. et al. Complete chloroplast genome sequence of Fortunella venosa (Champ. ex benth.) (Rutaceae): Comparative analysis, phylogenetic relationships, and robust support for its status as an independent species. Forests 12, 996 (2021).
doi: 10.3390/f12080996
Polonsky, J. Quassinoid bitter principles II. In Progress in the Chemistry of Organic Natural Products 222–259 (1985).
Alves, I. A. B. S., Miranda, H. M., Soares, L. A. L. & Randau, K. P. Simaroubaceae family: Botany, chemical composition and biological activities. Revista Brasileira de Farmacognosia 24, 481–501 (2014).
doi: 10.1016/j.bjp.2014.07.021
Gazoni, V. F. et al. Assessment of toxicity and differential antimicrobial activity of methanol extract of rhizome of Simaba ferruginea A. St.-Hil. and its isolate canthin-6-one. J. Ethnopharmacol. 223, 122–134 (2018).
pubmed: 29772356
doi: 10.1016/j.jep.2018.05.014
Gomes, M. C. A. R., Paula, V. F., Moreira, A. A., Castellani, M. A. & Macedo, G. E. L. Toxicity of plant extracts from Bahia, Brazil, to Atta sexdens sexdens (Hymenoptera: Formicidae) workers. Sociobiology 63, 770–776 (2016).
doi: 10.13102/sociobiology.v63i2.936
Devecchi, M. F., Thomas, W. W., Plunkett, G. M. & Pirani, J. R. Testing the monophyly of Simaba (Simaroubaceae): Evidence from five molecular regions and morphology. Mol. Phylogenet. Evol. 120, 63–82 (2018).
pubmed: 29222065
doi: 10.1016/j.ympev.2017.11.024
Majure, L. C., Clase, T., Blankenship, A. & Noa-Monzón, A. A new species of Picrasma, P. nanophylla (Simaroubaceae), from the Dominican Republic. Brittonia 73, 334–342 (2021).
doi: 10.1007/s12228-021-09656-x
Clayton, J. W., Soltis, P. S. & Soltis, D. E. Recent long-distance dispersal overshadows ancient biogeographical patterns in a pantropical angiosperm family (Simaroubaceae, Sapindales). Syst. Biol. 58, 395–410 (2009).
pubmed: 20525593
doi: 10.1093/sysbio/syp041
Cronquist, A. Studies in the Simaroubaceae-II. The genus Simarouba. Bull. Torrey Bot. Club 71, 226–234 (1944).
doi: 10.2307/2481702
Franceschinelli, E. V., Yamamoto, K. & Shepherd, G. J. Distinctions among three Simarouba species. Syst. Bot. 23, 479 (1999).
doi: 10.2307/2419379
Devecchi, M. F., Pirani, J. R. & Thomas, W. W. Simaroubaceae in Flora do Brasil. Jardim Botânico do Rio de Janeiro (2020).
Pirani, J. R., Majure, L. C. & Devecchi, M. F. An updated account of Simaroubaceae with emphasis on American taxa. Revista Brasileira de Botanica https://doi.org/10.1007/s40415-021-00731-x (2021).
doi: 10.1007/s40415-021-00731-x
Franceschinelli, E. V. & Yamamoto, K. Taxonomic use of leaf anatomical characters in the genus Simarouba Aublet (Simaroubaceae). Flora 188, 117–124 (1993).
doi: 10.1016/S0367-2530(17)32255-7
Hardesty, B. D., Dick, C. W., Kremer, A., Hubbell, S. & Bermingham, E. Spatial genetic structure of Simarouba amara Aubl. (Simaroubaceae), a dioecious, animal-dispersed Neotropical tree, on Barro Colorado Island, Panama. Heredity (Edinb.) 95, 290–297 (2005).
pubmed: 16094303
doi: 10.1038/sj.hdy.6800714
Waghmode, V. A., Kute, N. S. & Ban, Y. G. Reproductive biology of oilseed tree Simarouba glauca DC. Acta Hortic. 1241, 459–463 (2019).
doi: 10.17660/ActaHortic.2019.1241.67
Ferreira, I. N. M. et al. Two dioecious Simarouba species with a specialized pollination system and low reproductive efficacy in Central Brazil. Rodriguésia https://doi.org/10.1590/2175-7860202273030 (2022).
doi: 10.1590/2175-7860202273030
Romero-da-Cruz, M. V., Guimarães, R., Devecchi, M. F., Pirani, J. R. & Forni-Martins, E. R. Chromosome numbers in Homalolepis Turcz. and their significance in Simaroubaceae evolution. Revista Brasileira de Botanica https://doi.org/10.1007/s40415-021-00729-5 (2021).
doi: 10.1007/s40415-021-00729-5
Baratakke, R. C. & Patil, C. G. Cytological investigations in poly-gamo-dioecious tree Simarouba glauca DC. The Nucleus 53, 33–36 (2010).
doi: 10.1007/s13237-010-0008-7
Saina, J. K., Li, Z. Z., Gichira, A. W. & Liao, Y. Y. The complete chloroplast genome sequence of tree of heaven (Ailanthus altissima (mill.) (sapindales: Simaroubaceae), an important pantropical tree. Int. J. Mol. Sci. 19, 929 (2018).
pubmed: 29561773
pmcid: 5979363
doi: 10.3390/ijms19040929
Ng, W. L., Lee, S. Y. & Yeap, S. K. Characterization of the complete chloroplast genome of an important Southeast Asian medicinal plant, Eurycoma longifolia (Simaroubaceae). Mitochondrial DNA B Resour. 4, 128–129 (2019).
doi: 10.1080/23802359.2018.1540263
Qin, L. et al. The complete chloroplast genome sequence of Picrasma quassioides (D. Don) Benn. 1844 (Simaroubaceae). Mitochondrial DNA B Resour. 7, 1114–1116 (2022).
pubmed: 35783065
pmcid: 9245974
doi: 10.1080/23802359.2022.2087545
Mader, M. et al. Complete chloroplast genome sequences of four Meliaceae species and comparative analyses. Int. J. Mol. Sci. 19, 701 (2018).
pubmed: 29494509
pmcid: 5877562
doi: 10.3390/ijms19030701
Zhang, J., Li, Y. & Wang, Y. The complete chloroplast genome sequence of Aglaia odorata. Mitochondrial DNA B Resour. 5, 472–473 (2020).
pubmed: 33366607
pmcid: 7748849
doi: 10.1080/23802359.2019.1704649
Dobrogojski, J., Adamiec, M. & Luciński, R. The chloroplast genome: a review. Acta Physiol. Plant 42, 1–13 (2020).
doi: 10.1007/s11738-020-03089-x
Bock, R. & Knoop, V. Genomics of Chloroplasts and Mitochondria Vol. 35 (Springer, 2012).
doi: 10.1007/978-94-007-2920-9
Pacheco, T. G. et al. The complete plastome of Passiflora cirrhiflora A. Juss.: Structural features, RNA editing sites, hotspots of nucleotide diversity and molecular markers within the subgenus Deidamioides. Revista Brasileira de Botanica 43, 839–853 (2020).
Jansen, R. K. & Ruhlman, T. A. Plastid Genomes of Seed Plants.103–126 (2012). https://doi.org/10.1007/978-94-007-2920-9_5 .
Liu, T. J. et al. Complete plastid genome sequence of Primula sinensis (Primulaceae): Structure comparison, sequence variation and evidence for accD transfer to nucleus. PeerJ 2016, e2101 (2016).
doi: 10.7717/peerj.2101
Millen, R. S. et al. Many parallel losses of InfA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13, 645 (2001).
pubmed: 11251102
pmcid: 135507
doi: 10.1105/tpc.13.3.645
Ueda, M. et al. Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. Gene 402, 51–56 (2007).
pubmed: 17728076
doi: 10.1016/j.gene.2007.07.019
Daniell, H., Lin, C. S., Yu, M. & Chang, W. J. Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol. 17, 1–29 (2016).
doi: 10.1186/s13059-016-1004-2
Iwata, S. & Barber, J. Structure of photosystem II and molecular architecture of the oxygen-evolving centre. Current Opin. Struct. Biol. 14, 447–453. https://doi.org/10.1016/j.sbi.2004.07.002 (2004).
doi: 10.1016/j.sbi.2004.07.002
Chisholm, D. & Williams, J. G. K. Nucleotide sequence of psbC, the gene encoding the CP-43 chlorophyll a-binding protein of Photosystem II, in the cyanobacterium synechocystis 6803. Plant Mol. Biol. 10, 293–301 (1988).
pubmed: 24277560
doi: 10.1007/BF00029879
Hankamer, B., Barber, J. & Boekema, E. J. Structure and membrane organization of photosystem II in green plants. Annu. Rev. Plant Biol. 48, 641–671 (1997).
doi: 10.1146/annurev.arplant.48.1.641
Jo, S., Kim, Y. K., Cheon, S. H., Fan, Q. & Kim, K. J. Characterization of 20 complete plastomes from the tribe Laureae (Lauraceae) and distribution of small inversions. PLoS ONE 14, e0224622 (2019).
pubmed: 31675370
pmcid: 6824564
doi: 10.1371/journal.pone.0224622
Maurya, S. et al. Plastome characterization of Musa indandamanensis, an endemic banana in Andaman and Nicobar Islands, India. Nucleus 66, 117–126 (2023).
doi: 10.1007/s13237-023-00418-6
Xu, W. et al. Comparative plastome analyses and evolutionary relationships of all species and cultivars within the medicinal plant genus Atractylodes. Ind. Crops Prod. 201, 116974 (2023).
doi: 10.1016/j.indcrop.2023.116974
Sawicki, J., Krawczyk, K., Ślipiko, M., Szandar, K. & Szczecińska, M. Comparative analysis of Apopellia endiviifolia plastomes reveals a strikingly high level of differentiation between its terrestrial and water form. Diversity (Basel) 13, 674 (2021).
doi: 10.3390/d13120674
Liu, M. L. et al. Evolutionary analysis of plastid genomes of seven Lonicera L. species: Implications for sequence divergence and phylogenetic relationships. Int. J. Mol. Sci. 19, 4039 (2018).
pubmed: 30558106
pmcid: 6321470
doi: 10.3390/ijms19124039
Komenda, J. et al. Accumulation of the D2 protein is a key regulatory step for assembly of the photosystem II reaction center complex in synechocystis PCC 6803. J. Biol. Chem. 279, 48620–48629 (2004).
pubmed: 15347679
doi: 10.1074/jbc.M405725200
Fu, H. Y. et al. The availability of neither D2 nor CP43 limits the biogenesis of photosystem II in tobacco. Plant Physiol. 185, 1111–1130 (2021).
pubmed: 33793892
doi: 10.1093/plphys/kiaa052
Bricker, T. M. & Frankel, L. K. The structure and function of CP47 and CP43 in photosystem II. Photosynth. Res. 72, 131–146 (2002).
pubmed: 16228513
doi: 10.1023/A:1016128715865
Logacheva, M. D. & Shipunov, A. B. Phylogenomic analysis of Picramnia, Alvaradoa, and Leitneria supports the independent Picramniales. J. Syst. Evol. 55, 171–176 (2017).
doi: 10.1111/jse.12246
Cauz-Santos, L. A. et al. The chloroplast genome of Passiflora edulis (Passifloraceae) assembled from long sequence reads: Structural organization and phylogenomic studies in malpighiales. Front. Plant Sci. 8, 334 (2017).
pubmed: 28344587
pmcid: 5345083
doi: 10.3389/fpls.2017.00334
Da Silva, R. S. et al. The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae). PLoS ONE 16, e0256373 (2021).
doi: 10.1371/journal.pone.0256373
Yu, X. et al. Transcriptome and comparative chloroplast genome analysis of vincetoxicum versicolor: Insights into molecular evolution and phylogenetic implication. Front. Genet. 12, 1–13 (2021).
doi: 10.3389/fgene.2021.602528
Belinky, F., Rogozin, I. B. & Koonin, E. V. Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions. Sci. Rep. 7, 12422 (2017).
pubmed: 28963504
pmcid: 5622118
doi: 10.1038/s41598-017-12619-6
Watanabe, K. & Suzuki, T. Genetic code and its variants. eLS https://doi.org/10.1038/npg.els.0000810 (2001).
doi: 10.1038/npg.els.0000810
Looman, A. C. & van Knippenberg, P. H. Effects of GUG and AUG initiation codons on the expression of lacZ in Escherichia coli. FEBS Lett. 197, 315–320 (1986).
pubmed: 2419166
doi: 10.1016/0014-5793(86)80349-0
Ping, J. et al. The molecular evolution pattern of rps12 gene in gymnosperms. Kexue Tongbao/Chin. Sci. Bull. 66, 3182–3193 (2021).
Yan, W., Shi, W., Tian, Q., Li, Z. & Gao, H. The complete chloroplast genome sequence of Melilotoides ruthenica: structural comparative and phylogenetic analysis in Leguminosae. In IOP Conference Series: Earth and Environmental Science vol. 697 (IOP Publishing Ltd, 2021).
Long, M., Betrán, E., Thornton, K. & Wang, W. The origin of new genes: Glimpses from the young and old. Nat. Rev. Genet. 4, 865–875. https://doi.org/10.1038/nrg1204 (2003).
doi: 10.1038/nrg1204
pubmed: 14634634
Zaita, N., Torazawa, K., Shinozaki, K. & Sugiura, M. Trans splicing in vivo: Joining of transcripts from the ‘divided’ gene for ribosomal protein S12 in the chloroplasts of tobacco. FEBS Lett. 210, 153–156 (1987).
doi: 10.1016/0014-5793(87)81326-1
Hildebrand, M., Hallick, R. B., Passavant, C. W. & Bourque, D. P. Trans-splicing in chloroplasts: The rps 12 loci of Nicotiana tabacum. Proc. Natl. Acad. Sci. U.S.A. 85, 372–376 (1988).
pubmed: 3422433
pmcid: 279550
doi: 10.1073/pnas.85.2.372
Nunes, R. et al. Complete chloroplast genome sequence of Caryocar brasiliense camb. (caryocaraceae) and comparative analysis brings new insights into the plastome evolution of Malpighiales. Genet Mol. Biol. 43, 1–7 (2020).
doi: 10.1590/1678-4685-gmb-2019-0161
Trad, R. J., Cabral, F. N., Bittrich, V., Silva, S. R. D. & Amaral, M. D. C. E. D. Calophyllaceae plastomes, their structure and insights in relationships within the clusioids. Sci. Rep. 11(1), 20712 (2021).
pubmed: 34671062
pmcid: 8528878
doi: 10.1038/s41598-021-99178-z
de Souza, U. J. B., Nunes, R., Targueta, C. P., Diniz-Filho, J. A. F. & de Telles, M. P. C. The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae-Caesalpinioideae): Comparative analysis with related Mimosoid species. Sci. Rep. 9, 1–12 (2019).
doi: 10.1038/s41598-019-50620-3
Kim, K. S. & Sappington, T. W. Microsatellite data analysis for population genetics. Methods Mol. Biol. 1006, 271–295 (2013).
pubmed: 23546798
doi: 10.1007/978-1-62703-389-3_19
Singh, K. P., Kumari, P., Raipuria, R. K. & Rai, P. K. Development of genome-specific SSR markers for the identification of introgressed segments of Sinapis alba in the Brassica juncea background. 3 Biotech 12, 332 (2022).
pubmed: 36325472
pmcid: 9618473
doi: 10.1007/s13205-022-03402-0
Borlay, A. J., Mweu, C. M., Nyanjom, S. G., Omolo, K. M. & Omire, A. Molecular characterization of doum palm (Hyphaene compressa) from selected regions of Kenya using chloroplast simple sequence repeats (cpSSR) markers. Pak. J. Bot. 55, 1013 (2023).
doi: 10.30848/PJB2023-3(19)
Hardesty, B. D., Hubbell, S. P. & Bermingham, E. Genetic evidence of frequent long-distance recruitment in a vertebrate-dispersed tree. Ecol. Lett. 9, 516–525 (2006).
pubmed: 16643297
doi: 10.1111/j.1461-0248.2006.00897.x
Hardesty, B. D. et al. Geographic influence on genetic structure in the widespread Neotropical tree Simarouba amara (Simaroubaceae). Trop. Plant Biol. 3, 28–39 (2010).
doi: 10.1007/s12042-010-9044-3
Areces-Berazain, F., Wang, Y., Hinsinger, D. D. & Strijk, J. S. Plastome comparative genomics in maples resolves the infrageneric backbone relationships. PeerJ 8, e9483 (2020).
pubmed: 32742784
pmcid: 7365138
doi: 10.7717/peerj.9483
Yang, J., Hu, G. & Hu, G. Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. BMC Genomics 23, 27 (2022).
pubmed: 34991482
pmcid: 8734052
doi: 10.1186/s12864-021-08259-w
Zhou, S. M. et al. Phylogenomics and plastome evolution of Indigofera (Fabaceae). Front. Plant Sci. 14, 1186598 (2023).
pubmed: 37346129
pmcid: 10280451
doi: 10.3389/fpls.2023.1186598
Sun, K. et al. Comparative analysis and phylogenetic implications of plastomes of five genera in subfamily amyridoideae (Rutaceae). Forests 12, 1–14 (2021).
doi: 10.3390/f12030277
Ahmad, W., Asaf, S., Al-Rawahi, A., Al-Harrasi, A. & Khan, A. L. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci. Rep. 13, 7436 (2023).
pubmed: 37156827
pmcid: 10167353
doi: 10.1038/s41598-023-34477-1
Guisinger, M. M., Kuehl, J. V., Boore, J. L. & Jansen, R. K. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage. Mol. Biol. Evol. 28, 583–600 (2011).
pubmed: 20805190
doi: 10.1093/molbev/msq229
Zhao, Y. J., Liu, J., Yin, G. S. & Gong, X. Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications. BMC Plant Biol. 23, 303 (2023).
pubmed: 37280518
pmcid: 10245475
doi: 10.1186/s12870-023-04323-7
Quiroga, M. P., Zattara, E. E., Souza, G., Pedrosa-Harand, A. & Premoli, A. C. Plastome sequencing of South American Podocarpus species reveals low rearrangement rates despite ancient Gondwanan disjunctions. Mol. Biol. Rep. 50, 309–318 (2023).
pubmed: 36331753
doi: 10.1007/s11033-022-07969-y
Mauad, A. V. S. R. et al. Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data. PLoS ONE 16, e0256126 (2021).
doi: 10.1371/journal.pone.0256126
Kim, Y. K., Cheon, S. H., Hong, J. R. & Kim, K. J. Evolutionary patterns of the chloroplast genome in Vanilloid Orchids (Vanilloideae, Orchidaceae). Int. J. Mol. Sci. 24, 3808 (2023).
pubmed: 36835219
pmcid: 9966724
doi: 10.3390/ijms24043808
Raman, G., Nam, G. H. & Park, S. J. Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes. Front. Plant Sci. 13, 132 (2022).
doi: 10.3389/fpls.2022.1043740
Claude, S. J., Park, S. & Park, S. J. Gene loss, genome rearrangement, and accelerated substitution rates in Plastid genome of Hypericum ascyron (Hypericaceae). BMC Plant Biol. https://doi.org/10.1186/s12870-022-03515-x (2022).
doi: 10.1186/s12870-022-03515-x
pubmed: 35321651
pmcid: 8941745
Yu, J. et al. Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae). BMC Plant Biol. 23, 132 (2023).
pubmed: 36882685
pmcid: 9993602
doi: 10.1186/s12870-023-04148-4
Wang, Z. X., Wang, D. J. & Yi, T. S. Does IR-loss promote plastome structural variation and sequence evolution?. Front. Plant Sci. https://doi.org/10.3389/fpls.2022.888049 (2022).
doi: 10.3389/fpls.2022.888049
pubmed: 37082513
pmcid: 9838571
Jin, D. M. et al. The loss of the inverted repeat in the Putranjivoid clade of Malpighiales. Front. Plant Sci. https://doi.org/10.3389/fpls.2020.00942 (2020).
doi: 10.3389/fpls.2020.00942
pubmed: 33613580
pmcid: 7752781
Palmer, J. D. Chloroplast DNA exists in two orientations. Nature 301, 92–93 (1983).
doi: 10.1038/301092a0
Vera, A., Matsubayashi, T. & Sugiura, M. Active transcription from a promoter positioned within the coding region of a divergently oriented gene: The tobacco chloroplast Rp132 gene. Mol. General Genet. MGG 233, 151–156 (1992).
doi: 10.1007/BF00587573
Boudreau, E. et al. A large open reading frame (Orf1995) in the chloroplast DNA of Chlamydomonas reinhardtii encodes an essential protein. Mol. General Genet. MGG 253, 649–653. https://doi.org/10.1007/s004380050368 (1997).
doi: 10.1007/s004380050368
Drescher, A., Stephanie, R., Calsa, T., Carrer, H. & Bock, R. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J. 22, 97–104 (2000).
pubmed: 10792825
doi: 10.1046/j.1365-313x.2000.00722.x
Neuhaus, H. & Link, G. The chloroplast tRNALys (UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Curr. Genet. https://doi.org/10.1007/BF00355398 (1987).
doi: 10.1007/BF00355398
pubmed: 2834093
Xie, H. et al. Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species. BMC Genomics 23, 716 (2022).
pubmed: 36261795
pmcid: 9583488
doi: 10.1186/s12864-022-08934-6
Castro, A. A. et al. Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily. Sci. Rep. https://doi.org/10.1038/s41598-023-34334-1 (2023).
doi: 10.1038/s41598-023-34334-1
pubmed: 38086916
pmcid: 10716247
Moghaddam, M., Wojciechowski, M. F. & Kazempour-Osaloo, S. Characterization and comparative analysis of the complete plastid genomes of four Astragalus species. PLoS ONE 18, e0286083 (2023).
pubmed: 37220139
pmcid: 10204964
doi: 10.1371/journal.pone.0286083
Dong, W. et al. ycf1, the most promising plastid DNA barcode of land plants. Sci. Rep. 5, 8348 (2015).
pubmed: 25672218
pmcid: 4325322
doi: 10.1038/srep08348
Li, H. et al. The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants. Sci. Rep. 11, 1424 (2021).
pubmed: 33446865
pmcid: 7809279
doi: 10.1038/s41598-021-81087-w
CBOL Pant Working Group. A DNA barcode for land plants. PNAS 106, 12794–12797 (2009).
doi: 10.1073/pnas.0905845106
Neubig, K. M. et al. Phylogenetic utility of ycf1 in orchids: A plastid gene more variable than matK. Plant Syst. Evolut. 277, 75–84 (2009).
doi: 10.1007/s00606-008-0105-0
Amar, M. H. ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica. J. Genetic Eng. Biotechnol. 18, 42 (2020).
doi: 10.1186/s43141-020-00057-3
Corvalán, L. C. J. et al. Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae. Front. Plant Sci. 14, 1258794 (2023).
pubmed: 37822334
pmcid: 10562606
doi: 10.3389/fpls.2023.1258794
Wang, Y. C., Zhou, H. Y. & Liu, X. Q. Chloroplast genomic variation in Euonymus maackii Rupr. and its differentiation time in Euonymus. Forests 13, 265 (2022).
doi: 10.3390/f13020265
Cai, X. L. et al. Plastome structure and phylogenetic relationships of Styracaceae (Ericales). BMC Ecol. Evol. 21, 103 (2021).
pubmed: 34049486
pmcid: 8161964
doi: 10.1186/s12862-021-01827-4
Yu, X., Tan, W., Gao, H., Miao, L. & Tian, X. Development of a specific mini-barcode from plastome and its application for qualitative and quantitative identification of processed herbal products using DNA metabarcoding technique: A case study on Senna. Front. Pharmacol. 11, 585687 (2020).
pubmed: 33390955
pmcid: 7773718
doi: 10.3389/fphar.2020.585687
Bedoya, A. M. et al. Plastid genomes of five species of riverweeds (podostemaceae): Structural organization and comparative analysis in malpighiales. Front. Plant. Sci. 10, 1–14 (2019).
doi: 10.3389/fpls.2019.01035
Yang, Z., Ferguson, D. K. & Yang, Y. New insights into the plastome evolution of Lauraceae using herbariomics. BMC Plant Biol. 23, 387 (2023).
pubmed: 37563571
pmcid: 10413609
doi: 10.1186/s12870-023-04396-4
Yun, S. & Kim, H. The complete plastome sequence of Monstera deliciosa (Araceae), an ornamental foliage plant. Mitochondrial. DNA B Resour. 8, 1301–1305 (2023).
pubmed: 38188432
pmcid: 10769524
doi: 10.1080/23802359.2023.2284415
Qin, H. H. et al. The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: Comparative analysis, phylogenetic implications, and adaptive evolution. BMC Plant. Biol. 23, 9 (2023).
pubmed: 36604614
pmcid: 9814190
doi: 10.1186/s12870-022-04027-4
Pham, M. H. et al. The complete chloroplast genome of an Ophiorrhiza baviensis drake species reveals its molecular structure, comparative, and phylogenetic relationships. Genes (Basel) 14, 227 (2023).
pubmed: 36672968
doi: 10.3390/genes14010227
Kaiser, J. C. & Heinrichs, D. E. Branching out: Alterations in bacterial physiology and virulence due to branched-chain amino acid deprivation. MBio 9(5), 10–1128 (2018).
doi: 10.1128/mBio.01188-18
Amorim Franco, T. M. & Blanchard, J. S. Bacterial branched-chain amino acid biosynthesis: Structures, mechanisms, and drugability. Biochemistry 56, 5849–5865. https://doi.org/10.1021/acs.biochem.7b00849 (2017).
doi: 10.1021/acs.biochem.7b00849
pubmed: 28977745
Brosnan, J. T. & Brosnan, M. E. Branched-chain amino acids: Metabolism, physiological function, and application. Renal Fail. 1, 2 (2006).
Xu, C. et al. Analysis of synonymous codon usage patterns in seven different citrus species. Evolut. Bioinform. 2013, 215–228 (2013).
Chi, X., Zhang, F., Dong, Q. & Chen, S. Insights into comparative genomics, codon usage bias, and phylogenetic relationship of species from biebersteiniaceae and nitrariaceae based on complete chloroplast genomes. Plants 9, 1–15 (2020).
doi: 10.3390/plants9111605
Wang, L., He, N., Li, Y., Fang, Y. & Zhang, F. Complete chloroplast genome sequence of Chinese lacquer tree (Toxicodendron vernicifluum, Anacardiaceae) and its phylogenetic significance. Biomed. Res. Int. 2020, 9014873 (2020).
pubmed: 32071921
pmcid: 7011389
Prosdocimi, F. & Ortega, J. M. The codon usage of Leucine, Serine and Arginine reveals evolutionary stability of proteomes and protein-coding genes. In Brazilian Symposium on Bioinfomatics (2007).
Salim, H. M. W. & Cavalcanti, A. R. O. Factors influencing codon usage bias in genomes. J. Braz. Chem. Soc. 19, 257–262 (2008).
doi: 10.1590/S0103-50532008000200008
Shah, P. & Gilchrist, M. A. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and Genetic drift. Proc. Natl. Acad. Sci. U.S.A. 108, 10231–10236 (2011).
pubmed: 21646514
pmcid: 3121864
doi: 10.1073/pnas.1016719108
Rapino, F. et al. Wobble tRNA modification and hydrophilic amino acid patterns dictate protein fate. Nat. Commun. 12, 2170 (2021).
pubmed: 33859181
pmcid: 8050329
doi: 10.1038/s41467-021-22254-5
Alberts, B. et al. Molecular biology of the cell. Ed. Artmed. 5ed, 1396 (2010).
Whittle, C. A., Kulkarni, A., Chung, N. & Extavour, C. G. Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes. BMC Genom. 22, 1 (2021).
doi: 10.1186/s12864-021-07411-w
Liu, C. et al. Plastome phylogenomics of the East Asian endemic genus Dobinea. Plant Divers. 43, 35–42 (2021).
pubmed: 33778223
doi: 10.1016/j.pld.2020.05.002
Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Dierckxsens, N., Mardulyn, P. & Smits, G. NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucl. Acids Res. 45, e18 (2017).
pubmed: 28204566
Tillich, M. et al. GeSeq—Versatile and accurate annotation of organelle genomes. Nucl. Acids Res. 45, W6–W11 (2017).
pubmed: 28486635
pmcid: 5570176
doi: 10.1093/nar/gkx391
Kearse, M. et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).
pubmed: 22543367
pmcid: 3371832
doi: 10.1093/bioinformatics/bts199
Okonechnikov, K. et al. Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics 28, 1166–1167 (2012).
pubmed: 22368248
doi: 10.1093/bioinformatics/bts091
Greiner, S., Lehwark, P. & Bock, R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: Expanded toolkit for the graphical visualization of organellar genomes. Nucl. Acids Res. 47, W59–W64 (2019).
pubmed: 30949694
pmcid: 6602502
doi: 10.1093/nar/gkz238
Kurtz, S. et al. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucl. Acids Res. 29, 4633–4642 (2001).
pubmed: 11713313
pmcid: 92531
doi: 10.1093/nar/29.22.4633
Beier, S., Thiel, T., Münch, T., Scholz, U. & Mascher, M. MISA-web: A web server for microsatellite prediction. Bioinformatics 33, 2583–2585 (2017).
pubmed: 28398459
pmcid: 5870701
doi: 10.1093/bioinformatics/btx198
Darling, A. C. E., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: Multiple alignment of conserved genomic sequence with rearrangements Aaron. Genome Res. 14, 1394–1403 (2004).
pubmed: 15231754
pmcid: 442156
doi: 10.1101/gr.2289704
Nei, M. & Li, W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U.S.A. 76, 5269–5273 (1979).
pubmed: 291943
pmcid: 413122
doi: 10.1073/pnas.76.10.5269
Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 20, 1160–1166 (2018).
doi: 10.1093/bib/bbx108
Rozas, J. et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34, 3299–3302 (2017).
pubmed: 29029172
doi: 10.1093/molbev/msx248
R Core Team. R: A language and enviroment for statistical computing. Preprint at (2016).
Yang, Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
pubmed: 17483113
doi: 10.1093/molbev/msm088
Sharp, P. M., Tuohy, T. M. F. & Mosurski, K. R. Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucl. Acids Res. 14, 5125–5143 (1986).
pubmed: 3526280
pmcid: 311530
doi: 10.1093/nar/14.13.5125
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
pubmed: 29722887
pmcid: 5967553
doi: 10.1093/molbev/msy096
Nylander, J. A. A. catfasta2phyml. Preprint at https://github.com/nylander/catfasta2phyml (2010).
Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).
pubmed: 10742046
doi: 10.1093/oxfordjournals.molbev.a026334
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
pubmed: 25371430
doi: 10.1093/molbev/msu300