Two chloroplast genomes with reduced inverted repeat regions in Mammillaria series Stylothelae (Cactaceae)

keywords: isomeric plastomes, ndh genes, plastome, structure


Background: The chloroplast genomes of Cactaceae exhibit boundary modifications in the inverted repeat regions (IRs), gene inversions, and deletions. Among nine Mammillaria species, three distinct chloroplast structures have been identified, although not all of these correspond to the morphology-based classification of the genus.

Question: Is there a distinct chloroplast genome structure in the species of Mammillaria series Stylothelae?

Studied species: Mammillaria bocasana and M. erythrosperma.

Study site and dates: Mexico from 2019 to 2023.

Methods: Chloroplast DNA was sequenced, and chloroplast genomes were de novo assembled using the Fast-Plast program. Complete plastome sequences were annotated and verified. The sequences were aligned in MAUVE program to detect possible structural changes. A maximum likelihood phylogeny was executed to evaluate the relationships of the studied species.

Results: The plastomes ranged from 107,368 bp in Mammillaria bocasana to 108,069 bp in M. erythrosperma. Both presented a quadripartite structure and contained 108 genes. The IRs were ~ 1,600 bp long and included the genes rpl2, rpl23 (pseudo), and trnI-CAU. MAUVE identified a ~ 21 kb inversion in the large single copy containing a block of genes related to photosynthesis. The phylogenetic analysis placed both species in a single clade separated from the other species within Mammillaria subg. Mammillaria.

Conclusions: The studied species of Mammillaria series Stylothelae exhibited a different and synapomorphic chloroplast genome structure. Other Mammillaria chloroplast genome structures have evolved independently in different lineages.


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Two chloroplast genomes with reduced inverted repeat regions in <em>Mammillaria</em> series <em>Stylothelae</em> (Cactaceae)


Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics. (accessed July 18, 2023)

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19: 455-477. DOI:

Blazier JC, Guisinger MM, Jansen RK. 2011. Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae). Plant Molecular Biology 76: 263-272. DOI:

Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina Sequence Data. Bioinformatics 30: 2114-2120. DOI:

Bravo-Hollis H, Sánchez-Mejorada H. 1991. Las cactáceas de México: volumen III. DF, México: Universidad Nacional Autónoma de México. ISBN: 968-36-1760-3

Breslin PB, Wojciechowski MF, Majure LC. 2021. Molecular phylogeny of the Mammilloid clade (Cactaceae) resolves the monophyly of Mammillaria. TAXON 70: 308-323. DOI:

Butterworth CA, Butterworth KM, Fitz-Maurice WA, Fitz-Maurice B. 2007. A localized loss of the chloroplast rpl16 intron in Mammillaria series Stylothelae (Cactaceae) delineates members of the M. crinita group. Bradleya 25: 187-192. DOI:

Butterworth CA, Wallace RS. 2004. Phylogenetic studies of Mammillaria (Cactaceae): insights from chloroplast sequence variation and hypothesis testing using the parametric Bootstrap. American Journal of Botany 91: 1086-1098. DOI:

Braukmann TWA, Kuzmina M, Stefanović S. 2009. Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Current Genetics 55: 323-337. DOI:

Braukmann T, Kuzmina M, Stefanović S. 2013. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss. Journal of Experimental Botany 64: 977-989. DOI:

Campagna ML, Downie SR. 1998. The intron in chloroplast gene rpl16 is missing from the flowering plant families Geraniaceae, Goodeniaceae, and Plumbaginaceae. Transactions of the Illinois State Academy of Science 91: 1-11.

Cao DL, Zhang XJ, Qu XJ, Fan SJ. 2022. Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae). Frontiers in Plant Science 13: 1046253. DOI:

Cauz-Santos LA, Portugal da Costa Z, Callot C, Cauet S, Zucchi MI, Bergés H, van den Berg C, Carneiro-Vieira ML. 2020. A repertory of rearrangements and the loss of an Inverted Repeat region in Passiflora chloroplast genomes. Genome Biology and Evolution 12: 1841-1857. DOI:

Cervantes CR, Hinojosa-Alvarez S, Wegier A, Rosas U, Arias S. 2021. Evaluating the monophyly of Mammillaria series Supertextae (Cactaceae). PhytoKeys 177: 25-42. DOI:

Chincoya DA, Arias S, Vaca-Paniagua F, Dávila P, Solórzano S. 2023. Phylogenomics and biogeography of the Mammilloid Clade revealed an intricate evolutionary history arose in the Mexican Plateau. Biology 12: 512. DOI:

Chincoya DA, Sanchez-Flores A, Estrada K, Díaz-Velásquez CE, González-Rodríguez A, Vaca-Paniagua F, Dávila P, Arias S, Solórzano S. 2020. Identification of high molecular variation loci in complete chloroplast genomes of Mammillaria (Cactaceae, Caryophyllales). Genes 11: 830. DOI:

Daniell H, Lin C-S, Yu M, Chang W-J. 2016. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology 17: 134. DOI:

Darling ACE, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research 14: 1394-1403. DOI:

Fitz-Maurice WA, Fitz-Maurice B. 2006. Mammillaria series Stylothelae. Mammillaria Journal 46: 3-8.

Frailey DC, Chaluvadi SR, Vaughn JN, Coatney CG, Bennetzen JL. 2018. Gene loss and genome rearrangement in the plastids of five hemiparasites in the family Orobanchaceae. BMC Plant Biology 18: 30. DOI:

González-Zamora P, Aquino D, Mohl J, Sánchez D. 2022. A new endemic species of Mammillaria (Cactaceae) from San Luis Potosí, Mexico. Willdenowia 52: 359-372. DOI:

González-Zamora P, Aquino D, Rodríguez A, Sánchez D. 2023. Mammillaria monochrysacantha (Cactaceae), a new endemic species from Guanajuato, Mexico. Phytotaxa 618: 243-253. DOI:

Greiner S, Lehwark P, Bock R. 2019. Organellar Genome DRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research. 47: W59-W64. DOI:

Guo W, Grewe F, Cobo-Clark A, Fan W, Duan Z, Adams RP, Schwarzbach AE, Mower JP. 2014. Predominant and substoichiometric isomers of the plastid genome coexist within Juniperus plants and have shifted multiple times during Cupressophyte evolution. Genome Biology Evolution 6: 580-590. DOI:

Hinojosa-Alvarez S, Arias S, Ferran S, Purugganan MD, Rozas J, Rosas, Wegier A. 2020. The chloroplast genome of the pincushion cactus Mammilllaria haageana subsp. san-angelensis, a Mexican endangered species. Mitochondrial DNA Part B 5: 2038-2039. DOI:

Hunt D, Taylor N, Charles G. 2006. The New Cactus Lexicon: Descriptions and Illustrations of the Cactus Family. Milborne Port, UK: DH Books. ISBN: 0-9538134-5-2

Hunt D. 2016. CITES Cactaceae Checklist: Third Edition. UK: Royal Botanical Gardens Kew. ISBN: 978-0-9933113-2-1

Jin D-M, Wicke S, Gan L, Yang J-B, Jin JJ, Yi TS. 2020. The loss of the Inverted Repeat in the Putranjivoid clade of Malpighiales. Frontiers in Plant Science 11: 942. DOI:

Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160-1166. DOI:

Kim S-C, Ha Y-H, Park BK, Jang JE, Kang ES, Kim Y-S, Kimspe T-H, Kim H-J. 2023. Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. Plos One 18: e0289625. DOI:

Köhler M, Reginato M, Jin J-J, Majure LC. 2023. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). Annals of Botany 132: 771-786. DOI:

Köhler M, Reginato M, Souza-Chies TT, Majure LC. 2020. Insights into chloroplast genome evolution across Opuntioideae (Cactaceae) reveals robust yet sometimes conflicting phylogenetic topologies. Frontiers in Plant Sciences 11: 729. DOI:

Könyves K, Bilsborrow J, Christodoulou MD, Culham A, David J. 2021. Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq. PeerJ 9: e12400. DOI:

Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357-359. DOI:

Lee C, Choi I-S, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, Jansen RK, Ruhlman TA. 2021. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. The Plant Journal 107: 861-875. DOI:

Lin C-S, Chen JJW, Chiu C-C, Hsiao HCW, Yang C-J, Jin X-H, Leebens-Mack J, de Pamphilis8 CW, Huang Y-T, Yang L-H, Chang W-J, Kui L, Wong GK-S, Hu JM, Wang W, Shih M-C. 2017. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant Journal 90: 994-1006. DOI:

Lin C-S, Chen JJW, Huang Y-T, Chan M-T, Daniell H, Chang W-J, Hsu C-T, Liao DC, Wu F-H, Lin S-Y, Liao CF, Deyholos MK, Wong GK-S, Albert VA, Chou M-L, Chen C-Y, Shih M-C. 2015. The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Scientific Reports 5: 9040. DOI:

Majure LC, Baker MA, Cloud-Hughes M, Salywon A, Neubig KM. 2019. Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts. American Journal of Botany 106: 1327-1345. DOI:

Marçais G, Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27: 764-770. DOI:

Martín M, Funk HT, Serrot PH, Poltnigg P, Sabater B. 2009. Functional characterization of the thylakoid Ndh complex phosphorylation by site-directed mutations in the ndhF gene. Biochimica et Biophysica Acta 1787: 920-928. DOI:

Martín M, Sabater B. 2010. Plastid ndh genes in plant evolution. Plant Physiology and Biochemistry 48: 636e645. DOI:

McCoy SR, Kuehl JV, Boore JL, Raubeson LA. 2008. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evolutionary Biology 8: 130. DOI:

McKain. 2017. mrmckain/Fast-Plast: Fast-Plast v.1.2.6 (v.1.2.6). Zenodo.

Morais da Silva G,·de Santana-Lopes A, Gomes-Pacheco T, Lima de Godoy-Machado K, Silva MC, de Oliveira JD, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira-Pedrosa F, Rogalski M. 2021. Genetic and evolutionary analyses of plastomes of the subfamily Cactoideae (Cactaceae) indicate relaxed protein biosynthesis and tRNA import from cytosol. Brazilian Journal of Botany 44: 97-116. DOI:

Mower JP, Guo W, Partha R, Fan W, Levsen N, Wolff K, Nugent JM, Pabón-Mora N, González F. 2021. Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella. Molecular Phylogenetics and Evolution 162: 107217. DOI:

Ortiz-Brunel JP, Carrillo-Reyes P, Sánchez D, Ruíz-Sánchez E, Rodríguez A. 2023. A morphological analysis of the Mammillaria fittkaui species complex (Cactaceae) reveals a new species from Jalisco, Mexico. Botanical Sciences 101: 619-631. DOI:

Palmer JD. 1986. Chloroplast DNA exists in two orientations. Nature 301: 92-93. DOI:

Qu X-J, Wu C-S, Chaw S-M, Yi T-S. 2017. Insights into the existence of isomeric plastomes in Cupressoideae (Cupressaceae). Genome Biology and Evolution 9: 1110-1119. DOI:

Ranade SS, García‑Gil MR, Rosselló JA. 2016. Non‑functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes. Molecular Genetics and Genomics 291: 935-941:

Reppenhagen W. 1991. Die Gattung Mammillaria: Monographie. Band 1 und Band 2. Deutschland: Titisee-Neustadt, Druckerei Steinhart GmbH

Ruhlman TA, Chang WJ, Chen JJW, Huang Y-T, Chan M-T, Zhang J, Liao DC, Blazier JC, Jin X, Shih MC, Jansen RK, Lin C-S. 2015. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. BMC Plant Biology 15: 100. DOI:

Ruhlman TA, Zhang J, Blazier JC, Sabir JSM, Jansen RK. 2017. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. American Journal of Botany 104: 559-572. DOI:

Sabater B. 2021. On the edge of dispensability, the chloroplast ndh genes. International Journal of Molecular Sciences 22: 12505. DOI:

Sanderson MJ, Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Eguiarte LE, Kumar S, Lee HO, Lee J, McMahon M, Steele K, Wing R, Yang T-J, Zwickl D, Wojciechowski MF. 2015. Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): loss of the ndh gene suite and inverted repeat. American Journal of Botany 102: 1-13. DOI:

Shi C, Hu N, Huang H, Gao J, Chao Y-J, Gao L-Z. 2012. An improved chloroplast DNA extraction procedure for whole plastid genome sequencing. Plos One 7: e31468. DOI:

Silva SR, Diaz YCA, Alves-Penha H, Pinheiro DG, Fernandes CC, Miranda VFO, Michael TP, Varani AM. 2016. The chloroplast genome of Utricularia reniformis sheds light on the evolution of the ndh gene complex of terrestrial carnivorous plants from the Lentibulariaceae family. Plos One 11: e0165176. DOI:

Solórzano S, Chincoya DA, Sanchez-Flores A, Estrada K, Díaz-Velásquez CE, González-Rodríguez A, Vaca-Paniagua F, Dávila P, Arias S. 2019. De Novo assembly discovered novel structures in genome of plastids and revealed divergent inverted repeats in Mammillaria (Cactaceae, Caryophyllales). Plants 8: 392. DOI:

Strand DD, D’Andrea L, Bock R. 2019. The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics. Biochemical Journal 476: 2743-2756. DOI:

Su H-J, Liang S-L, Nickrent DL. 2021. Plastome variation and phylogeny of Taxillus (Loranthaceae). Plos One 16: e0256345. DOI:

Sun S-S, Fu P-C, Zhou X-J, Cheng Y-W, Zhang F-Q, Chen S-L, Gao Q-B. 2018. The complete plastome sequences of seven species in Gentiana sect. Kudoa (Gentianaceae): insights into plastid gene loss and molecular evolution. Frontiers in Plant Sciences 9: 493. DOI:

Sun Y, Moore MJ, Lin N, Adelalu KF, Meng A, Jian S, Yang L, Li J, Wang H. 2017. Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family. BMC Genomics 18: 592.

Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution 38: 3022-3027. DOI:

Thiers B. 2023. Index Herbariorum: A global directory of public herbaria and associated staff. New York: New York Botanical Garden’s Virtual Herbarium. (accessed October 21, 2023).

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq -versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45: W6-W11. DOI:

Walker JF, Jansen RK, Zanis MJ, Emery NC. 2015. Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes. American Journal of Botany 102: 1751-1752. DOI:

Wei N, Pérez-Escobar OA, Musili PM, Huang W-C, Yang J-B, Hu A-Q, Hu G-W, Grace OM, Wang Q-F. 2021. Plastome evolution in the hyperdiverse genus Euphorbia (Euphorbiaceae) using phylogenomic and comparative analyses: large-scale expansion and contraction of the Inverted Repeat region. Frontiers in Plant Science 12: 712064. DOI:

Wolfe KH, Morden CW, Palmer JD. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proceedings of the National Academy of Sciences 89: 10648-10652. DOI:

Yao G, Jin J-J, Li H-T, Yang J-B, Mandala VS, Croley M, Mostow R, Douglas NA, Chase MW, Christenhusz MJM, Soltis DE, Soltis PS, Smith SA, Brockington SF, Moore MJ, Yi T-S, Li D-Z. 2019. Plastid phylogenomic insights into the evolution of Caryophyllales. Molecular Phylogenetics and Evolution 134: 74-86. DOI:

Yu J, Li J, Zuo Y, Qin Q, Zeng S, Rennenberg H, Deng H. 2023. Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae). BMC Plant Biology 23:132. DOI:

Zhang F, Wang T, Shu X, Wang N, Zhuang W, Wang Z. 2020. Complete chloroplast genomes and comparative analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae). International Journal of Molecular Sciences 21: 5729. DOI:

How to Cite
Ortiz-Brunel, J. P., McKain, M. R., Zamora-Tavares, P., Ruiz-Sanchez, E., Sánchez, D., Sandoval-Padilla, I., MacNeill, B. N., & Rodríguez, A. (2024). Two chloroplast genomes with reduced inverted repeat regions in Mammillaria series Stylothelae (Cactaceae). Botanical Sciences, 102(2), 499-512.