Abdullah, Henrique CL, Mehmood F, Carlsen MM, Islam M, Waheed MT, Poczai P, Croat TB, Ahmed I. Complete chloroplast genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): unique inverted repeat expansion and contraction affect rate of evolution. J Mol Evol. 2020;88:562–74.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Amiryousefi A, Hyvönen J, Poczai P. IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018;34:3030–1.

Article  CAS  PubMed  Google Scholar 

Andrews S. FastQC: a quality control tool for high throughput sequence data. (2010). Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

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. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017;33:2583–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cai XL, Wang JH, Zhao KK, Wang HX, Zhu ZX, Wang HF. Complete plastome sequence of Arisaema ringens (Araceae): a dioecious herb disjunctly distributed in China, Japan and Korea. Mitochondrial DNA Part B. 2019;4:540–1.

Article  Google Scholar 

Charboneau JLM, Cronn RC, Liston A, Wojciechowski MF, Sanderson MJ. Plastome structural evolution and homoplastic inversions in Neo-Astragalus (Fabaceae). Genome Biol Evol. 2021;13:eva2b15.

Article  Google Scholar 

Choi IS, Jansen R, Ruhlman T. Lost and found: return of the inverted repeat in the legume clade defined by its absence. Genome Biol Evol. 2019;11:1321–33.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Croat T. Ecology and life forms of Araceae. Aroideana. 1988;11:4–52.

Google Scholar 

Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14:1394–403.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5(6):e11147.

Article  PubMed  PubMed Central  Google Scholar 

Díez Menéndez C, Poczai P, Williams B, Myllys L, Amiryousefi A. IRplus: an augmented tool to detect inverted repeats in plastid genomes. Genome Biol Evol. 2023;15:evad177.

Article  PubMed  PubMed Central  Google Scholar 

Ding Y, Fang Y, Guo L, Li Z, He K, Zhao Y, Zhao H. Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions. PeerJ. 2017;5:e4186.

Article  PubMed  PubMed Central  Google Scholar 

Dong W, Liu J, Yu J, Wang L, Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE. 2012;7(4):e35071.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Feulner PGD, De-Kayne R. Genome evolution, structural rearrangements and speciation. J Evol Biol. 2017;30(8):1488–90.

Article  CAS  PubMed  Google Scholar 

Frailey DC, Chaluvadi SR, Vaughn JN, et al. Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae. BMC Plant Biol. 2018;18:30.

Article  PubMed  PubMed Central  Google Scholar 

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32:W273–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Govaerts R, Bogner J, Boos J, Boyce P, Cosgriff B, Croat T, Goncalves E, Grayum M, Hay A, Hetterscheid W, Ittenbach S, Landolt E, Mayo S, Murata J, Nguyen VD, Sakuragui CM, Singh Y, Thompson S, Zhu G. World checklist of Araceae [online]. Available from http://apps.kew.org/wcsp/ [Accessed 1 May 2024] (2019)

Gruzdev EV, Kadnikov VV, Beletsky AV, Mardanov AV, Ravin NV. Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae. PeerJ. 2019;7:e7830.

Article  PubMed  PubMed Central  Google Scholar 

Gusman G, Gusman L. The genus Arisaema—a monograph for botanists and nature lovers, Second revised and enlarged edition. A.R.G. Gantner Verlag, Ruggell. (2006)

Henrique CL, Abdullah AI, Carlsen MM, Zuluaga A, Croat TB, McKain MR. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae). Planta. 2020;251:72.

Article  Google Scholar 

Henriquez CL, Abdullah AI, Carlsen MM, Zuluaga A, Croat TB, McKain MR. Evolutionary dynamics in chloroplast genome of subfamily Aroideae (Araceae). Genomics. 2020;112:2349–60.

Article  CAS  PubMed  Google Scholar 

Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020;21:241.

Article  PubMed  PubMed Central  Google Scholar 

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim SH, Yang JY, Park J, Yamada T, Maki M, Kim SC. Comparison of whole plastome sequences between thermogenic skunk cabbage Symplocarpus renifolius and nonthermogenic S. nipponicus (Orontioideae; Araceae) in East Asia. Int J Mol Sci. 2019;20:4678.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim W, Lautenschläger T, Bolin JF, et al. Extreme plastomes in holoparasitic Balanophoraceae are not the norm. BMC Genomics. 2023;24:330.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). Ann Bot. 2023;132:771–86.

Article  PubMed  PubMed Central  Google Scholar 

Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001;29:4633–42.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie. Nat Methods. 2012;9:357–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Low SL, Yu C-C, Ooi IH, Eiadthong W, Galloway A, Zhou Z-K, Xing Y-W. Extensive Miocene speciation in and out of Indochina: the biogeographic history of Typhonium sensu stricto (Araceae) and its implication for the assembly of Indochina flora. J Syst Evol. 2021;59:419–28.

Article  Google Scholar 

Ma ZX, Li H. The genus Arisaema (Araceae: Aroideae: Arisaemateae) in China—a taxonomic revision and annotated list of species. Aroideana. 2017;40:49–134.

Google Scholar 

Manudev KM, Arunkumar PG, Nampy S. Taxonomic revision of Arisaema sect. Sinarisaema in India. Rheedea. 2019;29:119–73.

Article  Google Scholar 

Mardanov AV, Ranin NV, Kuznestsov BB, Samigullin TH, Antonov AS, Kolganova TV, Skyabin KG. Complete sequence of the Duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other Angiosperms. J Mol Evol. 2008;66:555–64.

Article  CAS  PubMed  Google Scholar 

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4.

Article  CAS