References

Adler D. 1994. Idiogram album. http://www.pathology.washington.edu/research/cytopages/idiograms/human/
Carvalho R, Soares Filho WS, Brasileiro-Vidal AC, Guerra M. 2005. The relationships among lemons, limes and citron: A chromosomal comparison Cytogenetic and Genome Research, 109(1-3): 276–282. https://doi.org/10.1159/000082410
da Costa Silva S, Mendes S, Soares Filho W dos S, Pedrosa-Harand A. 2015. Chromosome homologies between Citrus and Poncirus—the comparative cytogenetic map of mandarin (Citrus reticulata) Tree Genetics & Genomes, 11(1): 811. https://doi.org/10.1007/s11295-014-0811-4. http://link.springer.com/10.1007/s11295-014-0811-4
da-Costa-Silva S, Mendes S, Régis T, Sampaio-Passos O, dos-Santos-Soares-Filho W, Pedrosa-Harand A. 2019. Cytogenetic Map of Pummelo and Chromosome Evolution of True Citrus Species and the Hybrid Sweet Orange Journal of Agricultural Science, 11(14): 148. https://doi.org/10.5539/jas.v11n14p148
Golczyk H, Hasterok R, Joachimiak AJ. 2005. FISH-aimed karyotyping and characterization of Renner complexes in permanent heterozygote Rhoeo spathacea Genome, 48(1): 145–153. https://doi.org/10.1139/g04-093
Guerra M. 1986. Reviewing the chromosome nomenclature of Levan et al. Brazilian Journal of Genetics, 9(4): 741–743
Höhna S, Landis MJ, Heath TA. 2017. Phylogenetic inference using RevBayes Current Protocols in Bioinformatics, 2017(March): 6.16.1–6.16.34. https://doi.org/10.1002/cpbi.22
Levan A, Fredga K, Sandberg AA. 1964. Nomenclature for centromeric position on chromosomes Hereditas, 52(2): 201–220. https://doi.org/10.1111/j.1601-5223.1964.tb01953.x. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1601-5223.1964.tb01953.x
Mendes S. 2016. Variabilidade Cariotípica da laranja-azeda (Citrus aurantium L.) e a origem do seu cariótipo heteromórfico Mapeamento citogenético em citrus: Análises evolutivas e integração com dados genômicos
Nguyen L-T, Schmidt HA, Haeseler A von, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies Molecular biology and evolution, 32(1): 268–274. https://doi.org/10.1093/molbev/msu300. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271533/
Robertson WRB. 1916. Chromosome studies. I. Taxonomic relationships shown in the chromosomes of tettigidae and acrididae: V-shaped chromosomes and their significance in acrididae, locustidae, and gryllidae: Chromosomes and variation Journal of Morphology, 27(2): 179–331. https://onlinelibrary.wiley.com/doi/abs/10.1002/jmor.1050270202
Romero-Zarco C. 1986. A new method for estimating karyotype asymmetry Taxon, 35(3): 526–530. https://onlinelibrary.wiley.com/doi/abs/10.2307/1221906
Watanabe K, Yahara T, Denda T, Kosuge K. 1999. Chromosomal evolution in the genus Brachyscome (Asteraceae, Astereae): statistical tests regarding correlation between changes in karyotype and habit using phylogenetic information Journal of Plant Research, 112: 145–161. https://link.springer.com/article/10.1007/PL00013869
Yasuda K, Yahata M, Shigyo M, Matsumoto R, Yabuya T, Kunitake H. 2010. Identification of parental chromosomes in sexual intergeneric hybrid progenies between citrus cultivar ’Nanpu’ tangor and Citropsis schweinfurthii in the subfamily aurantioideae Journal of the Japanese Society for Horticultural Science, 79(2): 129–134. https://doi.org/10.2503/jjshs1.79.129
Yi KU, Kim HB, Song KJ. 2018. Karyotype diversity of Korean landrace mandarins by CMA banding pattern and rDNA loci Scientia Horticulturae, 228(July 2017): 26–32. https://doi.org/10.1016/j.scienta.2017.10.001. http://dx.doi.org/10.1016/j.scienta.2017.10.001

R-packages

Csárdi G. 2017. Crayon: Colored terminal output. R package version 1.3.4. https://CRAN.R-project.org/package=crayon
Kassambara A. 2019. Ggpubr: ’ggplot2’ based publication ready plots. R package version 0.2.3. https://CRAN.R-project.org/package=ggpubr
R Core Team. 2019. R: A language and environment for statistical computing R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
Revell LJ. 2012. Phytools: An r package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3: 217–223. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00169.x
Roa F, PC Telles M. 2021. idiogramFISH: Shiny app. Idiograms with marks and karyotype indices Universidade Federal de Goiás, UFG, Goiânia. R-package. version 2.0.0. https://doi.org/10.5281/zenodo.3579417. https://ferroao.gitlab.io/manualidiogramfish/
Wickham H. 2011. The split-apply-combine strategy for data analysis Journal of Statistical Software, 40(1): 1–29. https://www.jstatsoft.org/article/view/v040i01
Wickham H. 2016. ggplot2: Elegant graphics for data analysis Springer-Verlag New York. https://ggplot2.tidyverse.org
Wickham H, Chang W, Henry L, Pedersen TL, Takahashi K, Wilke C, Woo K, Yutani H, Dunnington D. 2020. ggplot2: Create elegant data visualisations using the grammar of graphics. http://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2.
Wickham H, François R, Henry L, Müller K. 2019. Dplyr: A grammar of data manipulation. R package version 0.8.3. https://CRAN.R-project.org/package=dplyr
Wickham H, Henry L. 2020. Tidyr: Tidy messy data. R package version 1.0.2. https://CRAN.R-project.org/package=tidyr
Winter DJ. 2017. rentrez: An r package for the NCBI eUtils API The R Journal, 9: 520–526
Yu G, Lam TT-Y, Zhu H, Guan Y. 2018. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 35: 3041–3043. https://doi.org/10.1093/molbev/msy194. https://academic.oup.com/mbe/article/35/12/3041/5142656

Shiny App

Bihorel S. 2021. Rclipboard: Shiny/r wrapper for clipboard.js. R package version 0.1.3. https://github.com/sbihorel/rclipboard/
Chang W, Borges Ribeiro B. 2018. Shinydashboard: Create dashboards with shiny. R package version 0.7.1. http://rstudio.github.io/shinydashboard/
Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B. 2021. Shiny: Web application framework for r. R package version 1.6.0. https://shiny.rstudio.com/
Owen J. 2018. Rhandsontable: Interface to the handsontable.js library. R package version 0.3.7. http://jrowen.github.io/rhandsontable/
Warnes GR, Bolker B, Lumley T. 2020. Gtools: Various r programming tools. R package version 3.8.2. https://github.com/r-gregmisc/gtools

Documentation

Barnier J. 2020. Rmdformats: HTML output formats and templates for ’rmarkdown’ documents. R package version 0.3.7. https://CRAN.R-project.org/package=rmdformats
Temple Lang D, CRAN team the. 2019. RCurl: General network (HTTP/FTP/...) client interface for r. R package version 1.95-4.12. https://CRAN.R-project.org/package=RCurl
Wickham H, Bryan J. 2019. Usethis: Automate package and project setup. R package version 1.5.1. https://CRAN.R-project.org/package=usethis
Wickham H, Danenberg P, Eugster M. 2018. roxygen2: In-line documentation for r. R package version 6.1.1. https://CRAN.R-project.org/package=roxygen2
Wickham H, Hesselberth J. 2019. Pkgdown: Make static HTML documentation for a package. R package version 1.4.1. https://CRAN.R-project.org/package=pkgdown
Xie Y. 2015. Dynamic documents with R and knitr Chapman; Hall/CRC, Boca Raton, Florida. ISBN 978-1498716963. https://yihui.org/knitr/
Xie Y. 2016. Bookdown: Authoring books and technical documents with R markdown Chapman; Hall/CRC, Boca Raton, Florida. ISBN 978-1138700109. https://github.com/rstudio/bookdown
Xie Y, Allaire JJ, Grolemund G. 2018. R markdown: The definitive guide Chapman; Hall/CRC, Boca Raton, Florida. ISBN 9781138359338. https://bookdown.org/yihui/rmarkdown
Yu G. 2019b. Badger: Badge for r package. R package version 0.0.6. https://CRAN.R-project.org/package=badger
Yu G. 2019a. Rvcheck: R/package version check. R package version 0.1.6. https://CRAN.R-project.org/package=rvcheck
Zhu H. 2019. kableExtra: Construct complex table with ’kable’ and pipe syntax. R package version 1.1.0. https://CRAN.R-project.org/package=kableExtra