Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Overview

Journal Front Genet

Date 2020 Oct 26

PMID 33101394

Citations 129

Authors

Shuyu Zheng

Peter Poczai

Jaakko Hyvonen

Jing Tang

Ali Amiryousefi

Affiliations

Soon will be listed here.

Abstract

Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.

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References

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

Smith D . : the makings of a giant-sized chloroplast genome. AoB Plants. 2018; 10(5):ply058. PMC: 6205361. DOI: 10.1093/aobpla/ply058. View

Ponce-Toledo R, Deschamps P, Lopez-Garcia P, Zivanovic Y, Benzerara K, Moreira D . An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids. Curr Biol. 2017; 27(3):386-391. PMC: 5650054. DOI: 10.1016/j.cub.2016.11.056. View

Wang W, Lanfear R . Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants. Genome Biol Evol. 2019; 11(12):3372-3381. PMC: 7145664. DOI: 10.1093/gbe/evz256. View

Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T . The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986; 5(9):2043-2049. PMC: 1167080. DOI: 10.1002/j.1460-2075.1986.tb04464.x. View

Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L . CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 2019; 47(W1):W65-W73. PMC: 6602467. DOI: 10.1093/nar/gkz345. View

Wu C, Lai Y, Lin C, Wang Y, Chaw S . Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol. 2009; 52(1):115-24. DOI: 10.1016/j.ympev.2008.12.026. View

Greiner S, Lehwark P, Bock R . OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019; 47(W1):W59-W64. PMC: 6602502. DOI: 10.1093/nar/gkz238. View

Wolfsberg T, Schafer S, Tatusov R, Tatusov T . Organelle genome resource at NCBI. Trends Biochem Sci. 2001; 26(3):199-203. DOI: 10.1016/s0968-0004(00)01773-4. View

10.

Walker J, Jansen R, Zanis M, Emery N . Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes. Am J Bot. 2015; 102(11):1751-2. DOI: 10.3732/ajb.1500299. View

11.

Oldenburg D, Bendich A . The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication. Curr Genet. 2015; 62(2):431-42. DOI: 10.1007/s00294-015-0548-0. View

12.

Goulding S, Olmstead R, Morden C, Wolfe K . Ebb and flow of the chloroplast inverted repeat. Mol Gen Genet. 1996; 252(1-2):195-206. DOI: 10.1007/BF02173220. View

13.

Cheng S, Melkonian M, Smith S, Brockington S, Archibald J, Delaux P . 10KP: A phylodiverse genome sequencing plan. Gigascience. 2018; 7(3):1-9. PMC: 5869286. DOI: 10.1093/gigascience/giy013. View

14.

Lohse M, Drechsel O, Kahlau S, Bock R . OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013; 41(Web Server issue):W575-81. PMC: 3692101. DOI: 10.1093/nar/gkt289. View

15.

Bauman N, Akella S, Hann E, Morey R, Schwartz A, Brown R . Next-Generation Sequencing of Haematococcus lacustris Reveals an Extremely Large 1.35-Megabase Chloroplast Genome. Genome Announc. 2018; 6(12). PMC: 5864939. DOI: 10.1128/genomeA.00181-18. View

16.

Anderson S, Bankier A, Barrell B, de Bruijn M, Coulson A, Drouin J . Sequence and organization of the human mitochondrial genome. Nature. 1981; 290(5806):457-65. DOI: 10.1038/290457a0. View

17.

Jin J, Yu W, Yang J, Song Y, dePamphilis C, Yi T . GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21(1):241. PMC: 7488116. DOI: 10.1186/s13059-020-02154-5. View

18.

Dempewolf H, Kane N, Ostevik K, Geleta M, Barker M, Lai Z . Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol Ecol Resour. 2011; 10(6):1048-58. DOI: 10.1111/j.1755-0998.2010.02859.x. View

19.

Amiryousefi A, Hyvonen J, Poczai P . IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018; 34(17):3030-3031. DOI: 10.1093/bioinformatics/bty220. View

20.

Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G . MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2012; 69(2):313-9. DOI: 10.1016/j.ympev.2012.08.023. View