OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

Greiner, Stephan; Lehwark, Pascal; Bock, Ralph

doi:10.1093/nar/gkz238

Cited by 1,358 publications

(970 citation statements)

References 21 publications

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“…The ARAGORN v1.2.38 was chosen for tRNA annotation. The information of genes along the whole chloroplast genome were visualized by OGDRAW [38] with default settings. The IR (Inverted Repeat) boundaries in chloroplast sequences were identified by aligning the whole sequence with itself using BLAST (-p blastn -m 8 -F F -e 1).…”

Section: Methodsmentioning

confidence: 99%

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Shi

Han²,

Li³

et al. 2019

Preprint

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AbstractMangroves are main components of an ecosystem which connect land and ocean and is of significant ecological importance. They are found around the world and taxonomically distributed in 17 families. Until now there has been no evolutionary phylogenetic analyses on mangroves based on complete plastome sequences. In order to infer the relationship between mangroves and terrestrial plants at the molecular level, we generated chloroplast genomes of 14 mangrove species from eight families, spanning six orders: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, Thespesia populnea), Myrtales (Laguncularia racemose, Sonneratia ovata, Pemphis acidula), and Sapindales (Xylocarpus moluccensis). The whole-genome length of these chloroplasts is from 149kb to 168kb. They have a conserved structure, with two Inverted Repeat (IRa and IRb, ~25.8kb), a large single-copy region (LSC, ~89.0kb), a short single-copy (SSC, ~18.9kb) region, as well as ~130 genes (85 protein-coding, 37 tRNA, and 8 rRNA). The number of simple sequence repeats (SSRs) varied between mangrove species. Phylogenetic analysis using complete chloroplast genomes of 71 mangrove and land plants, confirmed the previously reported phylogeny within rosids, including the positioning of obscure families such as Linaceae within Malpighiales. Most mangrove chloroplast genes are conserved and we found six genes subjected to positive or neutral selection. Genomic comparison showed IR regions have lower divergence than other regions. Our study firstly reported several plastid genetic resource for mangroves, and the determined evolutionary locations as well as comparative analyses of these species provid insights into the mangrove genetic and phylogenetic research.

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Section: Methodsmentioning

confidence: 99%

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Shi

Han²,

Li³

et al. 2019

Preprint

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“…For both American elm genotypes a circular chloroplast genome map was drawn with OGDRAW (v. 1.3.1) (Greiner et al, 2019). A global pairwise sequence alignment of the two chloroplast genome sequences was produced using EMBOSS Stretcher (v. 6.6.0) with default parameters (Madeira et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species

Ebrahimi¹,

Antonides²,

Pinchot

et al. 2020

Preprint

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American elm, Ulmus americana L., was cultivated widely in USA and Canada as a landscape tree, but the genome of this important species is poorly characterized. For the first time, we describe the sequencing and assembly of the chloroplast genomes of two American elm genotypes (RV16 and Am57845). The complete chloroplast genome of U. americana ranged from 158,935-158,993 bp. The genome contains 127 genes, including 85 protein-coding genes, 34 tRNA genes and 8 rRNA genes. Between the two American elm chloroplasts we sequenced, we identified 240 sequence variants (SNPs and indels). To evaluate the phylogeny of American elm, we compared the chloroplast genomes of two American elms along with seven Asian elm species and twelve other chloroplast genomes available through the NCBI database. As expected, Ulmus was closely related to Morus and Cannabis, as all three genera are assigned to the Urticales. Comparison of American elm with Asian elms revealed that trnH was absent from the chloroplast of American elm but not most Asian elms; conversely, petB, petD, psbL, trnK, and rps16 are present in the American elm but absent from all Asian elms. The complete chloroplast genome of U. americana will provide useful genetic resources for characterizing the genetic diversity of U. americana and potentially help to conserve natural populations of American elm.

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“…GB2sequin was used to generate five column tab-delimited files from the annotated genomes for NCBI submission [45]. The circular map of these genomes was drawn by OrganellarGenomeDRAW (OGDRAW) [46].…”

Section: Genome Assembly and Annotationmentioning

confidence: 99%

Comparison among the first representative chloroplast genomes ofOrontium, Lasia, Zamioculcas, andStylochaetonof the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

Abdullah

Henriquez

Mehmood

et al. 2020

Preprint

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The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of the first representatives of four genera representing three subfamilies: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using the plastomes. The size of the chloroplast genomes ranged from 163,770-169,982 bp. These genomes comprise 114 unique genes, including 80 protein-coding, 4 rRNA, and 30 tRNA genes. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The junctions JSB (IRb/SSC) and JSA (SSC/IRa) are highly variable, as is oligonucleotide repeats content among the genomes. The patterns of inverted repeats contraction and expansion were shown to be homoplasious and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were shown for several genes in S. bogneri. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.Many other types of mutational events also take place within chloroplast genomes, including insertion-deletion (indels), substitutions, tandem repeat variations and variations in number and type of oligonucleotide repeats [11,[18][19][20]. The single parent inheritance of the chloroplast genome -paternally in some gymnosperms and maternally in most angiospermsalong with adequate levels of polymorphism make it suitable for studies of evolution, domestication, phylogeography, population genetics, and phylogenetics [7,10,11,[21][22][23][24].Araceae is an ancient and large monocot plant family, comprising 114 genera and 3750 species [25]. This family is subdivided into eight subfamilies: Gymnostachydoideae, Orotioideae, Lemnoideae, Pothoideae, Monsteroideae, Lasioideae, Zamioculcadoideae, and Aroideae [22,26,27]. Advancements in next generation sequencing have made genomic resources available for species of Lemnoideae [28], Monsteroideae [18,29,30], and Aroideae [10,31,32]; chloroplast genomes of Symplocarpus renifolius Schott ex Tzvelev and S. nipponicus Makino of Orotioideae have also been reported [33,34]. Previous studies provide insight into some unique evolutionary events of chloroplast genomes in Araceae, including IR contraction and expansion, gene rearrangement, and positive selection [10,18,28]. Moreover, loss/pseudogenation of some important genes are also reported in the genus Amorphophallus Blume (Aroideae) [17]. Nevertheless, data for the chloroplast genome ≥ 10, dinucleotide ≥ 5, trinucleotide ≥ 4, tetranucleotide, pentanucleotide and hexanucleotide ≥ 3. The forward and reverse oligonucleotide repeats were determined with length ≥ 14 bp with 1 editing site, initially. Later, we removed all repeats that contained mismatches from the analyses and left only those repeat pairs that exhibited 100% similarities, following Abdullah et al. 2020 [50].We determined transition substitutions (Ts), transvers...

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OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

Cited by 1,358 publications

References 21 publications

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species

Comparison among the first representative chloroplast genomes ofOrontium, Lasia, Zamioculcas, andStylochaetonof the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

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