Evolution of a Noncoding Region of the Chloroplast Genome

Golenberg, Edward M.; Clegg, Michael T.; Durbin, Mary L.; Doebley, John; Pow, Din

doi:10.1006/mpev.1993.1006

Cited by 203 publications

(153 citation statements)

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“…Multiple origins of such indels in intergenic spacers have been frequently observed (e.g. Golenberg et al 1993, Lowrey et al 2001). Indels 19 and 22 required reversals (Fig.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

Hadiah¹,

Quinn²,

Conn³

2003

Telopea

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using chloroplast DNA data. Telopea 10(1) [235][236][237][238][239][240][241][242][243][244][245][246]. Phylogenetic analyses of the Urticales, based on chloroplast DNA data, support the monophyly of the Urticaceae, Boehmeria, Pilea and Procris, but not of Elatostema. Our result suggests that the circumscription of Procris is to be extended or included within Elatostema. At the tribal level, both Boehmerieae and Lecantheae appear paraphyletic, although this may be an artefact of the low taxon sampling. Preliminary analyses of relationships within Elatostema do not support the recognition of the subgenus Pellionia.

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“…Multiple origins of such indels in intergenic spacers have been frequently observed (e.g. Golenberg et al 1993, Lowrey et al 2001). Indels 19 and 22 required reversals (Fig.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

Hadiah¹,

Quinn²,

Conn³

2003

Telopea

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“…There is no clear consensus about whether indels should be used for phylogenetic analyses (Bapteste and Philippe, 2002;Egan and Crandall, 2008;Zhang et al, 2011), although most arguments against them are according to studies using one or several DNA fragments. Some researchers have championed indels as phylogenetically reliable (Lloyd and Calder, 1991;Ingvarsson et al, 2003) while others suggest that indels are homoplasious or uninformative (Golenberg et al, 1993;Pearce, 2006). Genes in the cp genome contained both synapomorphic and homoplasious indels.…”

Section: Evolution Of the Five Oryzeae Chloroplast Genomesmentioning

confidence: 99%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

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Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and non-coding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.

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“…Insertions and deletions can have considerable value for phylogenetic inference (e.g., Golenberg et al 1993;Bayer and Starr 1998;Downie et al 1998), so one must consider Briggs et al (2000); c Designed or modified in this study; d White et al (1990). counting gaps as having the status of coded characters added in the sequence matrix. The exclusion of gaps and elimination of coded gap characters from a non-coding sequence has been recommended to assess the impact of point substitutions alone (e.g., Kelchner and Clark 1997).…”

Section: Molecular Techniquesmentioning

confidence: 99%

Phylogeny of Abildgaardieae (Cyperaceae) Inferred from ITS and trnL–F Data

Ghamkhar¹,

Marchant²,

Wilson³

et al. 2007

aliso

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Within the tribe Abildgaardieae, the relationships between Fimbristylis and its relatives have not been certain, and the limits of Fimbristylis have been unclear, with Bulbostylis and Abildgaardia variously combined with it and each other. The relationships and limits of tribes Abildgaardieae and Arthrostylideae and their genera were evaluated across 49 representative species using parsimony and maximum likelihood analyses of ITS (nuclear ribosomal) and trnL-F (plastid) DNA sequence data separately and combined. The evolutionary reconstructions derived from sequences of cpDNA and nrDNA disagree about the position of tribe Arthrostylideae relative to Abildgaardieae; Arthrostylis and Actinoschoenus are either nested within Abildgaardieae (trnL-F data) or very closely related to this tribe (ITS data). The reconstructions also disagree about the monophyly of genus Abildgaardia (excluding A. vaginata). Crosslandia and A. vaginata form a clade that is nested within Fimbristylis. Bulbostylis is monophyletic and clearly separated from Fimbristylis. Further sampling of taxa and characters is needed to resolve and/or strengthen support for some of these ''deep'' and fine-scale relationships.

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Evolution of a Noncoding Region of the Chloroplast Genome

Cited by 203 publications

References 0 publications

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

Phylogeny of Elatostema (Urticaceae) using chloroplast DNA data

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Phylogeny of Abildgaardieae (Cyperaceae) Inferred from ITS and trnL–F Data

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