Molecular Phylogeny of Dipetrocarpaceae in Southeast Asia Based on Nucleotide Sequences ofmatK,trnL Intron, andtrnL-trnF Intergenic Spacer Region in Chloroplast DNA

Kajita, Tadashi; Kamiya, Katsumasa; Nakamura, Kaho; Tachida, Hidenori; Ratnam, R Wickneswari V; Tsumura, Yoshihiko; Yoshimaru, Hiroshi; Yamazaki, Tsuneyuki

doi:10.1006/mpev.1998.0516

Cited by 75 publications

(84 citation statements)

References 20 publications

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“…The frequencies of the nucleotides were estimated and a similar composition has been reported for the trnL intron of cpDNA among Dipterocarpaceae species with frequencies of 0.40, 0.27, 0.15, and 0.17 for A, T, C, and G, respectively (Kajita et al, 1998) The trnL intron was considered a mosaic structure of conserved elements (internal guide sequence P, Q, R, and S) and common secondary structure elements, which are essential for correct splicing (Cech, 1990). In cases where variation in single nucleotides occurs, the secondary structure of the conserved motif of the intron is often retained.…”

Section: Discussionsupporting

confidence: 63%

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tRNALeu intron (UAA) of Ficus carica L.: genetic diversity and evolutionary patterns

2015

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ABSTRACT. Cytoplasmic chloroplast DNA was explored to establish genetic relationships among Ficus carica cultivars and elucidate the molecular evolution of the species. The results suggest the occurrence of haplotype and nucleotide diversity. Conserved group I intron sequence motifs were detected and showed a common secondary structure, despite the presence of some mutations on their sequences. The neighbor-joining dendrogram showed a continuous diversity that characterizes local resources. The maximum parsimony tree, with an RI index of 0.507, indicated minimal homoplasy within the data set. Furthermore, our results demonstrate that the trnL intron is the seat of numerous substitutions. Herein, new insight on the mechanism involved in the evolution of the trnL intron in the fig is presented. From the study, it appears that there is an explicit rejection of the null hypothesis in F. carica. A scenario of positive selection and recent expansion of F. carica genotypes across Tunisia seems to be retained.

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Section: Discussionsupporting

confidence: 63%

“…For Dipterocarpaceae species, the size of the intron trnL varies from 458 to 509 bp (Kajita et al, 1998). The length of this same region of the cpDNA was also reported for Triticum aestivum (587 bp), Hordeum vulgare (555 bp), Panicum virgatum L. (557 bp) (Missaoui et al, 2006), and Prunus spp (574 bp) (Ben Mustapha et al, 2013).…”

Section: Discussionsupporting

confidence: 52%

tRNALeu intron (UAA) of Ficus carica L.: genetic diversity and evolutionary patterns

2015

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“…Therefore they are potentially powerful tools for Ellegren et al (1997). Recently, molecular phylogenies of the same 30 species of Dipterocarpaceae were constructed using PCR-RFLP analysis of chloroplast genes (Tsumara et al, 1996) and sequence analysis of chloroplast DNA (Kajita et al, 1998). According to these studies, there are two major groups of Dipterocarpaceae: Shoreae, which includes Shorea, Hopea, Parashorea, Neobalanocarpus and Dryobalanops, and Dipterocarpeae, which includes Dipterocarpus, Anisoptera, Upuna and Cotylelobium.…”

Section: Discussionmentioning

confidence: 99%

Development and polymorphism of simple sequence repeat DNA markers for Shorea curtisii and other Dipterocarpaceae species

et al. 1998

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Nine simple sequence repeat (SSR) markers were developed from Shorea curtisii using two different methods. One SSR locus was isolated by the commonly used method of screening by colony hybridization, and the other eight loci were isolated by a vectorette PCR method. Primer pairs were designed based on the sequences of all these SSR loci. Analysis of 40 individuals of S. curtisii from natural forest in Malaysia revealed that all SSR loci were polymorphic. Four SSR markers, Shc01, Shc04, Shc07 and Shc09, were highly polymorphic. We have also tested the applicability of these SSR printers to other species of Dipterocarpaceae using PCR amplification. Because the flanking region sequences of the S. curtisii SSRs were well conserved within this family, the SSR primers for S. curtisii can be applied to almost all species of Dipterocarpaceae.

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“…The cpDNA markers provided data for reconstructing phylogeny among families of flowering plants (Kajita 1998). The sequences of trnL-F region of cpDNA are also frequently used in the phylogenetic studies at generic and specific levels (Alejanro et al 2005;Barfuss et al 2005;Shaw et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic analysis of Mangifera from central region of Sumatra using trnL-F intergenic spacer

et al. 2017

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Molecular Phylogeny of Dipetrocarpaceae in Southeast Asia Based on Nucleotide Sequences ofmatK,trnL Intron, andtrnL-trnF Intergenic Spacer Region in Chloroplast DNA

Cited by 75 publications

References 20 publications

tRNALeu intron (UAA) of Ficus carica L.: genetic diversity and evolutionary patterns

tRNALeu intron (UAA) of Ficus carica L.: genetic diversity and evolutionary patterns

Development and polymorphism of simple sequence repeat DNA markers for Shorea curtisii and other Dipterocarpaceae species

Phylogenetic analysis of Mangifera from central region of Sumatra using trnL-F intergenic spacer

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