Towards a more robust molecular phylogeny of Chinese Apiaceae subfamily Apioideae: Additional evidence from nrDNA ITS and cpDNA intron (rpl16 and rps16) sequences

Zhou, Jiawei; Gong, Xun; Downie, Stephen R.; Peng, Hua

doi:10.1016/j.ympev.2009.05.029

Cited by 97 publications

(139 citation statements)

References 52 publications

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“…To date, many gene markers have been employed in the phylogenetic study of the Apiaceae (Downie et al, 2001Kadereit and Kadereit, 2005;Zhou et al, 2008Zhou et al, , 2009Spalik et al, 2009Spalik et al, , 2014, such as nrDNA ITS region, chloroplast DNA gene (rbcL and matK), intergenic spacer (psbI-5'trnK and rps16-5'trnK), and intron (rpl16, rps16, and rpoC1) sequences. Among these, the ITS region is the most frequently used marker.…”

Section: Discussionmentioning

confidence: 99%

“…Oenanthe is a taxonomically complex genus due to its diverse morphology and widespread dispersal (Fu and Watson, 2005;Zhao, 2010;Spalik et al, 2014). In the last decade, great progress has been made in elucidating high-level phylogenetic relationships within the family Apiaceae, including Oenanthe, such as the tribe Oenantheae Spalik et al, 2009Spalik et al, , 2014 and the subfamily Apioideae (Downie and Katz-Downie, 1999;Zhou et al, 2008Zhou et al, , 2009 by polymerase chain reaction (PCR) and direct DNA sequencing. The phylogenetic position of Oenanthe in Apiaceae has been studied extensively in these studies.…”

Section: Introductionmentioning

confidence: 99%

“…The ITS region has also been successfully used for low-level phylogenetic analyses in the Apiaceae (Downie et al, 2001Kadereit and Kadereit, 2005;Zhou et al, 2008Zhou et al, , 2009Spalik et al, 2009). The numerous ITS sequences available in GenBank for almost all currently reported species of Oenanthe provide a reference for species discrimination.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Evaluation of the taxonomic status of water dropwort (Oenanthe, Apiaceae) accessions from East Asia based on nuclear rDNA internal transcribed spacer sequences

Long

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Oenanthe L. is a taxonomically complex genus, several species of which have long been used as vegetables and traditional medicines in East Asia. In order to clarify the taxonomic status of Oenanthe accessions and provide baseline data for the sustainable use of its genetic resources, we examined sequence variations in the internal transcribed spacer (ITS) region of Oenanthe accessions collected from a wide geographical area in China and its neighboring countries. For comparison, ITS sequences in GenBank for almost all currently reported species of Oenanthe were also included in our analyses. Both phylogenetic tree construction methods (Bayesian inference and maximum likelihood) revealed that the accessions tended to cluster into two groups, which were closely related to O. mildbraedii and O. sarmentosa. However, these two species have never been recorded in China or its neighboring countries. Therefore, it seems probable that in our sampled locations, Oenanthe accessions have been given an incorrect name, such as O. javanica. Future studies should carefully check the morphological characteristics of other Oenanthe species and sequence their ITS regions in order to clarify the taxonomic status of the genus.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Evaluation of the taxonomic status of water dropwort (Oenanthe, Apiaceae) accessions from East Asia based on nuclear rDNA internal transcribed spacer sequences

Long

et al. 2016

Genet. Mol. Res.

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“…Similar to the most traditional identifying of higher level taxa within Apiaceae, molecular systematic studies have revealed that the genus Pimpinella is polyphyletic, and taxonomic delimitation of the genus has not yet been resolved (Downie and Katz-Downie, 1999;Zhou et al, 2008Zhou et al, , 2009Downie et al, 2010). A recent molecular phylogenetic study of Pimpinella clearly showed it to be a non-monophyletic taxon Wang et al, 2014).…”

Section: Introductionmentioning

confidence: 97%

Phylogeny of the Southwest Asian Pimpinella and related genera based on nuclear and plastid sequences

2016

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ABSTRACT. Pimpinella L. is a large genus and arguably one of the most complex genera in the family Apiaceae. In this study, the infrageneric relationship between Southwest Asian Pimpinella species and their generic allies in the tribe Pimpinelleae Spreng were investigated using sequence data from the cpDNA (chloroplast DNA) rps16 exon and rpL16 intron and nuclear ribosomal DNA internal transcribed spacer regions. In total, 185 accessions representing 52 species of Pimpinella, 8 species of Aegopodium, and the monotypic Opsicarpium Mozaff. were analyzed using maximum parsimony and Bayesian methods. In our phylogenetic study, Pimpinella and Opsicarpium were considered together as a monophyletic group within the tribe Pimpinelleae. As a result, Opsicarpium insignis Mozaff has been formally transferred to Pimpinella. Our results indicate that the genera Pimpinella and Reutera Boiss formed a monophyletic group and also supported merging the

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“…Based on our previous work (Tan et al 2015), P. rhomboidea var. tenuiloba was treated as a synonym of Melanosciadium bipinnatum (Shan and Pu) Pimenov & Kljuykov, and has been corroborated to nest in Angelica sensu lato within Selineae (Zhou et al 2009, Liao et al 2013, Wang et al 2014. Here, we assembled the complete chloroplast genome of P. rhomboidea var.…”

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confidence: 97%

The complete chloroplast genome of Pimpinella rhomboidea var. tenuiloba

Tan

2018

Mitochondrial DNA Part B

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Pimpinella rhomboidea var. tenuiloba is an endemic species in China. The complete chloroplast genome sequence of P. rhomboidea var. tenuiloba was generated by de novo assembly using whole genome next generation sequencing. The genome was 146,655 bp in length, composed of four distinct regions such as large single copy (LSC) region of 94,684 bp, small single copy (SSC) region 17,537 bp and a pair of inverted repeat regions of 17,217 bp. The genome annotation predicted a total of 113 genes, including 80 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that P. rhomboidea var. tenuiloba has close relationship with genus Angelica .

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Towards a more robust molecular phylogeny of Chinese Apiaceae subfamily Apioideae: Additional evidence from nrDNA ITS and cpDNA intron (rpl16 and rps16) sequences

Cited by 97 publications

References 52 publications

Evaluation of the taxonomic status of water dropwort (Oenanthe, Apiaceae) accessions from East Asia based on nuclear rDNA internal transcribed spacer sequences

Evaluation of the taxonomic status of water dropwort (Oenanthe, Apiaceae) accessions from East Asia based on nuclear rDNA internal transcribed spacer sequences

Phylogeny of the Southwest Asian Pimpinella and related genera based on nuclear and plastid sequences

The complete chloroplast genome of Pimpinella rhomboidea var. tenuiloba

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