Phylogeny of Allium L. subgenus Anguinum (G. Don. ex W.D.J. Koch) N. Friesen (Amaryllidaceae)

Herden, Tobias; Hanelt, Peter; Friesen, Nikolai

doi:10.1016/j.ympev.2015.11.004

Cited by 67 publications

(57 citation statements)

References 49 publications

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“…& Godr.] known to represent one of the basal clades of Allium (Friesen et al 2006, Nguyen et al 2008, Li et al 2010, Herden et al 2016 was included as the outgroup. Sequencing of one or other markers in some important species was not successful (e.g.…”

Section: Taxon Samplingmentioning

confidence: 99%

“…Phylogenetic analyses were performed using three DNA fragments, known to be useful for studying the phylogeny of Allium (Li et al 2010, Herden et al 2016. The internal transcribed spacer (ITS) region of the nuclear ribosomal cistron (consisting of ITS1, the intervening 5.8S gene and ITS2), the plastid intron (rps16) and trnL-F intergenic spacer.…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

“…1, 2. There have been several molecular phylogenetic studies in Allium (Dubouzet and Shinoda 1998, 1999, Friesen et al 2006, Gurushidze et al 2007, Nguyen et al 2008, Hirschegger et al 2010, Li et al 2010, Choi et al 2012, Wheeler et al 2013, İpek et al 2014, Herden et al 2016, that addressed the infrageneric classification and the relationships in certain species groups. Based on a large-scale molecular systematic study, Allium has been classified into three evolutionary lines, 15 subgenera and 72 sections including A. subg.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences

Veiskarami

Khodayari

Heubl³

et al. 2019

Nordic Journal of Botany

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Allium is a particularly species rich (more than 800 species) and economically important genus, with numerous taxonomic problems at all levels of classification. In this study, we try to uncover the phylogenetic relationships of the common leek Allium ampeloprasum based on selected samples of this species and its putative relatives in A. sect. Allium from Iran. The silica‐dried leaf samples of 56 accessions representing 23 species of Allium were sequenced; 53 sequences of nrDNA ITS, 35 sequences of plastid rps16 and 52 sequences of trnL–F were generated and additional accessions were extracted from GenBank in order to cover all recognized main lineages in the genus. Maximum Parsimony and Bayesian Inference generated similar trees, but the placement of A. ampeloprasum and its relatives differed slightly between the nuclear and the plastid phylogenies. In the nrITS tree, A. ampeloprasum is retrieved as a highly supported clade with A. iranicum, while in the combined plastid tree A. ampeloprasum formed a highly supported clade with A. vineale. This supports the hypothesis of a possible hybrid origin of A. ampeloprasum. Allium iranicum formed a clade in the plastid tree, but was resolved as paraphyletic in the nrITS tree, probably due to presence of multiple non‐concerted copies of nrITS. Close relationships are suggested between the following species: A. aznavense and A. wendelboi with A. talyschense, A. erubescens and A. rotundum with A. scorodoprasum and A. abbasii with A. phanerantherum.

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Section: Taxon Samplingmentioning

confidence: 99%

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences

Veiskarami

Khodayari

Heubl³

et al. 2019

Nordic Journal of Botany

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“…ex W.D.J. Koch) (Herden et al 2016;Li et al 2016), and mainly concentrates on the Qinghai-Tibet Plateau and its adjacent regions. Allium prattii grows at an elevation from 2000 to 4900 m and adapts to very diverse habitats.…”

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confidence: 99%

Characterization of the complete chloroplast genome of Allium prattii

Jin

Xie

Zhou

et al. 2018

Mitochondrial DNA Part B

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The genus Allium is one of the world’s largest monocot genera. However, few reports on the complete chloroplast genome of Allium plants are reported. In this study, we reported the complete chloroplast genome of Allium prattii . The genome sequence was 154,482 bp in length, including a large single copy region (LSC) of 83,392 bp and a small single copy region (SSC) of 18,064 bp, which were separated by two inverted repeat (IR) regions of 26,513 bp. The complete chloroplast genome contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with several reported chloroplast genomes showed that A. prattii has a close genetic relationship with A. cepa and A. sativum .

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“…As one of the largest genera of the petaloid monocotyledons, Allium (Amaryllidaceae) comprises more than 920 species [1] and includes several economically important crops that are cultivated for consumption or medicinal uses, such as garlic ( A. sativum ), welsh onion ( A. fistulosum ), leek ( A. porrum ), Chinese chives ( A. tuberosum ), onion ( A. cepa ), Chinese jiaotou ( A. chinense ), and shallot ( A. ascalonicum ). Varied leaf shapes can be observed among Allium species, including flat, columnar, solid, and fistular morphologies.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium

et al. 2017

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BackgroundFistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported.ResultsIn this study, we characterized the leaf transcriptomes of nine Allium species, including six fistular- and three solid-leaved species. In addition, we identified orthologous genes and estimated their Ka and Ks values, in order to ascertain their selective pattern. Phylogenetic analysis based on the transcriptomes revealed that A. tuberosum was the most ancestral among the nine species, and analysis of orthologous genes between A. tuberosum and the other eight species indicated that 149 genes were subject to positive selection; whereas >3000 had undergone purifying selection in each species.ConclusionsWe found that many genes that are potentially related to programmed cell death either exhibited rapid diversification in fistular-leaved species, or were conserved in solid-leaved species in evolutionary history. These genes potentially involved in programmed cell death might play important roles in the formation of fistular leaf cavities in Allium, and the differing selection patterns in fistular- and solid-leaved species may be responsible for the evolution of fistular leaves.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3474-8) contains supplementary material, which is available to authorized users.

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Phylogeny of Allium L. subgenus Anguinum (G. Don. ex W.D.J. Koch) N. Friesen (Amaryllidaceae)

Cited by 67 publications

References 49 publications

Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences

Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences

Characterization of the complete chloroplast genome of Allium prattii

Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium

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