Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus

Viljoen, Erika; Odeny, Damaris Achieng; Coetzee, Martin Petrus Albertus; Berger, David Kenneth; Rees, D. J. G.

doi:10.1007/s00239-018-9837-9

Cited by 32 publications

(36 citation statements)

References 77 publications

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“…In the current study, we aligned the chloroplast matK marker sequences (434 bp) from 272 VA and 27 WA accessions, and found 96.8% constant and 3.2% variable sites. The length of the aligned sequence was much shorter than in previous studies on amaranth genetic diversity that used the matK marker (Viljoen et al 2018, Waselkov et al 2018; however, the percentage of parsimoniously informative sites in our study was higher than that in Viljoen et al (2018): about 2.5% vs. 2.15%. A phylogenetic tree was constructed by combining these sequences with those of 45 GRIN…”

Section: Discussioncontrasting

confidence: 72%

“…The interrelationships among the GRIN accessions, which include leafy amaranths (A. tricolor, A. blitum, A. viridis, and A. graecizans), weed amaranths (A. spinosus, A. retroflexus, and A. powellii), and A. dubius in our dendrogram were highly similar to those in the dendrogram in Fig. 4 in Viljoen et al (2018), which was based on whole chloroplast genome sequences. Most WA accessions of A. tricolor were assigned to the same group as the GRIN A. tricolor accessions, except that WA008 was in the same clade in our analysis as the A. blitum group, which was also determined in another study (our unpublished data).…”

Section: Analysis Of Genetic Diversity and Population Structure Of Thsupporting

confidence: 68%

“…However, Amaranthus has been widely considered as a "difficult" genus in terms of taxonomy and analysis of genetic variance using morphology alone because of the overall similarity among many species, small diagnostic parts, and the presence of intermediate forms (Achigan-Dako et al 2014, Assad et al 2017, Costea and Demason 2001. To overcome these difficulties, recent analyses of the genetic diversity of amaranths used chloroplast and nuclear DNA sequences (Stetter and Schmid 2017, Viljoen et al 2018, Waselkov et al 2018.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…The alignment sequences were used to produce a dendrogram with the Maximum Likelihood Algorithm in MEGA7. As references, we also used the matK sequences of 45 GRIN (Germplasm Resources Information Network) amaranth accessions (known species) deposited in GenBank (KX079543-KX079587; Viljoen et al 2018).…”

Section: Phylogenetic Analysis Of the Amaranth Collection By Using Thmentioning

confidence: 99%

“…Interestingly, Vietnamese accessions are genetically closer to the East Asian accessions (F ST = 0.078; Nei's distance = 0.042) than to the Southeast Asian accessions (F ST = 0.116; Nei's distance = 0.093), likely because all East Asian accessions originated from China (a neighbor of Vietnam), whereas no Southeast Asian accessions originated from two other neighbors, Laos and Cambodia. Another cause could be the dispersal events of amaranth from East Asia (China) to Vietnam, partly owing to the migrations of ancestors of amaranth accessions from the study of Viljoen et al (2018). The interrelationships among the GRIN accessions, which include leafy amaranths (A. tricolor, A. blitum, A. viridis, and A. graecizans), weed amaranths (A. spinosus, A. retroflexus, and A. powellii), and A. dubius in our dendrogram were highly similar to those in the dendrogram in Fig.…”

Section: Analysis Of Genetic Diversity and Population Structure Of Thmentioning

confidence: 99%

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Genetic diversity of leafy amaranth (<i>Amaranthus tricolor</i> L.) resources in Vietnam

Nguyen

Tran

et al. 2019

Breed. Sci.

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Leafy amaranths, which are consumed as traditional food in Asia and Africa, are now considered among the most promising vegetables. In Vietnam, leafy amaranths, particularly Amaranthus tricolor L., are important summer vegetables due to their excellent nutritional values and high tolerance to biotic and abiotic stresses. However, this species has not been subjected to systematic breeding. Here we describe species identification and evaluation of the genetic diversity of Vietnamese amaranth collection by using matK and simple sequence repeats (SSR) markers. Our phylogenetic analysis based on the matK marker classified the species of 68% of the accessions, of which 120 belonged to A. tricolor. We developed 21 SSR markers, which amplified a total of 153 alleles in 294 A. tricolor accessions originating from Vietnam and overseas, with a mean allelic richness of 7.29 per marker, observed heterozygosity of 0.14, expected heterozygosity of 0.38, and polymorphic information content of 0.35. The STRUCTURE and F ST analysis indicated a positive relationship between geographic distance and genetic differentiation among most of the overseas groups and the Vietnamese col lection, but not among geographic groups within the Vietnamese collection. Vietnamese amaranths could be divided into two major types, one common in East Asia and the other one unique to Vietnam.

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Section: Discussioncontrasting

confidence: 72%

Section: Analysis Of Genetic Diversity and Population Structure Of Thsupporting

confidence: 68%

Section: Phylogenetic Analysismentioning

confidence: 99%

Section: Phylogenetic Analysis Of the Amaranth Collection By Using Thmentioning

confidence: 99%

Section: Analysis Of Genetic Diversity and Population Structure Of Thmentioning

confidence: 99%

See 3 more Smart Citations

Genetic diversity of leafy amaranth (<i>Amaranthus tricolor</i> L.) resources in Vietnam

Nguyen

Tran

et al. 2019

Breed. Sci.

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Comparative study on chloroplast genome of Tamarix species

Liu,

Ding,

Liang

et al. 2024

Ecology and Evolution

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Tamaricaceae comprises about 120 species and has a long evolutionary history, Tamarix Linn accounts for approximately 75% of the total species in this family. It is the most widely distributed and diverse genus in the family. They have important ecological significance for transforming deserts and improving climate conditions. However, Tamarix is the most poorly classified genera among flowering plants owing to its large variability and high susceptibility to interspecific hybridization. In this study, the complete chloroplast genomes of three Tamarix species and one draft chloroplast genome were obtained in this study. Combined with eight chloroplast genomes deposited in GenBank, complete chloroplast sequences of 12 Tamarix species were used for further analysis. There are 176 non‐SSR‐related indels and 681 non‐indel‐related SSRs in the 12 Tamarix chloroplast genomes. The mononucleotide SSRs are the most prevalent among all types of SSRs. The mVISTA results indicate high sequence similarities across the chloroplast genome, suggesting that the chloroplast genomes are highly conserved, except for sample Tamarix androssowii (ENC850343). The IR regions and the coding regions are more conserved than the single‐copy and noncoding regions. The trnF‐ndhJ, ndhC‐trnM‐CAU, ycf1, and trnL‐UAG‐ndhF regions are the most variable and have higher variability than those of the universal DNA markers. Finally, the first phylogenetic tree of Tamaricaceae was constructed which confirmed the monophyly of Tamarix in Tamaricaceae. The first phylogenetic tree of Tamarix was based on the complete chloroplast genome to date, the changes in branch length and support rate can potentially help us clarify the phylogenetic relationships of Tamarix. All the obtained genetic resources will facilitate future studies in population genetics, species identification, and conservation biology of Tamarix.

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Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision

Huang

Chen

Hummer

et al. 2023

TAXON

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Rubus (Rosaceae), one of the most complicated angiosperm genera, contains about 863 species, and is notorious for its taxonomic difficulty. The most recent (1910–1914) global taxonomic treatment of the genus was conducted by Focke, who defined 12 subgenera. Phylogenetic results over the past 25 years suggest that Focke's subdivisions of Rubus are not monophyletic, and large‐scale taxonomic revisions are necessary. Our objective was to provide a comprehensive phylogenetic analysis of the genus based on an integrative evidence approach. Morphological characters, obtained from our own investigation of living plants and examination of herbarium specimens are combined with chloroplast genomic data. Our dataset comprised 196 accessions representing 145 Rubus species (including cultivars and hybrids) and all of Focke's subgenera, including 60 endemic Chinese species. Maximum likelihood analyses inferred phylogenetic relationships. Our analyses concur with previous molecular studies, but with modifications. Our data strongly support the reclassification of several subgenera within Rubus. Our molecular analyses agree with others that only R. subg. Anoplobatus forms a monophyletic group. Other subgenera are para‐ or polyphyletic. We suggest a revised subgeneric framework to accommodate monophyletic groups. Character evolution is reconstructed, and diagnostic morphological characters for different clades are identified and discussed. Based on morphological and molecular evidence, we propose a new classification system with 10 subgenera: R. subg. Anoplobatus, R. subg. Batothamnus, R. subg. Chamaerubus, R. subg. Cylactis, R. subg. Dalibarda, R. subg. Idaeobatus, R. subg. Lineati, R. subg. Malachobatus, R. subg. Melanobatus, and R. subg. Rubus. The revised infrageneric nomenclature inferred from our analyses is provided along with synonymy and type citations. Our new taxonomic backbone is the first systematic and complete global revision of Rubus since Focke's treatment. It offers new insights into deep phylogenetic relationships of Rubus and has important theoretical and practical significance for the development and utilization of these important agronomic crops.

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Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus

Cited by 32 publications

References 77 publications

Genetic diversity of leafy amaranth (<i>Amaranthus tricolor</i> L.) resources in Vietnam

Genetic diversity of leafy amaranth (<i>Amaranthus tricolor</i> L.) resources in Vietnam

Comparative study on chloroplast genome of Tamarix species

Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision

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