Two distinct groups of natural populations of Fagopyrum urophyllum (Bur. et Franch.) Gross revealed by the nucleotide sequence of a noncoding region in chloroplast DNA

Kawasaki, M.; Ohnishi, Ohmi

doi:10.1266/ggs.81.323

Cited by 9 publications

(8 citation statements)

References 16 publications

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“…Moreover, detecting the highly informative and variable genome regions can be important for diagnostic genetic marker development and DNA barcoding [ 27 ]. In Fagopyrum, plastome regions rbcL , accD , trnK (UUU) , trnC (GCA) - rpoB , matK , trnH-psbA , trnL , psbE-psbL, and ndhA intron have been widely used to construct the phylogeny at the species level, which is often supplemented with nrDNA ITS and/or nuclear gene sequences ( FLO/LFY , AG ) [ 12 , 15 – 17 , 19 , 49 , 50 ]. In general, there is a greater variation in intergenic regions than in gene regions, as has also been observed in this study (Table S 6 ).…”

Section: Discussionmentioning

confidence: 99%

Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa

Liu

Wang

et al. 2022

BMC Plant Biol

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Background Fagopyrum (Polygonaceae) is a small plant lineage comprised of more than fifteen economically and medicinally important species. However, the phylogenetic relationships of the genus are not well explored, and the characteristics of Fagopyrum chloroplast genomes (plastomes) remain poorly understood so far. It restricts the comprehension of species diversity in Fagopyrum. Therefore, a comparative plastome analysis and comprehensive phylogenomic analyses are required to reveal the taxonomic relationship among species of Fagopyrum. Results In the current study, 12 plastomes were sequenced and assembled from eight species and two varieties of Fagopyrum. In the comparative analysis and phylogenetic analysis, eight previously published plastomes of Fagopyrum were also included. A total of 49 plastomes of other genera in Polygonaceae were retrieved from GenBank and used for comparative analysis with Fagopyrum. The variation of the Fagopyrum plastomes is mainly reflected in the size and boundaries of inverted repeat/single copy (IR/SC) regions. Fagopyrum is a relatively basal taxon in the phylogenomic framework of Polygonaceae comprising a relatively smaller plastome size (158,768–159,985 bp) than another genus of Polygonaceae (158,851–170,232 bp). A few genera of Polygonaceae have nested distribution of the IR/SC boundary variations. Although most species of Fagopyrum show the same IRb/SC boundary with species of Polygonaceae, only a few species show different IRa/SC boundaries. The phylogenomic analyses of Fagopyrum supported the cymosum and urophyllum groups and resolved the systematic position of subclades within the urophyllum group. Moreover, the repeat sequence types and numbers were found different between groups of Fagopyrum. The plastome sequence identity showed significant differences between intra-group and inter-group. Conclusions The deletions of intergenic regions cause a short length of Fagopyrum plastomes, which may be the main reason for plastome size diversity in Polygonaceae species. The phylogenomic reconstruction combined with the characteristics comparison of plastomes supports grouping within Fagopyrum. The outcome of these genome resources may facilitate the taxonomy, germplasm resources identification as well as plant breeding of Fagopyrum.

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Section: Discussionmentioning

confidence: 99%

Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa

Liu

Wang

et al. 2022

BMC Plant Biol

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“…The multi-base indels detected within trnH-psbA were excluded from the data analyses. However, one or more of these may yet prove useful in future examinations of the phylogeny of the C. annuum complex, in studying diversity within this genus at other levels [29], or for the characterization of the new species of Capsicum that have been recently described [30,31].…”

Section: Discussionmentioning

confidence: 99%

DNA Barcoding in a Crop Genebank: The Capsicum annuum Species Complex

Jarret¹

2008

TOBIOJ

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Variability within eight cpDNA introns including trnS trnCrpoB, rps16 and matK, and the nuclear waxy introns was examined in seven species of Capsicum (C. annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense and C. rhomboideum) in order to evaluate the feasibility of utilizing these loci for DNA barcoding within the C. annuum complex. Numerous insertions/deletions (indels) and substitutions were detected in all cpDNA introns. However, none was sufficient to differentiate the individual members of the C. annuum complex (C. annuum, C. chinense and C. frutescens). Variation within trnL-trnT, trnF-trnL and trnH-psbA enabled the differentiation of the complex from the other taxa examined. In contrast, single base indels and substitutions within the waxy introns permitted the differentiation of all taxa within the plant materials examined. The use of trnH-psbA or trnL-trnT, and the waxy introns is proposed for barcoding members of the C. annuum complex.

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“…Systematic studies have shown that a perennial species F. urophyllum is comprised of two subgroups highly differentiated from each other (Ohsako and Ohnishi 2000, Yasui and Ohnishi 1998a, 1998b). Kawasaki and Ohnishi (2006) investigated cpDNA variation within F. urophyllum using a total of 19 accessions covering the entire distribution range of the species. They confirmed that the accessions are separated into two phylogeographic groups, the Kunming and the Dali groups.…”

Section: Differentiation Within Speciesmentioning

confidence: 99%

Classification and systematics of the <i>Fagopyrum</i> species

Ohsako

2020

Breed. Sci.

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Fagopyrum (Polygonaceae) is a small genus including less than 30 species, mostly endemic to southern China. The genus includes two cultivated species, common buckwheat F. esculentum and Tartary buckwheat F. tataricum. Fagopyrum is clearly distinguished from other genus in Polygonaceae by the central position of embryo in achene. The genus is divided into two major groups, namely the cymosum group and the urophyllum group, based on morphological characters and molecular systematics. In the last three decades the number of species in the genus has doubled by the discovery of new species by Japanese and Chinese groups. Most of them are revealed to be included in the urophyllum group based on morphological and molecular genetic analyses. Molecular systematic surveys have also detected inappropriate treatment of some non-Fagopyrum species as new species or combination in the genus.

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Two distinct groups of natural populations of Fagopyrum urophyllum (Bur. et Franch.) Gross revealed by the nucleotide sequence of a noncoding region in chloroplast DNA

Cited by 9 publications

References 16 publications

Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa

Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa

DNA Barcoding in a Crop Genebank: The Capsicum annuum Species Complex

Classification and systematics of the <i>Fagopyrum</i> species

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