Research Article |
Corresponding author: Meiliang Zhou ( zhoumeiliang@caas.cn ) Corresponding author: Bo Li ( hanbolijx@163.com ) Academic editor: Alexander Sukhorukov
© 2023 Daozhang Min, Wei Shi, Mohammad Mehdi Dehshiri, Yuting Gou, Wei Li, Kaixuan Zhang, Meiliang Zhou, Bo Li.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Min D, Shi W, Dehshiri MM, Gou Y, Li W, Zhang K, Zhou M, Li B (2023) The molecular phylogenetic position of Harpagocarpus (Polygonaceae) sheds new light on the infrageneric classification of Fagopyrum. PhytoKeys 220: 109-126. https://doi.org/10.3897/phytokeys.220.97667
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In the context of the molecular phylogeny of Polygonaceae, the phylogenetic positions of most genera and their relationships have been resolved. However, the monotypic genus Harpagocarpus has never been included in any published molecular phylogenetic studies. In the present study, we adopt a two-step approach to confirm the phylogenetic placement of Harpagocarpus using two datasets: (1) a concatenated dataset of three chloroplast DNA (cpDNA) regions (matK, rbcL and trnL-F) for Polygonaceae and (2) a combined cpDNA dataset of five sequences (accD, matK, psbA-trnH, rbcL and trnL-F) for Fagopyrum. Our analyses confirm the previous hypothesis based on morphological, anatomical and palynological investigations that Harpagocarpus is congeneric with Fagopyrum and further reveal that H. snowdenii (≡ F. snowdenii) is sister to the woody buckwheat F. tibeticum. Within Fagopyrum, three highly supported clades were discovered and the first sectional classification was proposed to accommodate them: sect. Fagopyrum comprises the two domesticated common buckwheat (F. esculentum and F. tataricum) and their wild relatives (F. esculentum subsp. ancestrale, F. homotropicum and F. dibotrys) which are characterised by having large corymbose inflorescences and achenes greatly exceeding the perianth; sect. Tibeticum, including F. snowdenii and F. tibeticum, is characterised by the achene having appurtenances along the ribs, greatly exceeding the perianth and the perianth accrescent in fruit; sect. Urophyllum contains all other species of which the achenes were completely enclosed in the perianth. This study is very helpful to understand the phylogeny of the Fagopyrum and sheds light on the future study of taxonomy, biogeography, diversification and character evolution of the genus.
buckwheat, cpDNA, Fagopyreae, morphology, new section
Polygonaceae, a family of the flowering plants known as the buckwheat family, can be easily distinguished by its ocrea, orthotropous ovules, trigonal (typically) achenes and quincuncial aestivation (
The genus Harpagocarpus was established on the basis of its distinct fruit morphology (
In the protologue, Harpagocarpus was morphologically compared to Polygonum L. and Fagopyrum Mill., but it was thought to resemble the latter considerably more on its broad cotyledons, large and obviously exerted fruits and the shape and venation of the leaves (
In the present study, we obtained a few precious pieces of leaf materials of H. snowdenii from the specimen Marshall A.R. WK 374 (detailed information available from: http://legacy.tropicos.org/image/100427626), which provided us an invaluable opportunity to investigate the phylogenetic position of Harpagocarpus, based on additional molecular data. We adopted two steps of phylogenetic analyses to infer the generic and specific affinities of H. snowdenii. Firstly, we used three chloroplast DNA (cpDNA) markers (matK, rbcL and trnL-F) to present the backbone phylogeny of Polygonaceae and affirmed the position of Harpagocarpus in Fagopyrum. Subsequently, based on five cpDNA regions (accD, matK, psbA-trnH, rbcL and trnL-F), we further reconstructed the phylogeny of Fagopyrum and clarified the accurate specific relationships of F. snowdenii within Fagopyrum.
We employed matK, rbcL and trnL-F sequences, which have been extensively used in previous studies (e.g.
As the analyses of the D1 dataset demonstrated that Harpagocarpus is nested within Fagopyrum, we designed another dataset (D2) using five cpDNA regions (accD, matK, psbA-trnH, rbcL and trnL-F), with an expanded sampling of Fagopyrum aiming for a more accurate placement of H. snowdenii (= F. snowdenii). The ingroups of D2 dataset included 33 taxa of Fagopyrum covering most of the recognised species in the genus and the outgroup taxon was set as Pteroxygonum giraldii Damm. et Diels according to the results presented in
Total genomic DNA was extracted from fresh or silica gel dried leaves following the manufacturer’s specifications of the DNEasy Plant Mini Kit (Qiagen, Valencia, CA, USA). After extraction, the DNA was resuspended in double-distilled water and kept at -40 °C for polymerase chain reaction (PCR). The PCR reactions and amplification protocol followed
Sequencher version 5.4.6 (
Phylogenetic analyses were conducted, based on the combined cpDNA dataset D1 and D2. The cpDNA regions were supposedly safe to be combined in phylogenetic analyses (
ML and BI analyses were carried out using RAxML-HPC2 version 8.2.9 (
The concatenated cpDNA dataset D1 has 78 aligned sequences and comprises 4167 characters (1585 bp for matK, 1432 bp for rbcL and 1150 bp trnL-F, respectively), of which 1756 are variable (42.14%) and 1181 are parsimony-informative (28.34%). The ML and BI analyses, based on dataset D1, generated nearly identical topologies (Suppl. material
Maximum Likelihood phylogram of Polygonaceae as inferred from analysis of the combined cpDNA dataset of matK, rbcL and trnL-F. Support values ≥ 50% BS or 0.90 PP are displayed above the branches, respectively. The tribal classification of Eriogonoideae followed
The combined dataset D2 has 31 aligned sequences and comprises 6378 characters (1425 bp for accD, 2278 bp for matK, 513 bp for psbA-trnH, 1278 bp for rbcL and 883 bp for trnL-F), of which 735 are variable (11.52%) and 428 are parsimony-informative (6.71%). ML and BI trees generated from the D2 dataset yielded similar topologies (Suppl. material
Maximum Likelihood phylogram of Fagopyrum as inferred from analysis of the combined cpDNA dataset of accD, matK, psbA-trnH, rbcL and trnL-F. Support values ≥ 50% BS or 0.90 PP are displayed above the branches, respectively. The two black boxes covered the cymosum group and the urophyllum group as defined in
After 20 years of molecular reconstruction of Polygonaceae (e.g.
Morphologically, H. snowdenii has sagittate to ovate-triangular leaf blades, seven palmate veins, large and clearly exerted fruits from the persistent tepals and broad cotyledons, which are very similar to those traits presented in Fagopyrum species (
It is noteworthy to point out that our molecular analyses not only supported the amalgamation of Harpagocarpus with Fagopyrum, but also clarified the accurate specific relationships of F. snowdenii within Fagopyrum, which was stably supported to be a sister of F. tibeticum using cpDNA sequences (Figs
The inclusion of F. tibeticum in Fagopyrum has updated our knowledge of morphology in the genus, but now, the sister relationships between F. snowdenii and F. tibeticum, revealed in our molecular analyses, would not only further expand the morphological variation of Fagopyrum, but also shed light on the thinking of the biogeographical origin of the genus, because F. snowdenii is the only species of Fagopyrum distributed in Africa, while all other congeneric taxa occur mainly in East Asia.
Fagopyrum is a small genus comprised of ca. 25 species according to the most updated classification (
Within Fagopyrum, two groups have been recognised in classical taxonomy, based on the morphology of inflorescence and the achene size: one group was mainly represented by F. cymosum (Trevir.) Meisn. (= F. dibotrys), F. esculentum and F. tataricum and characterised by having corymbose inflorescences with many branching and dense flowers and the achene greatly exceeding the perianth, while the other group is composed of other species (including F. urophyllum (Bureau & Franch.) H.Gross) having raceme-like inflorescences with sparse flowers and the achene completely enclosed in perianth (
In our present analyses, the above-mentioned two clades were recovered too, but the third clade, formed by F. snowdenii and F. tibeticum, was discovered, which is sister to the ‘Urophyllum’ clade (Fig.
Fagopyrum Mill., Gard. Dict. Abr., ed. 4, 495. 1754 [≡ Polygonum sect. Fagopyrum (Mill.) Meisn., Monogr. Polyg. 43, 61. 1826.] – Type: Fagopyrum esculentum Moench (≡ Polygonum fagopyrum L.).
= Harpagocarpus Hutch. & Dandy, Bull. Misc. Inform. Kew. 364. 1926 – Type: Harpagocarpus snowdenii Hutch. & Dandy [≡ Fagopyrum snowdenii (Hutch. & Dandy) S.P.Hong].
= Parapteropyrum A.J.Li, Acta Phytotax. Sin. 19: 330. 1981 – Type: Parapteropyrum tibeticum A.J.Li [≡ Fagopyrum tibeticum (A.J.Li) Adr.Sanchez & Jan.Burke].
Fagopyrum esculentum Moench. (≡ Polygonum fagopyrum L.).
This section is characterised by having large corymbose inflorescences with many branches and dense flowers and large achenes greatly exceeding the persistent perianth.
F. dibotrys, F. esculentum subsp. esculentum, F. esculentum subsp. ancestrale, F. homotropicum and F. tataricum.
Bhutan, India, Myanmar, Nepal, Pakistan, Thailand and Vietnam of southern and south-eastern Asia and southern and south-western China.
Fagopyrum tibeticum (A.J.Li) Adr. Sanchez & Jan. Burke (≡ Parapteropyrum tibeticum A.J.Li).
The new section is characterised by having raceme-like inflorescences with sparse flowers, large achenes with appurtenances (wings or setae) along the ribs and greatly exceeding the perianth and persistent perianth accrescent in fruit.
F. snowdenii and F. tibeticum.
Cameroon, Kenya, Rwanda, Tanzania and Uganda of Africa (F. snowdenii) and Tibet of south-western China (F. tibeticum).
Fagopyrum urophyllum (Bureau & Franch.) H.Gross (≡ Polygonum urophyllum Bureau & Franch.).
This new section is characterised by having raceme-like, spicate, capitate or paniculate inflorescences with mostly sparse or rarely dense flowers and achenes completely enclosed in the persistent perianth.
F. callianthum Ohnishi, F. capillatum Ohnishi, F. caudatum (Sam.) A.J.Li, F. crispatifolium J.L.Liu, F. densovillosum J.L.Liu, F. gilesii (Hemsl.) Hedberg, F. gracilipedoides Ohsako & Ohnishi, F. gracilipes (Hemsl.) Dammer, F. jinshaense Ohsako & Ohnishi, F. leptopodum var. leptopodum, F. leptopodum var. grossii (Lévl.) Lauener & D.K.Ferguson, F. lineare (Sam.) Haraldson, F. longistylum M.L.Zhou & Y.Tang, F. longzhoushanense J.R.Shao, F. luojishanense J.R.Shao, F. macrocarpum Ohsako & Ohnishi, F. pleioramosum Ohnishi, F. pugense Y.Tang, F. qiangcai D.Q.Bai, F. rubifolium Ohsako & Ohnishi, F. statice H.Gross, F. urophyllum (Bureau & Franch.) H.Gross, F. wenchuanense J.R.Shao.
Guizhou, Sichuan and Yunnan Provinces of southwest China.
1 | Achenes completely enclosed in the perianth | sect. Urophyllum |
– | Achenes greatly exceeding the perianth | 2 |
2 | Raceme-like inflorescences with sparse flowers and achenes having appurtenances (wings or setae) along the ribs | sect. Tibeticum |
– | Corymbose inflorescences with dense flowers and achenes without appurtenances | sect. Fagopyrum |
The authors are grateful to administrators of the Missouri Botanical Garden Herbarium (MO) for providing the specimen sample of Harpagocarpus snowdenii, to Dr. Tanja M. Schuster in the Naturhistorisches Museum Wien for sharing molecular data of Polygonaceae and to Vincent Droissart in the Institut de Recherche pour le Développement (IRD, France) for providing field photos of H. snowdenii. This study was jointly supported by the National Key R&D Program of China (2021YFD1200100/2021YFD1200105) and the National Natural Science Foundation of China (32160047, 31900181, 32161143005).
Supplementary information
Data type: tables, figures (Pdf file)
Explanation note: Taxa, GenBank accession numbers of DNA sequences with their vouchers or source of publication used in the molecualr dataset and phtlogenetic trees generated from BI and ML analyses.