The proximity of Hydrocotyle umbellata L. with araliaceae as evident from plastome and phylotranscriptomic analyses

1 Introduction

The order Apiales [(Nakai, Hisi-Shokubutsu 58 (1930)] which includes seven families {[i.e. 1. Apiaceae [(Lindl., Intr. Nat. Syst. Bot. (ed. 2) 21, (1836)], 2. Araliaceae [(Juss., Gen. Pl. 217, (1789)], 3. Griseliniaceae [(Akht., Sist. Magnol. 209 (1987)], 4. Myodocarpaceae [(Doweld, Prosyllab. Tracheophyt. Lii (2001)], 5. Pennantiaceae [(J. Agardh, Theoria Syst. Pl. 301 (1858)], 6. Pittosporaceae [(R. Br., Voy. Terra Austral. 2: 542 (1814)], and 7. Torricelliaceae [(H.H. Hu, Bull. Fan Mem. Inst. Biol., Bot. 5: 311, 1934)]} have been placed within the Asterid group of Eudicots as circumscribed by group Campanulids (APG IV, 2016). The family ‘Apiaceae Lindley / Umbelliferae Jussieu’ (with approx. c. 434 genera and c. 3700 species) and Araliaceae Jussieu (with approx. c. 43 genera, c.1450 species; APG IV, 2016; https://www.mobot.org/mobot/research/apweb/) resemble each other in the structure of their gynoecia, and were placed in the order Ariales, superorder Araliiflorae (Dahlgren, 1980), and are closely related (Plunkett et al., 2004). The family Araliaceae with the subfamily 1. Hydrocotyloideae Link, 2. Harmsiopanax Harms and 3. Aralioideae Eaton accepted as a monophyletic branch within the Apiales (Kim et al., 2017), an order within the Asterids (APG IV, 2016). Of these, the genus Hydrocotyle L. which comprises c.130 species (Hiroe, 1979; Pimenov and Leonov, 1993; Du and Ren, 2010; APG IV, 2016, https://www.mobot.org/mobot/research/apweb/) from Hydrocotyloideae Link of the family Apiaceae transferred to the family Araliaceae based on molecular phylogenetic studies (Lowry et al., 2004; Plunkett et al., 2004). The recent massive development in the next-generation sequencing platforms and bioinformatics tools including cloud-based bioinformatic analyses has proven extremely useful in understanding the deeper-level phylogenetic relationships of angiosperms (Ali, 2021). The present study evaluates the proximity of Hydrocotyle umbellata with Araliaceae based on plastome and phylotranscriptomic analyses.

2 Materials and methods

3 Results

3.1

3.1 Plastome and phylotranscriptome dataset characteristics

The present phylotranscriptomic analyses is from 11,495 parsimony informative sites out of a total of 1,42,796 positions in the aligned (the aligned data set contains 85,153 conserved, 48,037 variable and 35,240 singleton sites, Fig. 1) transcriptome dataset of A. archangelica (Apiaceae), C. asiatica (Apiaceae), H. umbellate (Araliaceae), H. helix (Araliaceae), G. littoralis (Griseliniaceae), G. racemose (Griseliniaceae), P. corymbosa (Pennantiaceae), P. sahnianum (Pittosporaceae), P. resiniferum (Pittosporaceae) and D. asper (Caprifoliaceae).

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Fig. 1

The aligned transcriptome data set showing several different sites. A total number of 11,495 parsimony informative sites out of a total number of 14,27,95 sites were used in phylogenetic analysis.

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3.2

3.2 Phylotranscriptomic analyses

The phylotranscriptomic analyses recovered the MPT with tree length of 0.628 [consistency index 0.689, retention index 0.404, composite index 0.362]. The MPT revealed the proximity (bootstrap support 99%) of H. umbellata (ex Apiaceae, Araliaceae) with H. helix (Araliaceae), while A. archangelica (Apiaceae), C. asiatica (Apiaceae) clade (supported by 99% bootstrap support)- P. sahnianum (Pittosporaceae)- G. littoralis (Griseliniaceae)- P. corymbosa (Pennantiaceae) shows proximity of Araliaceae clade (70% bootstrap support) (Fig. 2), which is also evident from the estimates of evolutionary divergence between the sequences (Table 3) and the alignment of plastome of A. dahurica (Apiaceae), P. crispum (Apiaceae), E. senticosus (Araliaceae), H. sibthorpioides (Araliaceae) and K. septemlobus (Araliaceae). The Araliaceae clade [constitute with E. senticosus (Araliaceae) - H. sibthorpioides (Araliaceae) with branch length 0.08] clade with K. septemlobus (Araliaceae) (branch length 0.15), while A. dahurica (Apiaceae) (branch length 0.15) clade together with P. crispum (Apiaceae) (branch length 0.17) (Fig. 3). In the maximum likelihood analyses, the tree topology and the proximity of H. umbellata with the taxon included in the analyses found similar to MPT.

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Fig. 2

The evolutionary tree to evaluates the proximity of the genus Hydrocotyle with Araliaceae based on phylotranscriptomic analyses.

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Table 3 The estimates of evolutionary divergence between the sequences (Zuckerkandl and Pauling, 1965) used to infer the phylogeny using MEGA X (Kumar et al., 2018).

	G. littoralis	P. sahnianum	H. umbellata	P. corymbosa	H. helix	A. archangelica	C. asiatica	D. asper
G. littoralis
P. sahnianum	0.145
H. umbellata	0.164	0.171
P. corymbosa	0.150	0.182	0.202
H. helix	0.118	0.134	0.123	0.168
A. archangelica	0.187	0.193	0.201	0.220	0.180
C. asiatica	0.158	0.167	0.179	0.198	0.146	0.195
D. asper	0.223	0.243	0.248	0.211	0.231	0.269	0.252

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Fig. 3

The plastome alignment of the representative of the family Apiaceae and Araliaceae using MAUVE (Darling et al., 2004). Alignment Lane1: Eleutherococcus senticosus, 2. Kalopanax septemlobus, 3. Hydrocotyle sibthorpioides, 4. Petroselinum crispum, 5. Angelica dahurica.

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4 Discussion

The phylogenetic reconstruction of evolutionary histories in plants based on molecular data has been based largely on nuclear sequences or chloroplast/plastid DNA markers (Ali et al., 2014). The recent massive development in the next-generation sequencing platforms has brought cost-effective sequencing of genome or organelle genome e.g. chloroplast and mitochondria, which have proven extremely useful in understanding the deeper-level phylogenetic relationships of angiosperms (Ali, 2021). The transcriptome/ RNA-Seq (Wang et al., 2009) have attracted the attention for the reconstruction of evolutionary histories in plants because it allows massively parallel sequencing of expressed genes within a single genome which offers a powerful means of investigating the signals for evolutionary implications in higher taxonomic level such as Charophytes, Caryophyllales, Vitaceae, Brassicaceae, Betulaceae, Asteraceae, Hydnoraceae, Asclepias, Ferns; at a lower taxonomic level such as Camelina sativa, Artemisia tridentata, Ranunculus, Flaveria, or at angiosperms level; and have also been proven very useful in comparative transcriptomics, character evolution, domestication of crops and genome evolution (Wen et al., 2014).

The present phylotranscriptomic analyses revealed the proximity of H. umbellata (ex Apiaceae, Araliaceae) with H. helix (Araliaceae). The family Araliaceae (-Ginseng family) have distributed mostly in tropical regions, consists of c. 41 plus genera under Subfamily Aralioideae (1. Anakasia Philipson, 2. Aralia L., 3. Astrotricha DC., 4. Brassaiopsis Decne. & Planch., 5. Cephalaralia Harms, 7. Cheirodendron Nutt. ex Seem., 8. Cussonia Thunb., 9. Dendropanax Decne. & Planch., 10. Eleutherococcus Maxim., 11. Fatsia Decne. & Planch., 12. Gamblea C.B. Clarke, 13. Harmsiopanax Warb., 14. Hedera L., 15. Heteropanax Seem., 16. Hunaniopanax C.J. Qi & T.R. Cao, 17. Kalopanax Miq., 18. Macropanax Miq., 19. Megalopanax Ekman ex Harms, 20. Merrilliopanax H.L. Li, 21. Meryta J.R. Forst. & G. Forst., 22. Metapanax J. Wen & Frodin, 23. Motherwellia F. Muell., 24. Oplopanax (Torr. & A. Gray) Miq., 25. Oreopanax Decne. & Planch., 26. Osmoxylon Miq., 27. Panax L., 28. Plerandra A. Gray, 29. Polyscias J.R. Forst. & G. Forst., 30. Pseudopanax C. Koch, 31. Raukaua Seem., 32. Schefflera J.R. Forst. & G. Forst., 33. Sciadodendron Griseb., 34. Seemannaralia R. Vig., 35. Sinopanax H.L. Li, 36. Stilbocarpa (Hook. f.) Decne. & Planch., 37. Tetrapanax (K. Koch) K. Koch, 38. Trevesia Vis., 39. Woodburnia Prain) and Subfamily Hydrocotyloideae: 40. Hydrocotyle, 41. Trachymene (APG, 2016); out of these, some possess immense medicinal impotence such as Hedera sp., Panax sp. (Ginseng), and Eleutherococcus senticosus (Wen et al., 2000; Plunkett et al., 2004), are distinctive in being palmate or pinnate leaves, heads, reduced calyx, apopetalous to sympetalous corolla, and a 1–∞-carpellate inferior ovary, apical-axile placentation, fruit a berry, drupe, or schizocarp (Plunkett et al. 2004). The family Araliaceae show considerable floral variation. The family Apiaceae and Araliaceae resemble each other in the structure of their gynoecia, and are closely related (Plunkett et al., 2004), the family Araliaceae with the subfamily Hydrocotyloideae, Harmsiopanax and Aralioideae accepted as a monophyletic branch within the Apiales, an order within the Asterids; of these, Hydrocotyle from Hydrocotyloideae of Apiaceae transferred to Araliaceae based on molecular phylogenetic studies (Lowry et al., 2004; Plunkett et al., 2004). The Hydrocotyloideae are sister to the rest of the family (Chandler and Plunkett, 2004; Plunkett et al., 2004; Nicolas and Plunkett, 2009), the species of the genus Hydrocotyle are highly polyploidy (Yi et al., 2004), show early corolla tube initiation (Leins and Erbar, 1997; Erbar and Leins, 2004), calyx remains absent (Tseng, 1967), and possess has trilacunar nodes, laterally flattened fruits with a sclerified endocarp and stipules are cauline or borne on the leaf base (Sinnott and Bailey 1914).

In conclusion, the present study evaluates the proximity of Hydrocotyle with Araliaceae based on plastome and phylotranscriptomic analyses using the minimum evolution method. The family ‘Apiaceae/Umbelliferae and Araliaceae resemble each other in the structure of their gynoecia, and were placed in the order Apiales, and are closely related. The family Araliaceae with the subfamily 1. Hydrocotyloideae Link, 2. Harmsiopanax Harms and 3. Aralioideae Eaton accepted as a monophyletic branch within the Apiales, an order within the Asterids. Of these, Hydrocotyle L. from Hydrocotyloideae Link of Apiaceae transferred to Araliaceae based on molecular phylogenetic studies. The present analyses revealed the nesting of the Hydrocotyle under Araliaceae in the MPT, and the proximity is further supported by the evolutionary divergence between the sequences and plastome alignment.