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Begonia bangsamoro subp. bagasa Naive, subsp. nov. (Fig. 2) The new subspecies differs from Begonia bangsamoro subsp. bangsamoro in having staminate and pistillate flowers with much narrower and elongate tepals. Type: — PHILIPPINES. Mindanao, Zamboanga del Sur, Tigbao, Timolan, Mt. Timolan Protected Landscape, elev. 830 m, 31 January 2022, MAK Naive 127 (holotype PNH; isotype HNUL). Terrestrial, monoecious, perennial herb, up to 30 cm long. Stem erect to ascending, terete, 1.0– 3.5 mm in diameter, olive green to reddish green, densely hirsute, hairs pale green to pale red, 0.5–2.0 mm long, nodes slightly swollen, internodes up to 4 cm long. Stipules persistent, lanceolate, concave, 4.0– 7.5 mm long by 1.5–3 mm wide, pale green to reddish pale green, canaliculate, glabrous adaxially, keeled, hirsute along the center abaxially, margin entire, membranaceous, apex aristate, arista up to 2 mm long. Leaves alternate, petiolate, 6.0– 6.5 cm long; petiole terete, succulent, 3.0– 10.5 mm long, 1.0– 1.5 mm in diameter, olive green to reddish green, densely hirsute; lamina asymmetric, basifixed, lanceolate, 5.5–6.0 cm long by 2.5–3.1 cm wide, chartaceous, green adaxially, pale green abaxially, hirsute to sparsely hirsute adaxially, glabrous (except the veins) abaxially, margin distantly serrate to biserrate, densely ciliate, base asymmetrically cordate, apex acute to attenuate; venation basally palmate, with 5 majour lateral veins, actinodromous, branching dichotomously, basal half purplish red, green towards the apex, hirsute, channeled, adaxially, densely appressed hirsute, protruding abaxially. Inflorescence short, terminal, cymose, protogynous, bisexual, 4–5 cm long; peduncle 8–13 mm long, 1.0– 1.3 mm in diameter, terete, hirsute, fleshy, green to greenish red; rachis bearing up to 10 staminate flowers, 2.8–3.2 cm long, terete, glabrous, branching; bracts persistent, narrowly ovate, 2–3 mm long by 1.0– 1.3 mm wide, glabrous both sides, deflexed, green, margin entire, apex attenuate to acuminate. Staminate flower basal, longer than pistillate flower, dichotomously branching, with 4 tepals; pedicel 4.0– 4.5 mm long, 0.5 mm in diameter, terete, fleshy, glabrous, pinkish white; outer tepals 2, narrowly lanceolate, recurved, 6.5–8.0 mm long by 3.0– 3.5 mm wide, pale pink to pinkish white, glabrous adaxially, sparsely echinate abaxially, margin entire, apex obtuse to acute; inner tepals 2, linear, 5.8–6.3 mm long by 1.0– 1.5 mm wide, pinkish white, glabrous both sides, margin entire, apex rounded to obtuse; androecium actinomorphic, 1.5–2.0 mm across, the stamens ca. 20, lemon yellow; anthers obovoid, 0.2–0.5 mm long. Pistillate flower solitary, basal to staminate cymes, pink to pale pink, with 5 tepals; pedicel 7.5 mm long, 1.2–1.5 mm in diameter, terete, fleshy, hirsute, red to pale red; outer tepals 2, narrowly elliptic to linear, 9–10 mm long by 2.0– 2.5 mm wide, glabrous adaxially, sparsely or occasionally echinate abaxially, margin entire, revolute, apex acute; inner tepals 3, narrowly elliptic to linear, 9–10 cm long by 1.0– 1.5 cm wide; ovary stout, triquetrous-ellipsoid, 5–7 mm long by 2.0– 2.5 mm wide (wings excluded), hirsute, green with a hint of red in the wings, 3-locular, wings 3, subequal, triangular, apex obtuse to rounded, placentation axile, bilamellate; style 3, 3.0– 3.5 mm long, bifid, apically forked; stigmas spirally twisted, papillose all around. Fruit 1.5–1.8 cm long, stout, reclinate; pedicel 5–6 mm long, 1.0– 1.3 mm in diameter, hispid, reddish green; tepals deciduous; capsule 5.0– 5.5 mm long by 3.0– 3.5 mm wide (wings excluded), hirsute, reddish green, wings 3, subequal, 3–5 mm long by 3–4 mm wide, broadly triangular to subrhomboid, apex proximally obtuse. Distribution: —Endemic to the Zamboanga Peninsula. At present, the new subspecies can only be found from its type locality at Mt. Timolan Protected Landscape, Municipality of Tigbao, Zamboanga del Sur, Western Mindanao (Fig. 3). Habitat: —The subspecies was found in deeply shaded lower montane forest with damp soil growing along the trail with an elevation of 700–900 m a.s.l. It was also found growing as a terrestrial, lithophyte and as a climber on tree ferns. The new subspecies was found growing together with Begonia affinis Merr. (1912: 308). Phenology: —Buds, flowers and fruits were observed in the months of January and February. Etymology: —The subspecific epithet “ bagasa ” was used as a noun in apposition. It is a Subanen word meaning thin, alluding to the tepals of the staminate and pistillate flowers of this new subspecies. Subanen is one of the Philippine ethnic tribes that inhabits areas in the Zamboanga Peninsula and the montane areas of Misamis Occidental, island of Mindanao (Viernes-Enriques 1990). Proposed conservation assessment: — Following the IUCN Standards and Petitions Committee (2019), we herein propose this subspecies to be treated as ‘ Least concern’ (LC). At present, it is only known from the type collection site (Mt. Timolan Protected Landscape) with about 50 individuals observed. It is likely that other populations exist in the neighboring forests and mountains of Zamboanga Peninsula. Although the subspecies is quite uncommon at the type locality and it is mostly found along the trail of the forest, Mt. Timolan Protected Landscape (MTPL) is one of the protected areas of the Philippines declared last August 14, 2000 through proclamation order no. 354 issued by President Joseph Estrada. Other specimens examined: — Begonia bangsamoro subs. bangsamoro: PHILIPPINES, Mindanao, Bukidnon, Valencia City, Lourdes, elev. 1484 m, 10 June 2021, M. A . Cababan 4 (HNUL); Bukidnon, Pangantucan, Portulin, Mt. Kalatungan Range Natural Park, elev. 1500 m, 17 April 2018, MAK Naive s.n., photographic record; Misamis Oriental, Gingoog City, 2 October 2021, M . Baul s.n., photographic record. Notes: —Aside from morphological differences, Begonia bangsamoro subsp. bangsamoro can be usually found at higher elevations (≥ 1000 m) (Buenavista et al. 2021) whilst our newly discovered subspecies is usually growing at elevations of B. bangsamoro subsp. bangsamoro is restricted to the central and northern part of Mindanao island whereas our new subspecies is so far only been found in Zamboanga Peninsula (Fig. 3). It has long been supposed that Philippine archipelago consists of small centres of endemism, one of the reasons for the great diversity in the country. The Zamboanga Peninsula is a separate terrane and considered as the centre of endemism in Mindanao. It is a Miocene microcontinental block that may have been part of Palawan, and areas east of it are composed of younger ophiolitic deposits with a striking botanical affinity to Borneo (Hall 1996, 1998; Yumul et al. 2004). At present, Zamboanga peninsula harbours 16 species and 1 subspecies of Begonia (17 taxa), of which mostly are found to be endemic in the region. As shown in Table 1, of the 17 Begonia taxa recorded in Zamboanga Peninsula, only eight have an IUCN conservation assessment and the rest are not yet evaluated. Three are considered Critically Endangered namely B. amamampang Mazo & Rubite (2022: 164), B. parvilimba (1925: 481) and B. turugsoy Mazo & Rubite (2022: 166); three are Endangered which are B. affinis (Naive et al. 2022), B. tinuyopensis (Mazo et al. 2021), and B. oblongata (Naive et al. 2022); and two are Least Concern which are B. bangsamoro subsp. bagasa (this study) and B. contracta (Rubite 2013). The need to recollect Begonia species in Mindanao most especially in Zamboanga peninsula is urgent in order for us understand their distribution, identification and conservation status., Published as part of Naive, Mark Arcebal K., Calimbo, Liberty Grace L., Cudal, Maricris G., Alejandro, Grecebio Jonathan D. & Yu, Wen-Bin, 2022, Taxonomy of the genus Begonia (Begoniaceae) in Mindanao, Philippines IV: Begonia bangsamoro subsp. bagasa (Begonia section Petermannia), a new subspecies from Zamboanga del Sur, pp. 88-94 in Phytotaxa 559 (1) on pages 90-92, DOI: 10.11646/phytotaxa.559.1.10, http://zenodo.org/record/7009268, {"references":["Buenavista, D. P., Ang, Y. P., Pranada, M. A. K., Salas, D. A., Mollee, E. & McDonald, M. (2021) Begonia bangsamoro (Begoniaceae, section Petermannia), a new species from Mindanao Island, the Philippines. Phytotaxa 497 (1): 39 - 48. https: // doi. org / 10.11646 / phytotaxa. 497.1.4","Hall, R. (1996) Reconstructing Cenozoic SE Asia. In: Hall, R. & Blundell, D. (eds.) Tectonic Evolution of Southeast Asia 1. Geological Society of London, London, pp. 153 - 184.","Hall, R. (1998) The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. In: Hall, R. & Holloway, J. D. (eds.) Biogeography and Evolution of SE Asia. Backhuys Publisher, Leiden, pp. 99 - 131.","Yumul, G. P., Dimalanta, C. B., Tamayo, R. A., Maury, R. C., Bellon, H., Polve, M., Maglambayan, V. B., Querubin, C. L. & Cotten, J. (2004) Geology of the Zamboanga Peninsula, Mindanao, Philippines: an enigmatic South China continental fragment? Geological Society, London, Special Publications 226: 289 - 312. https: // doi. org / 10.1144 / GSL. SP. 2004.226.01.16","Mazo, K. R. & Rubite, R. R. (2022) Two new species of Begonia (section Petermannia, Begoniaceae) from the Zamboanga Peninsula, Philippines, and a redescription of Begonia parvilimba. Phytotaxa 538 (2): 163 - 171. https: // doi. org / 10.11646 / phytotaxa. 538.2.9","Naive, M. A. K., Mazo, K. R. F. & Hughes, M. (2022) Taxonomy of the genus Begonia (Begoniaceae) in Mindanao, Philippines II: Lectotypification of two Begonia section Petermannia species from Zamboanga Peninsula. Kew Bulletin 77: 139 - 146. https: // doi. org / 10.1007 / s 12225 - 022 - 10008 - 5","Mazo, K. R., Aribal, L. G., Bustamante, R. A. A. & Ang, Y. P. (2021) Begonia tinuyopensis (sect. Petermannia, Begoniaceae), a new species from Zamboanga Del Norte, Philippines. Phytotaxa 516 (1): 101 - 107. https: // doi. org / 10.11646 / phytotaxa. 516.1.8","Rubite, R. R. R. (2013) Begonia section Petermannia of Luzon Island, The Philippines. Philippine Journal of Science 142: 183 - 197."]}

Additional file 13: Figure S12. Family relationships within the pruned angiosperm subdataset. In this tree, bootstrap/gCF/sCF scores are shown for each branch.

Additional file 7: Figure S6. Phylogenetic tree of 4792 plastomes of 445 families (including 12 gymnosperm families) of seed plants.

Additional file 9: Figure S8. Phylogenetic tree of 4792 plastomes with successive removal of the long branch forming a sister relationship with a ���clade��� of Mitrastemonaceae, Thismiaceae, Apodanthaceae, and Balanophoraceae.

Zingiberaceae are well known for their medicinal and economic significance across the world yet remained poorly known and studied and unfortunately considered one of the most threatened plant families in the Philippines. Such is the case for the genus Etlingera, where its taxonomy and nomenclature are much disputed particularly for several species in the archipelago that have been studied very little for over a century. Here, we report the seven newly sequenced Etlingera plastomes obtained through genome skimming using next generation sequencing. All plastomes displayed a typical quadripartite structure and their size ranges from 163,615–164,641 bp which encoded 113 different genes (80 protein-coding, 30 tRNA, and four rRNA genes) with 36.1% GC content. Gene content, gene order, and GC content were highly similar among these genomes. The maximum likelihood tree of the seven Etlingera within the family showed that plastomes can be used as a super-barcode to identify Etlingera spp. and provides an important reference and solid foundation in the establishment of species identification and phylogeny ofZingiberaceae. In addition, recent fieldwork in Mindanao resulted in the discovery of a new species (Etlingera dostseiana Naive, Demayo & Alejandro) and a new species record (E. pilosa A.D.Poulsen & Docot).

Additional file 3: Figure S2. Phylogenetic tree of 4782 plastomes of 445 families (including 12 gymnosperm families) of seed plants. Five problematic families (Rafflesiaceae, Apodanthaceae, Balanophoraceae, Mitrastemonaceae, and Thismiaceae) were added manually (see Results for details).

Additional file 8: Figure S7. Phylogenetic tree of 4792 plastomes of 4660 species of seed plants. All bootstrap values are shown.

Additional file 6: Figure S5. Phylogenetic tree of 4792 plastomes of 76 orders (including eight gymnosperm orders) of seed plants.

Additional file 5: Figure S4. Phylogenetic tree of 4782 plastomes (with ten plastomes of five problematic families excluded) of 4650 species of seed plants. Bootstrap values are shown.