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Research Article
Systematic reinstatement of the Sumatra endemic species Mangifera sumatrana Miq. (Anacardiaceae)
expand article infoFitmawati Fitmawati‡, Erwina Juliantari§, Mega Silvia‡
‡ Universitas Riau, Riau, Indonesia
§ Faculty of Mathematics and Natural Sciences IPB University, Bogor, Indonesia

Corresponding author: Fitmawati Fitmawati ( fitmawati2008@yahoo.com )

Academic editor: Hugo de Boer
© 2022 Fitmawati Fitmawati, Erwina Juliantari, Mega Silvia.
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: Fitmawati F, Juliantari E, Silvia M (2022) Systematic reinstatement of the Sumatra endemic species Mangifera sumatrana Miq. (Anacardiaceae). PhytoKeys 199: 129-140. https://doi.org/10.3897/phytokeys.199.80727
Open Access

Abstract

Mangifera sumatrana Miq. is an endemic species from Sumatra. The taxonomic status of M. sumatrana remains unclear and is currently treated as a synonym of M. laurina. The present study employed morphological and palynological characters and molecular analyses to address the delimitation between the two species. Pollen observations were carried out with a Scanning Electron Microscope (SEM). Phylogenetic relationships were investigated using the ITS and the trnl-F intergenic spacer markers. M. sumatrana differs from M. laurina by having pyramidal panicles with a low density of pale yellow flowers pale, sepals 3–3.5 × 1.7–2 mm, fruit roundish to flattened with pale yellow pulp, a rough fibre texture, and pollen with a prolate spheroidal shape. The MP phylogenetic tree showed a divergent boundary between the two species suggesting that M. sumatrana could be an independent species, not a variety of M. laurina. The present study supports the view that these two taxa can be treated as different species.

Keywords

Accepted name, barcoding DNA, morphology, palynology, phylogeny

Introduction

Mango (Mangifera spp.) has become a major fruit crop of the tropics and subtropics, particularly in Asia. The mango has always been one of the most important fruit crops and it has been considered the ‘king of fruits’. The genus Mangifera is one of the 73 genera belonging to the Anacardiaceae family in the order Sapindales. The latest classification of Mangifera by Kostermans and Bompard (1993) describes 69 species.

Morphologically, closely-related Mangifera are quite difficult to distinguish, leading to species complexity and misidentification. This is due to the continuity of the characters and the high morphological plasticity of Mangifera, as well as the diversity of species boundaries (Fitmawati and Hartana 2010). Continuity of characters or plasticity due to interspecific hybridisation is common in Mangifera and can occur due to a chromosomal match between Mangifera species, i.e. species are allotetraploids with 40 chromosomes, and these have polembrionic seeds (Litz 2004).

According to Kostermans and Bompard (1993), based on morphological characteristics, there is a species boundary between M. laurina Bl., M. indica L. and M. lalijiwa Kosterm., so that these three Mangifera species are separated, but for M. sumatrana Miq., which is identical to M. laurina Bl. and, until now, the taxonomic status of M. sumatrana is synonymous (POWO 2019). Before then, this species was treated as a synonym of M. longipes Griff. by Mukherjee (1953) and Hou (1978).

According to Konchummen (1996), M. laurina is a variation of M. indica and is a synonym of M. indica. Phenetic analysis, based on morphological characters, also showed that M. sumatrana Miq. has a close relationship with M. indica L. and M. laurina Bl (Fitmawati et al. 2013). However, based on molecular analysis using the ITS sequence by Fitmawati et al. (2016), the results identified that M. sumatrana Miq. did not form a clade with either M. indica L. or M. laurina Bl. M. sumatrana is rarely found in nature, so it is important to clarify its taxono­mic status.

Differences of opinion regarding the taxonomic status of M. sumatrana and its relatives are caused by differences in the sources of taxonomic evidence used as the basis for compiling different classifications and the rationale for classifying these plants is also different. Therefore, a more comprehensive source of evidence is needed to strengthen the taxonomic status of M. sumatrana and its relatives.

Conflicts have also developed amongst taxonomists regarding the taxonomic status of the species M. sumatrana due to the great rarity of the species. Therefore, we propose that this species needs to be evaluated using morphological methods, palynological characteristics and molecular phylogeny to confirm the identity of M. sumatrana. We hope this study can provide an outstanding example for re-evaluating synonyms for M. sumatrana.

Materials and methods

Fresh leaf samples of M. sumatrana were collected from Sumatra, Indonesia. We have been doing exploration since 2013–2017. The voucher specimens of M. sumatrana (sheets: HR20130073, HR20130094, HR20160096, HR20170124) were generated and deposited at the Herbarium Riauense, Indonesia.

Morphological and palynological analysis

The morphological characters observed in this study were qualitative and quantitative characters comprising stems, leaves, fruits and seeds. Morphological comparisons were made through herbarium studies and field observations. Herbarium studies were conducted in Herbarium Riauense, ANDA, BO and Kew (https://powo.science.kew.org/). A total of 2000 Mangifera spp. and 30 M. sumatrana collections number loaned from the following herbaria were examined for morphological data. Morphological characters are referred to as descriptors of mango (International Plant Genetic Resources Institute 2006) and Kosterman and Bompard 1993). We evaluated the conservation status of species using IUCN Red List categories (IUCN 2012). Pollen observations were carried out with a Scanning Electron Microscope (SEM) and consisted of preparation, mounting, coating, photographing of pollen and data analysis. Pollen grains were prepared in glycerine jelly and measured using an eyepiece (ocular) with a scale and then the measurement results were converted into micrometre units.

Molecular methods and phylogenetic relationship analyses

Samples used in this study represent each section of Mangifera species obtained from Genbank. Fresh leaves of M. sumatrana used in this study were collected from Sumatra. Two genera from Anacardiaceae were used as an outgroup (Table 1). The DNA was amplified in a specific target area using the internal transcribed spacer (ITS) and the trnL-F intergenic spacer (IGS) marker. DNA extraction using the CTAB method of Doyle and Doyle (1987) with modification, was undertaken by using ethanol 96% for about 24 h at 4 °C. Barcoding sequence amplification was done through the PCR technique. The genomic DNA was amplified using universal primers ITS5F (5’-GGAAGTAAAAGTCGTAACAAGG-3’) and ITS4R (5’-TCCTCCGCTTATTGATATGC-3’) (White et al. 1990) (for the entire ITS regions, nrDNA) and primer E (5’-GGTTCAAGTCCCTCTATCCC-3’) and primer F (5’-ATTTGAACTGGTGACACGAG-3’) (Small et al. 2004) (for the entire trnL-F intergenic spacer region, cpDNA). PCR products were sent to First Base Laboratories, Malaysia. PCR Clean-Up was then used to purify the amplified products by Gel Extraction, depending on visualisation results for Single Pass DNA Sequencing.

Table 1.
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Sources of Mangifera sequences and their locality.

Species Genbank Acc. No. Locality Species Genbank Acc. No. Locality
ITS sequences trnL-F sequences
M. sumatrana Miq. MF990366 Indonesia M. sumatrana Miq. MF997590 Indonesia
M. indica L. KX347960 Indonesia M. indica L. KY392616 Indonesia
M. zeylanica (Bl) Hook. f. KX347962 Indonesia M. zeylanica (Bl) Hook. f. MF997591 Indonesia
M. laurina Bl. MF678498 Indonesia M. laurina Bl. KY392609 Indonesia
M. lalijiwa Kosterm. MF678504 Indonesia M. lalijiwa Kosterm. MF997587 Indonesia
M. torquenda Kosterm. MF990365 Indonesia M. quadrifida Jack. KY392614 Indonesia
M. quadrifida Jack. MF678511 Indonesia M. foetida Lour. MF997585 Indonesia
M. casturi Kosterm. MF678493 Indonesia M. odorata Griff. MF945595 Indonesia
M. foetida Lour. MF678506 Indonesia M. kemanga Bl. MF919594 Indonesia
M. odorata Griff. KX347957 Indonesia M. andamanica King AB598013 India
M. kemanga Bl. MF990368 Indonesia M. camptosperma AB598010 India
M. oblongifolia Hook. f. AB071682 Thailand M. flava Evrard. MF945595 India
M. gedebe Miq. AB071681 Thailand M. griffithi Hook. f. AB598012 Vietnam
M. macrocarpa Bl. AB071688 Thailand M. reba Pierre KY067415 Vietnam
M. sylvatica Roxb. AB071689 Thailand
M. cochinchinensis Engler. AB071675 Thailand
M. griffithii Hook. f. AB071685 Thailand
M. flava Evrard. AB071679 Thailand
M. pentandra Hooker f. AB071684 Thailand
M. pajang Kosterm. MF444896 India

DNA sequences were aligned with ClustalW Multiple Alignment used Molecular Evolutionary Genetics Analysis (MEGA) software (Tamura et al. 2013; Kumar et al. 2016). Phylogenetic relationships analysis was performed using the Maximum Parsimony (MP) with the PAUP programme (Swofford 2002).

Results and discussion

Morphology

Mangifera sumatrana Miq. first published in Fl. Ned. Ind. 1(2): 630 (1859)

Fig. 1

Type

Indonesia. Sumatra, Riau, Pekanbaru, tropical lowland, alt. 32 m, 3 October 2016, Fitmawati 152 (holotype HR20130073!).

Diagnosis

Mangifera sumatrana has been considered as a synonym of Mangifera laurina Bl. The distinctive characteristics of the M. sumatrana are panicles pyramidal and not dense, large and flat fruit, prominent fruit beak type, a quantity of fibre in pulp and high stone. M. laurina panicles are conical and dense, with small and thick fruit, round in shape and fruit break type is perceptible (Figs 1, 2).

Figure 1. 

Mangifera sumatrana A habit B adaxial and abaxial surface of leaf C pyramidal panicles D flowers E flowers after anthesis; F ovary with swollen disc G roundish fruit H flattened fruit I pulp.

Figure 2. 

Mangifera laurina A conical panicles B flowers C roundish thick fruit.

Description

Tree up to 40 m tall and 100–140 cm in diam., growth habit spreading, bark brownish-white with cream sap, the shoot brownish-yellow and crown semi-circular. Leaves dark green, scattered, semi-drooping on branch, chartaceous, oblong-ovate, apex acuminate, base acute, both surfaces smooth, 14.9–15.4 × 4.51–5 cm, thickness 0.12–0.2 cm, mid-rib 13.7–14.2 cm in length, above and below mid-rib prominent, nerves 21–23 pairs, areola reticulation dense, slightly prominent, two branches. Petiole 2.8–3 cm in length, 0.19–0.22 cm in diameter. Panicles terminal, semi-erect, yellowish-cream, pyramidal, 9.5–12 cm long, 14.30–15.55 g, non-glomerulate, low flower density. Flowers pale yellow with light yellow tinge, 5-merous, after anthesis, pale yellow with orangish-yellow tinge, 0.1–0.2 g, 6–6.5 × 5.5–6.2 cm. Bract yellowish-green, 5, 2.6–3.1 × 1.4–1.6 mm, broadly triangular acuminate, even and hairy, both dorsal and ventral smooth. Sepals light green, 5, 3–3.5 × 1.7–2 mm, broad ovate, acute and hairy and smooth. Petals pale yellow, 5, 5–5.4 × 2–2.3 mm, curved-reflexed outwards, elliptic, apex blunt, not hairy, ridges 5. Disc swollen, broader than ovary. Stamen fertile 1, 2.5–2.8 mm long, staminodes 4–5, filaments adnate to the base, 0.7–0.78 × 0.4–0.5 mm. Ovary rather round, lateral-frontal. Stylus slightly to the side and curved, 2–2.5 mm long. Fruits pale yellow, roundish flattened, thickness 0.2–0.3 cm, apex round, 160.41–182 g, 10.8–11.6 × 4.51–5.4 cm, 5.44–6 cm, skin surface texture smooth, non-waxy, density of lenticels on fruit skin sparse, beak pointed, sinus shallow, slope of fruit central shoulder rising and then rounded, fruit stalk insertion oblique, neck prominence absent. Pulp yellow, texture soft, adherence intermediate, quantity of fibre low, 6.13–6.4 cm long, juicy and sweet. 15.5° Brix. Stones oblong, 23.51–25 g, 8.7–9 × 4.22–4.5 cm, 1.14–1.3 cm thickness, fibre texture rough, adherence of fibre to stone weak, veins on stone depressed and pattern of stone venation forked. Polyembryony, 2.22–3 g. Leaf anatomy Anomocytic stomata type. Simple epidermis. Simple palisade mesophyll. Upper mid-rib of M. sumatrana has convex and lower mid-rib has concave shape.

Distribution and habitat

M. sumatrana is an endemic species only found in lowland areas in Sumatra (less than 100 m a.s.l.), collected in southern Sumatra and central Sumatra, but is more commonly found in Riau Province, Sumatra, Indonesia.

Chemotaxonomy

In addition, several compounds from the alkaloid, alkane, amino acids, benzene, benzoic acid and fatty acyl groups are only found in M. sumatrana Miq. Conversely, several compounds from the phenolic group (gallic acid), amino acids, benzene and benzoic acid are only found in M. laurina Bl (Fitmawati et al. 2021). Therefore, it can be reported that M. sumatrana Miq. is not a synonym of M. laurina Bl and contradicts the morphological classification of Kostermans and Bompard (1993).

Notes

Geographically, the distribution of M. sumatrana and M. laurina is also different. M. sumatrana is found in lowland areas of Sumatra (less than 100 m a.s.l.), while M. laurina is a cosmopolitan species and is not only found in Sumatra, but also in the Maleisiana area, especially in the highlands (altitude up to 2000 m a.s.l.) (Fitmawati et al. 2013).

Palynology

Mukherjee (1953) investigated the pollen morphology of mango and 12 other Mangifera species. Their pollen grains were tricolpate of almost the same size. Mondal (1982), cited in Kostermans and Bompard (1993), attempted to correlate pollen morphology with taxonomic relationships of 17 Mangifera species, based upon different characteristics of the exine and sporoderm. They demonstrated that all of the species of section II (subgenus Limus) possess a coarse exine, whereas there was no clear correlation with pollen type in species within section I (subgenus Mangifera).

Figure 3. 

Pollen polarity and pollen aperture of the four types Mangifera, by electron microscope (A1–B1). Surface ornamentation of Mangifera pollen (A2–B2) A M. sumatrana and B M. laurina.

Mangifera are closely related morphologically and are quite difficult to distinguish, causing differences of opinion amongst experts regarding the taxonomic position of several Mangifera species. Therefore, more comprehensive and stable additional data are needed to strengthen the taxonomic status of Mangifera, namely using micromorphological pollen characters.

Based on the results of the study, there were five similarities in the characteristics of pollen morphology, namely pollen monad unit, angular polar view, circular/oval equatorial view, isopolar pollen polarity and tricolpate pollen aperture type, while the differences were pollen size, pollen shape and pollen ornamentation, polar diameter, equatorial length and exine thickness.

The relationship, based on a study of pollen micromorphology, shows that the pollen characteristics of M. sumatrana are very different from M. indica, while the difference between M. sumatrana, M. laurina, and M. odorata lies in the type of pollen ornamentation. M. laurina has the closest relationship with M. odorata. The results of this study can be a source of supporting evidence in clarifying the taxonomic status of M. sumatrana and showing that it differs from its relatives.

M. sumatrana has a striate-microreticulate ornamentation type, while M. laurina has a striate-reticulate ornamentation type, so that this pollen ornamentation feature can be a source of new taxonomic evidence for refuting the theory of Kostermans and Bompard (1993) which states that M. sumatrana is a synonym of M. laurina, based on morphological characteristics. This statement is also supported by research conducted by Fitmawati et al. (2018) which states that M. laurina and M. sumatrana are different and M. laurina is not a synonym for M. sumatrana, based on an analysis using ITS. This finding can be a source of supporting evidence in clarifying the taxonomic status of M. sumatrana and showing that it differs from its relatives (Table 2).

Table 2.
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Morphological and palynological differences between Mangifera sumatrana and M. laurina.

Taxonomic traits Mangifera sumatrana Mangifera laurina
Panicle shape Pyramidal Conical
Panicle density Low (14.30–15.55 g) Medium (15.56–16.81 g)
Flowers’ colour Pale yellow Yellow-orange
Bractea Yellowish-green (2.6–3.1 × 1.4–1.6 mm) Green (2–2.5 mm × 1.1–1.3 mm)
Sepal size 3–3.5 × 1.7–2 mm 1.3–1.8 mm × 0.7–1 mm
Fruit shape Roundish flattened Roundish thicked
Fruit stalk insertion Oblique Vertical
Fruit neck prominence Absent Slightly prominent
Pulp colour Pale yellow Yellow-orange
Fibre texture in the pulp Rough Soft
Pollen ornamentation type Striate-microreticulate Striate-reticulate

Phylogenetic relationship analysis

ITS sequences were obtained for all 24 species of Mangifera and two genera from Anacardiaceae were used as an outgroup. Alignment samples yielded 672 nucleotide sites distributed in the ITS region. The aligned ITS contained 452 (67.2%) conserved sites, 123 (18.3%) variable informative sites and 97 (14.5%) parsimony-informative site characters that were assumed to be informative for phylogenetic analysis using the parsimony method. The research resulted in a length of 369 steps and had a consistency index (CI) and retention index (RI) of 0.726 and 0.690, respectively (Table 3).

Table 3.
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Properties of the two candidate DNA barcoding loci in M. sumatrana with its relative species.

Parameter ITS regions trnL-F IGS ITS+ trnL-F IGS
Sequences length 672 411 1582
Conserved sites (%) 67.20 90.75 89.60
Variable informative sites (%) 18.30 5.35 5.69
Parsimony-informative sites (%) 14.50 3.50 4.62
Tree length 534 60 221
Consistency index (CI) 0.72 0.67 0.91
Retention index (RI) 0.69 0.50 0.80

trnL-F IGS sequences were obtained for all 14 species of Mangifera and two genera from Anacardiaceae were used as an outgroup. Alignment samples yielded 411 nucleotide sites distributed in the trnL-F IGS. The aligned ITS contained 373 (90.75%) conserved sites, 22 (5.35%) variable informative sites and 16 (3.5%) parsimony-informative characters that were assumed to be informative for phylogenetic analysis using the parsimony method. The analysis resulted in a length of 369 steps and had a consistency index (CI) and retention index (RI) of 0.67 and 0.50, respectively.

The aligned matrix for the combined analysis comprised 1582 characters, of which 89.6% were conserved region and 4.62% parsimony informative. We found one of the most parsimonious trees with a length of 221 steps, CI of 0.91 and RI of 0.80 (Table 3). Additional analysis of genus M. sumatrana to its closely related species based on ITS region of nrDNA and trnL-F IGS of chloroplast DNA using MP methods showed that the cladogram was monophyletic. The strict consensus tree is reconstructed by the parsimony method shown in Fig. 4.

Figure 4. 

Phylogenetic tree of M. sumatrana and Mangifera taxa using maximum parsimony analysis derived from: A ITS sequences B trnL-F IGS C combination ITS+trnL-F IGS sequences. Numbers below branches showed bootstrap values.

Maximum parsimony analysis of the branch leading to M. sumatrana with other Mangifera species provided a clear resolution. The M. sumatrana Miq. is a unique species found in Sumatra and was treated as a synonym of M. laurina Bl., based on morphological characters in the latest classification by Kostermans and Bompard (1993) and palynological characters. Based on molecular analysis, using ITS, trnL-F IGS sequence and a combination of both, the results can support different species based on morphological and palynological characters (Fig. 4).

The result of BLAST indicated that Mangifera sumatrana Miq. ITS sequences (Genbank acc. no. MF990366.1) and trnL-F IGS (Genbank acc. no. MF990366.1) have a high similarity to M. indica (Table 4). Corresponding to the tree MP, using ITS and trnL-F IGS sequence and data from BLAST parameters, M. sumatrana Miq. is not a synonym of M. laurina Bl (Fig. 4B).

Table 4.
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BLAST analysis of ITS and trnl-F IGS sequences of Mangifera sumatrana Miq.

Description Max score Total score Query cover (%) Ident Accession
Mangifera indica ITS1 (partial), 5.8S rRNA gene, and ITS2 partial), cultivated variety Dasheri. 841 841 100 98.14 AJ890466.1
Mangifera indica cultivar MKR 8 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence. 833 833 99 97.93 OL960632.1
Mangifera indica cultivar Tuong BP small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer. 830 830 100 97.72 MN011941.1
Mangifera indica cultivar Gadung internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence. 830 830 98 98.11 MH037250.1
Mangifera laurina internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence. 830 830 100 97.72 MF678508.1
Mangifera indica trnL-trnF intergenic spacer, partial sequence; chloroplast. 725 725 97 99.25 MF997590.1
Mangifera indica cultivar Arunika trnA-Leu (trnL) gene, partial sequence; trnL-trnF intergenic spacer, complete sequence; and trnA-Phe (trnF) gene, partial sequence; chloroplast. 723 723 96 99.50 JX185679.1
Mangifera lalijiwa trnL-trnF intergenic spacer, partial sequence; chloroplast. 684 684 91 99.47 MF997587.1
Mangifera zeylanica trnL-trnF intergenic spacer, partial sequence; chloroplast. 721 721 96 99.50 MF997591.1
Mangifera foetida trnL-trnF intergenic spacer, partial sequence; chloroplast. 723 723 96 99.50 MF997585.1

Identification, using DNA barcodes, shows that M. sumatrana is related to M. indica, M. zeylanica, M. laurina and M. lalijiwa. Based on floral morphological characteristics, these five species of Mangifera are grouped with two distinguishing characteristics: panicles glomerulate (M. indica and M. zeylanica), while M. laurina, M. sumatrana and M. lalijiwa have non-glomerular panicles. However, M. laurina was very different from the distinctive features of conical panicles. Meanwhile, the distinguishing feature of M. lalijiwa and M. sumatrana species is that the crown shape distinguishes between M. lalijiwa and M. sumatrana species, which are spherical (M. lalijiwa) and semi-circular (M. sumatrana) crowns. M. sumatrana is different. Based on fruit morphological characteristics, M. sumatrana has a fruit shape that is very different from other species, namely the fruit is roundish and flattened, a distinguishing feature which is stable and genetic. The differences in M. sumatrana shows clearly that M. sumatrana is a different species, not a synonym of M. laurina. Hence, we propose that M. sumatrana is a distinct species amongst the M. laurina complex species.

M. sumatrana is a narrowly distributed species. It is only found in central Sumatra, with a population of fewer than 100 individuals. Following the Categories and Criteria of the IUCN Red List (IUCN 2012), we categorise M. sumatrana as critically endangered according to criteria B and D.

1 Panicles glomerulate, horizontal axis 2
– Panicles not glomerulate, semi-erect axis 3
2 Leaves lanceolate to oblong, fruits green, ovate-oblong M. indica
– Leaves spathulate to oblanceolate, fruits yellow orange, cordate M. zeylanica
3 Crown shape semi-circular, leaves semi-drooping on branch, panicles terminal, greenish yellow to yellowish-cream, large up 40 cm long 4
– Crown shape spherical, leaves semi-erect on branch panicles pseudo-terminal, light green, large up 20 cm long M. lalijiwa
4 Panicles conical, medium densely, flowers yellow-orange small sepal 1.3–1.8 mm × 0.7–1 mm, fruit roundish thickened, pulp yellow-orange, fibre texture soft M. laurina
– Panicles pyramidal, low densely, flowers pale yellow, large sepal 3–3.5 × 1.7–2 mm, fruit roundish flattened, pulp pale yellow, fibre texture rough M. sumatrana

Conclusion

M. sumatrana has a fruit shape that is very different from other species. Namely, the fruit is roundish and flattened, a distinguishing feature which is stable. M. sumatrana also has a prolate spheroidal pollen. Based on phylogenetic analysis, M. sumatrana is not in the same clade as M. laurina. The present study showed that ITS and trnL-F IGS DNA barcode markers in combination can be used as taxon-specific markers for Mangifera. The findings of this study support the view that M. sumatrana can be treated as a distinct species from M. laurina.

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