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. 2020 Dec 11;28(2):1487–1493. doi: 10.1016/j.sjbs.2020.12.008

Plastome of Saraca asoca (Detarioideae, Fabaceae): Annotation, comparison among subfamily and molecular typing

Mohammad Ajmal Ali a,⁎, Tapan Kumar Pan b, Arun Bahadur Gurung c,⁎, Mohammad Abul Farah d, Fahad Al-Hemaid a, Khalid Mashay Alanazi d, Meena Elangbam e, Joongku Lee f, Shankar Kumar Pandey g, M Oliur Rahman h, Soo-Yong Kim i
PMCID: PMC7878682  PMID: 33613076

Abstract

Saraca asoca (Roxb.) Willd. (subfamily Detarioideae, family Fabaceae) is a perennial evergreen sacred medicinal tree classified under ‘vulnerable’ by the IUCN. The chloroplast (cp) genome/plastome which follows uniparental inheritance contains many useful genetic information because of its conservative rate of evolution. The assembled cp genome of S. asoca which maps as a conserved circular structure revealed extensive rearrangement in gene organization, comprising total length 160,003 bp including LSC, SSC, IRa, and IRb, and GC content was 35.26%. Herein a set of rbcL and matK gene were established using molecular phylogenetic analyses for molecular typing of S. asoca.

Keywords: Plastome, Saraca asoca, Detarioideae, Fabaceae, Molecular authentication, Simple sequence repeat, Genomic rearrangement

1. Introduction

Saraca asoca (Roxb.) de Wilde [family Fabaceae, subfamily Detarioideae (APG IV, 2016, LPWG, 2017)], commonly known as ‘asoca’ (Fig. 1A-B), indigenous to Assam, E. Pakistan, Upper Burma, Malaya, Ceylon and South India (Singh et al., 2015), is one of the most sacred tree of the Indian subcontinent (Murthy et al., 2008, Mollik et al., 2010). Apart from its various pharmacological significance e.g. antimicrobial (Seetharam et al., 2003, Shirolkar et al., 2013), anticancer (Cibin et al., 2012), anti-inflammatory (Cibin et al., 2012, Saha et al., 2012), antiarthritic (Preethi and Krishnakumar, 2011) activities, the barks, leaves, flowers, and seeds of ‘asoca’ have extensively been used against uterine infections and as astringent in the cases of the internal haemorrhoids in modern as well as in the Indian traditional systems of medicine (Nudrat et al., 2005, Singh et al., 2015).

Fig. 1.

Fig. 1

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Saraca asoca. A. The tree in the flowering stage. B. An enlarged view of inflorescence.

The continuous development in the next-generation sequencing (NGS) platforms (Shendure et al., 2017), and bioinformatics tools (Yang and Rannala, 2012) including cloud computing for genomic data analysis (Kwon et al., 2015, Langmead and Nellore, 2018) during last two decades have (a) greatly propelled to sequencing of the organellar genome e.g. mitochondria (Kozik et al., 2019), chloroplast (Daniell et al., 2016) and whole genome (Chen et al., 2018), (b) revolutionized the understanding of various biological disciplines (Ali et al., 2020) e.g. tree of life (Philippe et al., 2005, Rokas, 2006), evolution of plant genomes (Wendel et al., 2016), gene families and gene function (Leebens-Mack et al., 2019), conservation biology (Johnson and Koepfli, 2014, Wambugu et al., 2018), and (c) alleviate the enhancement of the agronomic traits (Rogalski et al., 2015, Daniell et al., 2016, Lima et al., 2016). The over-exploitation of S. asoca from the wild habitat due to increasing commercial demand of the bark of ‘asoca’ as crude drug material leads it to vulnerable (IUCN, 2019); hence, the characterization of plastome/whole chloroplast (cp) genome of ‘asoca’ and its genetic comparison will facilitate the development of DNA markers for diversity assessment, conservation, and in unraveling function of genes and gene families to produce its enhanced agronomic traits through genetic engineering.

2. Materials and methods

2.1. Leaf sampling and DNA sequencing

The green young leaves material of S. asoca was collected [voucher information: ‘MAA & TKPAN-116′ (BHAG, KSUH)] from the tree growing at conservatory of the botanical garden, Tilka Manjhi Bhagalpur University (TMBU), Bhagalpur, India, without harming the plant, were used for the extraction of DNA using # DNeasy Plant Mini Kit (QIAGEN). The de novo sequencing (as a single end run of 51 bp) was performed at Illumina platform, Illumina Pipeline 1.3.2 (Nie et al., 2012) was used for base calling.

2.2. Cp genome assembly and annotation

The raw reads were first filtered using fastqc. The high-quality reads were then assembled using spades (Bankevich et al., 2012), and annotated using the online tool GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) at Tamarindus indica L. (GenBank NC_026685.1) as reference (Hansen et al., 2007, Tillich et al., 2017). The repeat structure and small inversion (Timme et al., 2007, Yang et al., 2010, Maia et al., 1991, Doorduin et al., 2011, Castro et al., 2013, Beier et al., 2017) in cp genome were analyzed.

2.3. Comparison of cp genome and phylogenetic analysis

The cp genome of S. asoca was compared with the five other complete Detarioideae (Fabaceae) cp genomes including Crudia harmsiana Wild., (NC_036743.1), Daniellia pilosa (J. Léonard) Estrella, (NC_036744.1), Guibourtia leonensis J. Leonard, (NC_036742.1) and Tamarindus indica L. (NC_026685.1) by aligning using Kalign (Lassmann and Sonnhammer, 2005) and UPGMA analysis (Sneath and Sokal, 1973) employing MEGA X (Kumar et al., 2018) followed by the verification of the taxon proximity under UPGMA tree with MAUVE alignment.

The plant DNA barcoding genes i.e. rbcL and matK of adulterant species (a) Bauhinia variegata L. (GU135196, GU135033), (b) Mesua ferrea L. (KY654490, JN114759), (c) Polyalthia longifolia (Sonn.) Thwaites (JX856748, AY518786), (d) Shorea robusta Gaertn. (KY654498, KY973059) and (e) Trema orientalis (L.) Blume (KY654502, AB924756) were retrieved from the GenBank, and analyzed together with the sequences of the S. asoca (KY678341, KC592386). The sequences were aligned (Thompson et al., 1994), and the molecular phylogenetic analyses by Maximum Evolution method (Rzhetsky and Nei, 1992) rooted using outgroup Sarcandra glabra [Clade: Angiosperms, Order: Chloranthales, Family: Chloranthaceae (KP208901, JN407112) were performed using MEGA X (Kumar et al., 2018).

3. Results and discussion

The assembled cp genome maps as a conserved circular structure (Fig. 2A), comprising total length 160,003 bp including LSC, SSC, IRa, and IRb, and GC content was 35.26% (NCBI GenBank accession number: MN866115) as similar to those of other angiosperms (Daniell et al., 2016). The cp genome possessed 111 genes (97 CDS, 29 tRNA, 4 rRNA genes) (Fig. 2B). Twelve of the CDS and eight of the tRNAs contain introns; 18 of these contain single intron, and two genes (ycf3 and clpP) possess 2 introns each (Fig. 2A).

Fig. 2.

Fig. 2

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A. The cp geneome map Saraca asoca, B. the genes of different groups are color-coded.

The tandem and dispersed repeats were analyzed for S. asoca cp genome. It is evident that the number of tandem and dispersed repeats were more in 15–20 bp and 31–40 bp category, respectively (Fig. 3A). The repeat structures of S. asoca and other five species of Fabaceae were analyzed by REPuter and were compared. The forward and palindrome repeats were common in these species (Fig. 3B-C). A total of 70 different SSR loci repeated more than 1 time (Table 1), contribute to the A–T richness of cp genome. The repeat regions play very significant roles in genome recombination (Yang et al., 2010). The SSRs are highly polymorphic due to higher mutation rate that affects the number of repeat units (Tsai et al., 2008).

Fig. 3.

Fig. 3

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The repeat structure analysis of the cp genome S. asoca. [A. The frequency of repeat by length; B. The repeat type; C. Comparison among six sequenced Fabaceae cp genomes (F: forward, P: palindrome, R: reverse, C: complement orientations)].

Table 1.

The SSR loci of S. asoca cp genome.

S. Type SSR Size Starts End
1 P1 (T)10 10 2993 3002
2 p2 (TA)6 12 3933 3944
3 p2 (CT)6 12 9477 9488
4 p2 (TA)6 12 9799 9810
5 p1 (A)11 11 11,185 11,195
6 p1 (A)10 10 11,518 11,527
7 p1 (T)10 10 14,444 14,453
8 p1 (A)10 10 15,746 15,755
9 c (T)11seq (T)14 105 16,111 16,215
10 c (T)15 seq (A)10 109 17,236 17,344
11 p1 (T)12 12 18,454 18,465
12 p1 (T)13 13 18,906 18,918
13 p1 (A)11 11 19,421 19,431
14 p1 (A)10 10 48,187 48,196
15 p1 (A)14 14 50,369 50,382
16 p1 (T)14 14 51,455 51,468
17 p2 (TA)8 16 51,746 51,761
18 p1 10(A) 10 53,129 53,138
19 p1 (T)10 10 53,454 53,463
20 p1 (T)14 14 54,019 54,032
21 c (AT)7 seq (T)11 119 59,271 59,389
22 p1 (T)10 10 59,795 59,804
23 c (AT)6 seq (AT)6 seq (AT)7 163 60,249 60,411
24 p3 (TAT)5 15 60,634 60,648
25 p1 (A)10 10 61,434 61,443
26 c (T)11 g(A)10 22 63,236 63,257
27 p1 (T)12 12 65,351 65,362
28 p1 (T)10 10 65,958 65,967
29 p4 (TTAA)6 24 69,696 69,719
30 p1 (T)12 12 73,240 73,251
31 p1 (T)10 10 74,761 74,770
32 c (A)10 seq (A)9 89 76,392 76,480
33 c (A)10 seq (AT)6 58 77,232 77,289
34 p1 (T)11 11 77,940 77,950
35 p1 (A)11 11 79,224 79,234
36 p1 (T)10 10 80,731 80,740
37 p1 (G)10 10 82,977 82,986
38 p1 (A)15 15 84,348 84,362
39 p1 (C)11 11 84,762 84,772
40 p2 (AT)6 12 85,254 85,265
41 p1 (A)10 10 91,245 91,254
42 p1 (T)10 10 91,781 91,790
43 p1 (T)13 13 92,481 92,493
44 p1 (A)14 14 93,452 93,465
45 p1 (A)12 12 93,799 93,810
46 p2 (AT)10 20 94,894 94,913
47 p2 (TA)6 12 96,515 96,526
48 p2 (AT)6 12 96,648 96,659
49 p1 (A)12 12 101,516 101,527
50 p1 (T)10 10 103,439 103,448
51 p2 (TA)7 14 103,785 103,798
52 p1 (T)15 15 105,822 105,836
53 p1 (T)10 10 106,166 106,175
54 p2 (AT)6 12 106,328 106,339
55 p1 (T)12 12 108,073 108,084
56 p1 (T)10 10 109,129 109,138
57 c (A)11 seq (T)10 38 109,557 109,594
58 p1 (A)13 13 112,044 112,056
59 p2 (AT)6 12 112,200 112,211
60 c (AT)7 t(TA)7 29 112,852 112,880
61 p1 (A)10 10 114,163 114,172
62 p1 (A)13 13 115,814 115,826
63 p1 (T)10 10 116,265 116,274
64 p1 (T)10 10 117,561 117,570
65 p1 (T)10 10 120,635 120,644
66 p1 (A)10 10 121,197 121,206
67 p1 (T)10 10 126,128 126,137
68 p1 (T)13 13 130,202 130,214
69 p1 (A)11 11 131,334 131,344
70 p1 (T)10 10 133,319 133,328
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The comparison of cp genome of S. asoca with the five other complete Detarioideae (Fabaceae) cp genomes e.g. C. harmsiana, D. pilosa, G. leonensis, and T. indica revealed extensive rearrangement in gene organization (Fig. 4). Further, the ME tree from the set of the GenBank accession number [Bauhinia variegata [(Clade: Rosids, Order: Fabales, Family: Fabaceae; GenBank accession number: GU135196, GU135033)], Mesua ferrea [Clade: Rosids, Order: Malpighiales, Family: Calophyllaceae; GenBank accession number: KY654490, JN114759)], Polyalthia longifolia [Clade: Magnoliids, Order: Magnoliales, Family: Annonaceae; GenBank accession number: JX856748, AY518786)], Shorea robusta [Clade: Rosids, Order: Malvales, Family: Dipterocarpaceae; GenBank accession number: KY654498, KY973059] and Trema orientalis [Clade: Rosids, Order: Rosales, Family: Cannabaceae; GenBank accession number: KY654502, AB924756)] of rbcL and matK [- the cp genes used in the plant DNA barcoding (CBOL, 2009)] with the sequence of S. asoca (KY678341, KC592386/MN866115) revealed the optimal tree with the sum of branch length 0.57133802 (Fig. 5), and have potential to be used as molecular typing of S. acoca from its adulterants (Hegde et al., 2018) as NMR spectroscopy (Urumarudappa et al., 2016) and rbcL-ISSR based DNA barcodes (Hegde et al., 2018) are least user-friendly.

Fig. 4.

Fig. 4

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The MAUVE alignment of cp genomes of five different Detarioideae, showing genomic rearrangement.

Fig. 5.

Fig. 5

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The minimum evolution tree based on combined sequence of rbcL and matK gene representative species of Rosids. (R, F, F: Clade: Rosids, Order: Fabales, Family: Fabaceae; R, M, C: Clade: Rosids, Order: Malpighiales, Family: Calophyllaceae; M, M, A: Clade: Magnoliids, Order: Magnoliales, Family: Annonaceae; R, M, C: Clade: Rosids, Order: Malvales, Family: Dipterocarpaceae; R, R, C: Clade: Rosids, Order: Rosales, Family: Cannabaceae).

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

The authors would like to extend their sincere appreciation to the Researchers Supporting Project number (RSP-2020/154), King Saud University, Riyadh, Saudi Arabia.

Footnotes

Peer review under responsibility of King Saud University.

Contributor Information

Mohammad Ajmal Ali, Email: ajmalpdc@gmail.cm.

Arun Bahadur Gurung, Email: arunbgurung@gmail.com.

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