Comparative analysis of cp genome of Fagonia indica growing in desert and its implications in pattern of similarity and variations

Abstract

The chloroplasts genome encodes several key proteins that involves in the process of the photosynthesis and also in other metabolic processes important for growth and development, yield, biomass, and plant interactions with their environment. The present study aimed to sequencing of cp genome of Fagonia indica Burm.f (Zygophyllaceae), -a plant that occurs even in the hot desert condition of the inner zone of Rub′ al-Khali (the Empty Quarter) of south-central Arabia, and its comparative analyses with the representative of the sequence of the different categories [viz. (a) with the other member of the family Zygophyllaceae, and with the representatives from: (b) different clade of the angiosperms, (c) flowering plants occurs in different major habitats, (d) different groups of plants, (e) different group of plants having range of biomass, (f) C3 and C4 plants, and (g) the representative from very common, rare and major high yielding crop of the world] to unravel the genetic pattern of similarity and variations. The comparison of F. indica genome in different categories showed strong evidence and further support for the conservative pattern of chloroplast genome, the coding and non-coding region remains conserved even in phylogenetically distant eukaryotic clades, and might not have the sole roles in organism′s yield, rarity or abundance and biomass, and in encountering the stress. Nevertheless, the result could be useful for molecular phylogenetic and molecular ecological and molecular mechanism of photosynthesis.

1. Introduction

Fagonia indica Burm.f. [family Zygophyllaceae; included in the Fabids (APG IV, 2016)] is a thorny medicinal herb possess anticancer activity (Lam et al., 2014), growing widely in Asian and African deserts (Beier, 2005), and able to grow even in the hot desert condition of the inner zone of Rub' al-Khali (the Empty Quarter) of south-central Arabia where annual precipitation generally less than 35 mm or sometimes very less or no rain for several years (Mandavil, 1986). Since the enhanced understanding of chloroplast biology came with the recent advances in biotechnology and bioinformatics during last two decades (Shendure and Ji, 2008, Shendure et al., 2017) have impact on various biotechnological applications including genetic engineering to enhance plant agronomic traits (Shintani and DellaPenna, 1998, Viitanen et al., 2004, Apel and Bock, 2009, Verma et al., 2010, Kwon et al., 2013, Kwon and Daniell, 2015, Jin et al., 2011, Jin and Daniell, 2014, Holtz et al., 2015, Brozynska et al., 2016, Daniell et al., 2016). The chloroplasts genome encodes several key proteins that involves in the process of the photosynthesis and in other metabolic processes important for the growth and development, and plant interactions with their environment like responses to heat, drought, salt, light, etc., (Bobik and Burch-Smith, 2015). The dynamics of genetic diversity have fascinated to naturalists for centuries, the present study aimed to comparative analyses of cp genome to unravel the genetic pattern of similarity and variations in context with organism’s yield, rarity or abundance and biomass, and in encountering the stress.

2. Materials and methods

2.1. cp genome sequencing

The leaf material of F. indica was collected, and stored at 4 °C for overnight. The modified Percoll gradient buffer method (Kim and Kim, 2013) was then applied to isolate the chloroplasts. The DNA was extracted from the isolated chloroplast using DNeasy Plant Mini Kit (Qiagen, Seoul, Korea). The Purified cp DNA was fragmented, and used to construct short-insert libraries following the manufacturer′s manual (Illumina). The sequencing was performed at DNA Illumina sequencing platform.

2.2. Assembly, annotation and comparative analyses of the cp genome

The high quality reads were assembled using spades (Bankevich et al., 2012). The assembled genome was annotated using GeSeq (Tillich et al., 2017), the cp genome sequence of Tibetia liangshanensis (NC_036109.1) was used as reference. The comparative analysis of the cp genome was analyzed using the mVISTA program in Shuffle-LAGAN mode (Brudno et al., 2003). For the comparative cp genomic analyses, the cp genome sequence of F. indica was compared with the Larrea tridentata (-a member of the Order Zygophyllales; Family Zygophyllaceae; sub family Larreoideae; GenBank NC_028023.1), and also with the representative of the sequence of the different categories [viz. i. the representatives from different clade of the angiosperms including Rosids (Annexure I), ii. the representative of flowering plants occurs in different major habitats such as in hot/desert habitat, temperate rain forest, temperate/tropical and sub-tropical regions, cold desert, wetland/aquatic, sea grass/aquatic/marine habitat (Annexure II), iii. the representative of different groups of plants such as Algae, Bryophytes, Pteridophyte and Gymnosperm (Annexure III), iv. the representative from range of biomass such as unicellular plant, plant having thalloid body, small size herbaceous plant, living giant Gymnosperm from desert habitat, smallest flowering plants, very rapidly growing medium sized herbs, trees occurs in desert and tree with large canopy (Annexure IV), v. the representative from C3 and C4 plant (Annexure V), and vi. the representative from common, rare and major high yielding crop of the world (Annexure VI)] were plotted using the mVISTA program (Brudno et al., 2003) with the annotation of F. indica as reference (Fig. 1), and the percent identity plot for comparison were drawn.

Fig. 1.

Percent identity plot for comparison of Fagonia indica chloroplast genome with the representative of plants (a) occurs in different major habitats, (b) of major eukaryotic clade [Algae to Angiosperm], (c) range of biomass [from unicellular to large canopy], (d) with major important crop [(Rice, Wheat and Maize), common plant (Cynodon) and rare plant (Berchemiella wilsonii].

Annexure I:- Apiales: Anethum graveolens (NC_029470), Daucus carota (NC_008325), Panax schinseng (NC_006290); Asterales: Helianthus annuus (NC_007977), Lactuca sativa (DQ383816), Trachelium caeruleum (NC_010442); Brassicales: Arabidopsis thaliana (NC_000932), Brassica rapa (DQ231548); Buxales: Buxus microphylla (EF380351); Caryophyllales: Spinacia oleracea (NC_002202); Cucurbitales: Cucumis sativus (NC_007144); Fabales: Glycine max (NC_007942), Lotus corniculatus (NC_002694), Medicago truncatula (NC_003119); Gentianales: Coffea arabica (NC_008535); Geraniales: Pelargonium × hortorum (NC_008454), Lamiales: Jasminum nudiflorum (NC_008407); Malphigiales: Manihot esculenta (EU117376), Passiflora biflora (NC_038120), Populus trichocarpa (NC_008235), Malvales: Gossypium hirsutum (NC_007944); Myrtales: Eucalyptus globulus (NC_008115), Oenothera elata (NC_002693); Proteales: Platanus occidentalis (NC_008335); Ranunculales: Nandina domestica (NC_008336), Ranunculus macranthus (NC_008796); Rosales: Morus indica (NC_008359); Sapindales: Citrus sinensis (NC_008334); Solanales: Atropa belladonna (NC_004561), Ipomoea purpurea (EU118126), Nicotiana sylvestris (NC_007500), N. tabacum (NC_001879), N. tomentosus (NC_007602), Solanum bulbocastanum (NC_007943), S. lycopersicum (DQ347959), S. tuberosum (NC_008096); Vitales: Vitis vinifera (NC_007957); Zygophyllales: Larrea tridentate (NC_028023).

Annexure II:- Hot/desert habitat: Haloxylon persicum (NC_027669); Temperate Rain forest: Panax vietnamensis (NC_033519); Temperate/tropical and sub-tropical regions: Praxelis clematidea (NC_023833); Cold desert: Arabis alpine (NC_023367); Wetland/Aquatic: Nelumbo nucifera (NC_025339); Sea grass/Aquatic/Marine habitat: Zostera marina (NC_036014).

Annexure III:- Algae: Chlamydomonas reinhardtii (BK000554); Bryophytes: Marchantia paleacea (NC_001319); Pteridophyte: Adiantum capillus-veneris (NC_004766); Gymnosperm: Welwitschia mirabilis (EU342371).

Annexure IV:- Unicellular plant: Algae- Chlamydomonas reinhardtii (BK000554); Thalloid plant body: Bryophytes- Marchantia paleacea (NC_001319); Small size herbaceous plant: Pteridophyte- Adiantum capillus-veneris (NC_004766); Living Gymnosperm from desert habitat: Gymnosperm- Welwitschia mirabilis (EU342371); Smallest flowering plants: Angiosperm- Wolffia australiana (NC_015899); Very rapidly growing medium sized herbs: Angiosperm- Praxelis clematidea (KF922320); Trees occurs in desert: Angiosperm- Haloxylon persicum (KF534479); Tree with large canopy: Angiosperm- Ficus religiosa voucher (NC_033979).

Annexure V:- C3 Plant: Poaceae- Oryza sativa (NC_008155), Triticum aestivum (NC_002762), Solanaceae- Solanum tuberosum (NC_008096), Nicotiana tabacum (Z00044), Fabaceae-Glycine max (NC_007942), Malvaceae- Gossypium thurberi (NC_015204), Fabaceae- Arachis hypogaea (NC_037358); C4 plant: Poaceae- Aristida ternipe (NC_037164), Zea mays (NC_001666), Saccharum officinarum (NC_035224), Amaranthaceae- Bienertia sinuspersici (KU726550), Euphorbiaceae- Euphorbia esula (NC_033910).

Annexure VI:- Rare: Berchemiella wilsonii var. wilsoni (KY926621); Major high yielding crop of the world: Oryza sativa (NC_008155), Triticum aestivum (NC_002762), Zea mays (NC_001666); Common: Cynodon dactylon (NC_034680).

3. Results and discussion

The high quality reads were de novo assembled, resulted into a contig of 128,379 bp with GC content of 34.02% which is consistent with the cp genome of L. tridentata (35.09%). The cp genome size of F. indica cp was approximately 7.5 kb, and smaller than L. tridentata cp genome. Interestingly, F. indica has single copy of inverted repeat resulting into the inverted gene order compared to its closest relative L. tridentata. The length of angiosperm cp genomes remains variable primarily due to expansion and contraction of the inverted repeat IR region and the single copy boundary regions. It is evident from the analysis that the coding region is less divergent than the non-coding region. However further analysis showed that clpP and accD were the most divergent coding regions.

With the increasing global population and demand for food, and the rising global temperatures and decreasing water resources, it is important to understand the genomic mechanisms of photosynthetic genes respond to abiotic and biotic stress which may lead to enhance the yield of the crops (Cushman, 2001, Berry et al., 2011, Berry et al., 2013). The genome annotation resulted a total of 115 unique coding genes were annotated which includes 80 protein coding (represent 80200 bp nucleotides coding for 42,793 codons), 31 tRNA and 4 rRNA genes. The gene order in F. indica was similar to the angiosperm’s gene order except for the loss of one copy of the IR and by the presence of a single, large inversion that reverses the order of the genes between rbcL and rps16, the similar cases have also been reported in some cp genome of legumes previously (Doyle et al., 1996, Kato et al., 2000, Saski et al., 2005, Guo et al., 2007).

The comparative analyses of cp genome of the representatives from different clade of the angiosperms including Rosids with F. indica as reference revealed that coding region was more conserved than the non-coding region; however, clpP (Clp protease proteolytic subunit), ycf1, ycf2 and ycf4 were the most divergent coding region among all taxa included in the analyses. The comparative analyses of the representatives from different habitats with F. indica as reference also revealed that coding regions were more conserved than the non-coding regions, but here in this case the ycf1 was the most divergent coding region among all taxa.

The percent identity plot of the representatives from different groups of plants and also the different group of plants having range of biomass with F. indica as reference revealed that coding regions were more conserved than the non-coding regions; however, it was interesting to note the considerable differences in between cp genome of F. indica and C. reinhardtii.

Further, the comparative analyses of cp genome of the representatives from C3 and C4 plant and the representative from common, rare and major high yielding crop of the world revealed that coding region was more conserved than the non-coding region as similar to the results of previous comparative analyses, and the ycf1 and ycf2 were the most divergent coding region. It was interesting to note that the loss of accD gene in rice, wheat, maize and Cynodon (the representative from common, major high yielding crop). The accD, ycf2 genes are exclusively transcribed by the nuclear-encoded plastid RNA polymerase (NEP) which plays a role in maintaining housekeeping functions in proplastids, and in plastid development from proplastids (Hajdukiewicz et al., 1997, Allison, 2000, Swiatecka-Hagenbruch et al., 2008).

In summary, the comparison of F. indica genome in different categories showed strong evidence and further support for the conservative pattern of chloroplast genome, the coding and non-coding region remains conserved even in phylogenetically distant eukaryotic clades, and might not have the sole roles in organism′s yield, rarity or abundance and biomass, and in encountering the stress. Further the present findings also support the anterograde and retrograde signaling which insures the highly coordinated expression of the photosynthetic genes (Jung and Chory, 2010).

Declaration of Competing Interest

The authors report no conflicts of interest in this work.