The complete mitochondrial genome of the biodiesel plant Jatropha curcas L.

Abstract

Jatropha curcas (Linnaeus, 1753) is a plant species in the order Malpighiales and the family Euphorbiaceae and is native to the tropical regions of America, such as Mexico and Argentina. Currently, this plant species inhabits tropical and subtropical regions of the world. Jatropha has been widely used as a biofuel plant to produce high-quality diesel engine fuel. In this study, the complete mitochondrial genome sequence of J. curcas was assembled into 561,839 bp circular nucleotides with a GC content of 44.6%. The mitochondrial genome of J. curcas comprises 33 known protein-coding genes, 22 tRNA genes, three rRNA genes, one ncRNA gene, and 85 open reading frame genes. Phylogenetic analysis showed this species is closely related to the castor bean (Ricinus communis).

Keywords:

• Jatropha curcas
• Malpighiales
• Euphorbiaceae
• biodiesel plant
• mitochondrial genome

Introduction

Jatropha curcas (Linnaeus, 1753) is a monoecious tree or shrub that originated in Central America and is widely distributed in tropical and subtropical regions. J. curcas belongs to the order Malpighiales and the family Euphorbiaceae. Euphorbiaceae is one of the prominent flowering plant families, including several economically important plant species such as, rubber trees (Hevea brasiliensis), cassava (Manihot esculenta), and castor bean (Ricinus communis) (Ha et al. 2019; Fayed et al. 2020). As a member of the Euphorbiaceae, J. curcas has been widely used as a biofuel plant to generate high-quality diesel fuel because it produces seeds that contain significant portions of non-edible oil (Ashraful et al. 2014; Takase et al. 2015). Jatropha seed oil contains oleic (18:1), linoleic (18:2), palmitic (16:0), and stearic acid (18:0), along with phorbol ester, a toxic compound, suggesting that it is a promising alternative to standard diesel fuel that does not compete for food security (Sinha et al. 2015; Gomes et al. 2022). Furthermore, the evolutionarily conserved succulent stem in Jatropha and some Euphorbiaceae plants makes Jatropha tolerant to drought stress and arid lands, facilitating marginal land use and reducing competition for arable land use in food cultivation (Maes et al. 2009; Santos et al. 2015; Della Torre et al. 2021).

The complete chloroplast genome sequence has played a crucial role in understanding the evolutionary relationships of various Euphorbiaceae plants (Zhang, Shi, et al. 2019; Zhang, Zhao, et al. 2019; Wang et al. 2020; Iwata et al. 2022). The whole reference genome sequences and complete circular chloroplast genome sequence of J. curcas have been reported recently, providing insights into its evolutionary history (Asif et al. 2010; Ha et al. 2019). However, the complete mitochondrial genome sequence has not been reported in Euphorbiaceae, except Ricinus communis (Rivarola et al. 2011). Here, we report the novel complete mitochondrial genome sequence of J. curcas as a second representative mitochondrial genome sequence in Euphorbiaceae plants.

Materials and methods

A specimen of J. curcas was determined by D. Burch and deposited at the Atlas of Florida Plants (https://florida.plantatlas.usf.edu/Default.aspx, Richard P. Wunderlin, [email protected]) under the accession number: 106202 (Figure 1(A)). The whole-genome sequence of J. curcas var. Chai Nat, widely cultivated in Chai Nat province (latitude 15.18567 and longitude 100.12367) of Thailand, has been reported previously (Ha et al. 2019) (Figure 1(B)). To investigate the mitochondrial genome sequence of J. curcas, we downloaded raw PacBio read sequences (SRR5974849) and Illumina paired-end sequences (SRR5974850) from PRJNA399212 of SRA (Ha et al. 2019). To assemble the mitochondrial genome, we corrected and trimmed the PacBio reads using Canu (Koren et al. 2017). Sequence reads carrying homologous sequences to the mitochondrial genes of Ricinus communis (NC_015141.1) were selected using TBLASTX (Camacho et al. 2009). The selected reads were initially assembled using FALCON (Chin et al. 2016). A total of nine contigs carrying the mitochondrial genes were identified. The assembled contigs were submitted as seed sequences to the short read assembly using NOVOPlasty (Dierckxsens et al. 2017). The assembled sequence was assessed by coverage and sequencing depth (https://www.protocols.io/view/generating-sequencing-depth-and-coverage-map-for-o-4r3l27jkxg1y/v1) (Supplemental figure 1). To validate the complete circular form of J. curcas mitogenome, sequence alignment and mapping depth around the merged position were examined using Samtools and IGV (Li et al. 2009; Thorvaldsdóttir et al. 2013) (Supplemental figure 2). Gene prediction and annotation were performed using MFannot (https://megasun.bch.umontreal.ca/apps/mfannot/) for protein-coding genes and transfer RNAs and GeSeq annotator for ribosomal RNAs (Tillich et al. 2017). A map of the complete mitochondrial genome sequence and genes was generated using OrganellarGenomeDRAW (Greiner et al. 2019). A molecular phylogenetic tree was constructed using the maximum-likelihood method with Jones–Taylor–Thornton (JTT) matrix-based model and 1000 bootstrap replications using MEGA software (Kumar et al. 2018).

Figure 1. The specimen and picture of the Jatropha curcas L. The specimen of J. curcas was deposited at the Atlas of Florida Plants, operated by the Institute for Systematic Botany at the University of South Florida (https://Florida.plantatlas.usf.edu/Default.aspx) under the accession number: 106202 (A). Picture of J. curcas was taken and provided by Won Joo Hwang (B).

Results

The complete mitochondrial genome of J. curcas spans 561,839 bp in length with 44.6% GC content and encodes 144 genes, including 33 known protein-coding genes, 22 tRNA genes, three rRNA genes, one ncRNA gene, and 85 open reading frame genes (ORFs) (Figure 2). Among the 33 known protein-coding genes, nad1 and cox1 (first copy) carried two exons, and nad4 and nad7 carried 4 and 5 exons, respectively (Supplemental figure 3). There were 15 duplicated gene pairs, including atp1, atp9, cox1, trnP, and 11 orf genes (orf99, orf101, orf105, orf107, orf110, orf111, orf114, orf115, orf118, orf142, and orf183), and four sets of triplicated orf genes (orf102, orf108, orf109, and orf130). Interestingly, two ORF genes (orf106 and orf103) were quadruplicated and hexaplicated, respectively. A set of trnM genes was presented as pentaplicated genes. The remaining 87 genes are presented as single copies.

Figure 2. Map of Jatropha curcas mitochondrial genome. The genes annotated outside the circular genome are in the forward orientation, whereas the genes inside the circle are in the reverse orientation. Genes with asterisk mark indicate cis-splicing genes.

A total 18 genes, including atp1 (second copy), atp4, atp6, ccmC, ccmF, cob, cox1 (first copy), cox2, cox3, nad4, nad6, nad7, nad9, orf206, orf294, orf326, orf653, and rps3 have substantially conserved over 11 plant species including nine Malpighiales plants and two outgroup plants: Arabidopsis thaliana (Sloan et al. 2018), Brassica napus (Handa 2003), Bruguiera sexangula (Zhang, Bai, Zhang 2020), Bruguiera x rhynchopetala (Zhang, Bai, Liu 2020), Populus alba (Brenner et al. 2019), Populus tremula (Kersten et al. 2016), Ricinus communis (Rivarola et al. 2011), Salix cardiophylla (Chen et al. 2020), Salix dunnii (He et al. 2021), and Salix wilsonii (Han et al. 2022). The phylogenetic tree showed that J. curcas was closely related to R. communis (Figure 3).

Figure 3. Unrooted phylogenetic tree of mitochondrial genome sequences of Malpighiales. The phylogenetic tree was constructed using the maximum-likelihood (ML) method with Jones–Taylor–Thornton (JTT) matrix-based model and 1000 times bootstrap replications. The protein sequences of mitochondrial genes from nine Malpighiales and two outgroup plants (Arabidopsis thaliana and Brassica napus) were used. Bootstrap values indicate the topology of the tree. The asterisk mark indicates the plant species investigated in this study.

Discussion and conclusions

We report the novel complete mitochondrial genome sequence of J. curcas as a second representative plant species in the Euphorbiaceae family. The complete mitochondrial genome sequence of J. curcas and its whole genome sequences provide an essential resource for phylogenomic analysis and will help elucidate the evolutionary relationship between the Malpighiales and the Euphorbiaceae family soon.

Author contributions

S.S. and J.H. conceptualized the study and conducted bioinformatics analyses. The manuscript was prepared by S.S. and revised by J.H.

Ethical approval

Any data from NCBI SRA does not need ethical approval.

Acknowledgements

We especially thank Won Joo Hwang for providing a picture of Jatropha curcas.

Disclosure statement

The authors declare no conflict of interest.

Data availability statement

The data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under accession no. OQ603497. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA399212, SRR5974849, SRR5974850, and SAMN07527279, respectively.

Additional information

Funding

This study was supported by the ‘2022 Research Grant’ from Kangwon National University [202203110001] to S.S. and a National Research Foundation of Korea (NRF) Grant funded by the Korean Government (MSIT) [No. 2021R1C1C1004233] to J.H.