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Sequencing the organelle genomes of Bougainvillea spectabilis and Mirabilis jalapa (Nyctaginaceae)

Abstract

Objectives

Mirabilis jalapa L. and Bougainvillea spectabilis are two Mirabilis species known for their ornamental and pharmaceutical values. The organelle genomes are highly conserved with a rapid evolution rate making them suitable for evolutionary studies. Therefore, mitochondrial and chloroplast genomes of B. spectabilis and M. jalapa were sequenced to understand their evolutionary relationship with other angiosperms.

Data description

Here, we report the complete mitochondrial genomes of B. spectabilis and M. jalapa (343,746 bp and 267,334 bp, respectively) and chloroplast genomes of B. spectabilis (154,520 bp) and M. jalapa (154,532 bp) obtained from Illumina NovaSeq. The mitochondrial genomes of B. spectabilis and M. jalapa consisted of 70 and 72 genes, respectively. Likewise, the chloroplast genomes of B. spectabilis and M. jalapa contained 131 and 132 genes, respectively. The generated genomic data will be useful for molecular characterization and evolutionary studies.

Objective

Organelle genomes such as chloroplast and mitochondrial genomes are highly conserved in plant species except for minor structural rearrangements reported in few species [1]. The conserved nature and rapid evolution rate of organelle genomes play a key role in understanding the evolutionary aspects of different species [2]. Chloroplast genomes generally have a quadripartite structure ranging from 107 to 217 kb [3]. In contrast, mitochondrial genomes are bigger in size (105 kb to 110 Mb) [4]. Compared to the nucleic genome, organelle genomes are ideal for studying phylogenetics [5,6,7,8,9].

The Nyctaginaceae family, known for its ornamental value and pharmaceutical properties, consists of hermaphroditic trees, shrubs, and herbs. M. jalapa and B. spectabilis originated from tropical America and have been widely adapted as ornamental plants for their vibrant colors, medicinal characteristics, and phytoremediation properties [10,11,12,13,14]. Antioxidative, antimicrobial, antibacterial, and antiviral effects of both species have also been reported [10, 15, 16]. Although both species have been well characterized for their bioactive components, genomic resources for molecular characterization and evolutionary analyses are rare in M. jalapa and B. spectabilis. In this study, we sequenced the chloroplast and mitochondrial genomes of M. jalapa and B. spectabilis. The generated datasets will be used to investigate the structural organization of their organelle genomes and the phylogenetic relationship with existing angiosperms.

Data description

The leaf samples from B. spectabilis and M. jalapa were collected from Qiannan Buyi and Miao Autonomous Prefecture (N: 26° 22 ′ 75.63 ″, E:107° 62 ′ 39.08 ″), Guizhou Province, China. The samples were obtained from the wild and no permissions were necessary to collect such samples. The formal identification of the samples was conducted by Prof Xiaozhong Lan and voucher specimens were deposited at Tibet Agriculture and Animal Husbandry University (http://www.taaas.org) under the voucher numbers: ZY20-082,503 and ZY20-082,504. The total genomic DNA (gDNA) was isolated from fresh leaf samples with the CTAB method using the Plant Genomic DNA Kit (DP305, TIANGEN, China). After the fragmentation of DNA, 300 bp short insert libraries were constructed. The expected size profile was verified using gel electrophoresis. The gDNA was sequenced on the Illumina NovaSeq 6000 platform at Wuhan bio-mall Biotechnology Co., Ltd (Wuhan, China), following the standard protocols. Quality control was performed using fastqc and NGSQC, and raw data were cleaned for low-quality reads. Chloroplast and mitochondrial genomes were assembled using SPAdes v3.9.0 [17] and MITObim v1.8. The annotation was performed using CpGAVAS [18].

The obtained circular mitochondrial genomes of B. spectabilis and M. jalapa were 343,746 bp and 267,334 bp long, respectively (Data files 1 and 2). GC contents in B. spectabilis and M. jalapa mitochondrial genomes were estimated to be 37% and 34.5%, respectively. B. spectabilis mitochondrial genome was annotated with 70 genes. Among these, we identified 42 protein-coding genes, 25 tRNA, and three rRNA. M. jalapa mitochondrial genome consisted of 72 genes with 40 protein-coding genes, 28 tRNA, and three rRNA. Strong evidence of expression supported most annotated genes.

The sequenced chloroplast genomes of B. spectabilis and M. jalapa were 154,520 bp (35.9% GC content) and 154,532 bp (35.9% GC content) long, respectively (Data file 3 and 4). The quadripartite structure of M. jalapa chloroplast genome contained two inverted repeats regions (25,428 bp), one large-single copy (85,908 bp), and one small-single copy (17,768 bp). A total of 131 genes were identified, including 86 protein-coding genes, eight rRNA, and 37 tRNA. The chloroplast genome of B. spectabilis encoded 132 genes, including 87 protein-coding genes, eight rRNA genes, and 37 tRNA genes. RPS12 gene had a trans-splicing in the two species. Similarly, in both genomes, a total of 15 genes (trnKUUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA) had a single intron while two genes (clpP and ycf3) had two introns.

The genomic data presented here are the first publicly available organelle genomes of B. spectabilis and M. jalapa. The datasets can be further exploited to investigate the evolutionary relationship of B. spectabilis and M. jalapa with existing Nyctaginaceae species and other angiosperms. It can also be used for the development of molecular markers and DNA barcoding applications.

Limitations

Organelle genomes have a lower mutation rate as compared to nucleic genomes. Therefore, organelle genomes are not suitable for studying differentiation within the species (Table 1).

Table 1 Overview of data files/data sets

Availability of data and materials

The data sets are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MW167296 (data set 1; Bio-project PRJNA682652) [19], https://www.ncbi.nlm.nih.gov/nuccore/MW295642 (data set 2; Bio-project PRJNA692028) [20], https://www.ncbi.nlm.nih.gov/nuccore/MW167297 (data set 3; Bio-project PRJNA682652) [21], and https://www.ncbi.nlm.nih.gov/nuccore/MW894644 (data set 4; Bio-project PRJNA720802) [22].

Abbreviations

GC:

Guanine-Cytosine

rRNA:

Ribosomal ribonucleic acid

tRNA:

Transfer ribonucleic acid

CTAB:

Cetyltrimethylammonium bromide

DNA:

Deoxyribonucleic acid

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Acknowledgements

We thank the staff of Norminkoda Biotechnology Co., Ltd. (Wuhan, China) for their assistance during the organelle the sequencing stage.

Funding

This work was funded by The Nyingchi City Science and Technology Plan Projects [Grant No. XDHZ-2020–01], The Tibet Autonomous Region Major Special Science and Technology Project [Grant No. XZ201901-GA-04]. The funders had no role in the design of this study, during its execution, analyses, interpretation of the data, or decision to publish the paper.

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Contributions

F Y conceived the project, performed the sampling, bioinformatics analysis and drafted the manuscript. X L conceived the project, guided and supervised the data analysis, provided funding support and revised the first drafts of the manuscript. All authors have read and approved the final version of this manuscript.

Corresponding author

Correspondence to Xiaozhong Lan.

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Yuan, F., Lan, X. Sequencing the organelle genomes of Bougainvillea spectabilis and Mirabilis jalapa (Nyctaginaceae). BMC Genom Data 23, 28 (2022). https://doi.org/10.1186/s12863-022-01042-0

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Keywords

  • Mitochondrial genome
  • Chloroplast genome
  • Phylogenetics
  • Traditional medicine
  • Ornamental plants
  • DNA barcoding