The first complete chloroplast genome of Pontederia cordata (Pontederiaceae)

Abstract

The order Commelinales comprises many species with important economic and ecological values and represents a striking case of morphologically convergent evolution in monocots. However, so far the genomic resources of species within Commelinales are limited and the deep level phylogeny of Commelinales has not been well resolved. Here we reported and characterized the first complete chloroplast (cp) genome of Pontederia cordata and analysed the phylogenomic relationship of Commelinids based on complete cp sequences. The complete cp genome of P. cordata is 162,234 bp in length with a typical quadripartite structure. The overall GC content is 36.2%. A total of 124 genes were annotated, including 85 encoding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. The inverted repeat regions contain six CDSs, eight tRNA genes and all the four rRNA genes. Phylogenetic study validated the phylogenetic position of P cordata and showed that the three species from Commelinales form a monophyletic group sister to Zingiberales with high support rate. Meanwhile, species from Zingiberales and Commelinale form a molophyletic group sister to the Poales clade.

Keywords:

• Commelinales
• Pontederia cordata
• chloroplast genome
• phylogeny

Pontederia cordata is a wetland plant species native to the North and South America which has now been widely cultivated in China for ornamental purposes. Since P. cordata can effectively inhibit the growth of algal, it is also considered as a promising plant for water environmental restoration currently (Qian et al. 2017). The order Commelinales represents a typical system of morphologically convergent evolution (Givnish et al. 1999). However, so far the deep level phylogeny of Commelinales has not been well resolved. To provide genomic resources for investigating the evolution of Commelinales, here we reported and characterized the complete chloroplast (cp) genome of P. cordata, the first plastome sequence in the Pontederiaceae family.

Leaf materials of P. cordata were collected on the Campus of Zhejiang University, Hangzhou city, Zhejiang, China. The corresponding specimen was deposited in the herbarium of Tarim University (TAU) (voucher number: Yang20180001). Total DNA was isolated using the DNA Plantzol Reagent (Invitrogen, Carlsbad, CA) and sent to BGI (Shenzhen, Guangdong, China) for next-generation sequencing on the Illumina Hiseq Platform (Illumina, San Diego, CA). The cp genome was assembled using NOVOPlasty (Dierckxsens et al. 2017) and annotated using Geneious version 11.0.4 (Biomatters Ltd., Auckland, New Zealand). The cp genome sequence of Xiphidium caeruleum (GenBank accession number: JX08669.1) was used as the reference (Barrett et al. 2013).

The cp genome of P. cordata is 162,234 bp in length with a typical quadripartite structure consisting of a large single copy of 90,112 bp, a small single copy region of 18,454 bp, and a pair of 26,834 bp inverted repeats (IRs). The GC content of the complete cp genome is 36.2%. The genome contains 124 genes, including 85 encoding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. The IR regions contain six coding sequences (CDSs), eight tRNA genes, and all the four rRNA genes. The cp genome structure, GC content, and gene locations of P. cordata are almost identical to the previously reported cp genomes of Xiphidium caeruleum and Hanguana malayana belonging to Commelinales (Barrett et al. 2013).

Phylogenomic analysis based on the complete cp genome was performed with the maximum likelihood (ML) and Bayesian inference (BI) methods (Ronquist and Huelsenbeck 2003; Stamatakis 2014) implemented on the CIPRES Science Gateway V.3.3 (Miller et al. 2010). Two species from Asparagales (Dendrobium bellatulum and Dendrobium candidum) were used as the outgroup. The cp genome sequences of P. cordata was submitted to GeneBank (accession number: xxxxx). The GenBank accession numbers of other species used for phylogenomic analysis are provided in Table 1. All the 20 genome sequences were aligned using MAFFT version 7.0 (Katoh et al. 2017).

Table 1. GenBank accession numbers of all the plastome sequences used for phylogenetic reconstruction.

Order	Species	GenBank accession number
Commelinales	Hanguana malayana	NC_029962.1
	Xiphidium caeruleum	JX088669.1
Zingiberales	Costus pulverulentus	KF601573.1
	Heliconia collinsiana	NC_020362.1
	Curcuma roscoeana	KF601574.1
	Maranta leuconeura	KF601571.1
	Monocostus uniflorus	KF601572.1
Poales	Otatea glauca	NC_028631.1
	Oryza sativa	NC_001320.1
	Pariana campestris	NC_027491.1
	Stipa magnifica	NC_037031.1
	Stipa narynica	NC_037032.1
Arecales	Acoelorraphe wrightii	NC_029973.1
	Borassus flabellifer	KP901247.1
	Chamaerops humilis	KT312935.1
	Baxteria australis	NC_029970.1
	Dasypogon bromeliifolius	JX088665.1
Asparagales	Dendrobium bellatulum	NC_037700.1
	Dendrobium candidum	NC_035745.1

The ML and BI analyses generated the same tree topology (Figure 1). Pontederia cordata and two other species from Commelinales form a monophyletic group sister to Zingiberales. The evolutionary relationships of Poales, Arecales, and Asparagales are consistent with the results from previous phylogenetic study (Barrett et al. 2013). The P. cordata plastome reported in this study may provide useful resources for the development of ornamental and ecological value as well as robust phylogenetic study at deep level of Commelinales in the future.

Figure 1. Molecular phylogeny of Commelinids based on the complete chloroplast genomes of 20 species, with Dendrobium bellatulum and Dendrobium candidum as the outgroup. Relative branch lengths are indicated below the phylogenetic tree. Numbers above each branch indicates the bootstrap values obtained from ML analysis (before the slash) and the posterior probabilities obtained from BI analysis (after the slash).

Disclosure statement

The authors are really grateful to the opened raw genome data from public database. The authors report no conflict of interest and are responsible for the content and writing of the paper.

Additional information

Funding

This research was supported by the National Natural Science Foundation of China [Grant No. 31800187], the Scientific Research Start-up Foundation of Zhejiang Shuren University [grant no. KXJ0517104], the National basic resource survey of China [Grant No. 2017FY100201], and the Natural Science Foundation of Zhejiang Province, China [Grant No. LQ19C020005].