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. 2021 Mar 16;6(3):927–928. doi: 10.1080/23802359.2021.1888331

The complete chloroplast genome sequence of Oryza sativa Temperate japonica

Qi Feng a, Wei-Cai Song a, Yun-Jiao Zhang b,✉, Chao Shi a,c,✉
PMCID: PMC7971287  PMID: 33796685

Abstract

In this study, the complete chloroplast genome of O. sativa Temperate Japonica YunJing-24 was assembled using Illumina sequencing data. The complete chloroplast (cp) genome is 134,556 bp in length, including a pair of invert repeats (IRA and IRB) regions of 20,797 bp, large single-copy (LSC) region of 80,615 bp, and small single-copy (SSC) region of 12,347 bp. A total of 129 genes were predicted in the genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the phylogenetic relationship between O. sativa Temperate Japonica and other representative species.

Keywords: Oryza sativa, Temperate japonica, chloroplast genome, Poaceae

Rice is one of the important plants of Poaceae and is the main food for human beings. Rice varieties are divided into two major subspecies, Indica and Japonica, which are different from each other in geographical distribution, morphological, and physiological aspects (Londo et al. 2006). Indica is suitable for high temperature, strong light, and wet tropical and subtropical regions. It has the characteristics of weak resistance to fertilizer, light green leaves, slender grains, and easy threshing. However, Japonica is suitable for Temperate and subtropical high-altitude areas, with strong cold resistance and fertilizer resistance, dark green leaves, short round grains, not easy to threshing. The O. sativa Temperate Japonica is one of the five kinds of O. sativa subsp. Japonica (Xiong et al. 2011; Cheng et al. 2019). The complete chloroplast genome of O. sativa Temperate Japonica provides significant information for further studies on its taxonomy and population genetics.

Fresh leaves of O. sativa Temperate Japonica YunJing-24 was collected from Kunming city, Yunnan province of China (24°23'N, 102°10'E), and the voucher specimen and DNA were deposited at Qingdao University of Science and Technology (specimen code HY0811). The total genomic DNA was extracted from fresh leaves of the sample using a modified CTAB method (Doyle and Doyle 1987). A genomic library with an insert size of 300 bp was constructed and the library was sequenced using the Illumina HiSeq platform in Novogene (Nanjing, China). A total of 945 Mb of 150 bp paired-end reads were generated.

The complete chloroplast genome sequence of O. sativa Temperate Japonica was assembled using the program NOVOPlasty4.2 software (Dierckxsens et al. 2017), with the chloroplast genome of O. sativa Tropical Japonica (GenBank Accession No. KT289404) as the reference sequences and ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) gene from O. sativa cultivar Vettuver (GenBank Accession No. MK932669) as the seed sequence. The final complete chloroplast genome annotation was performed using the GeSeq (Michael et al. 2017) and tRNAs were identified using the tRNAscan-SE v2.0.7 (Schattner et al. 2005).

The complete chloroplast genome of O. sativa Temperate Japonica (GenBank Accession No. MW001303) was 134,556 bp in length, with a GC content of 39.0%. The complete chloroplast genome shows a typical quadripartite structure with a pair of inverted repeats (IRs) of 20,797 bp, separated by a large single-copy region (LSC) of 50,615 bp and a small single-copy region (SSC) of 12,347 bp. A total of 129 genes were identified from O. sativa Temperate Japonica chloroplast genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, 8 classes of genes (rps16, atpF, petB, petD, rpl16, ndhB, ndhA, rpl2) were found to contain two exons.

The complete chloroplast genome sequence of O. sativa Temperate Japonica and other species selected from the Genus Oryza were used to construct phylogenetic tree (Figure 1). The sequences were downloaded from the GenBank database and were aligned using MAFFT version 7 (Katoh and Standley 2013) and then visualized and manually adjusted using BioEdit (Hall 1999). Mosel selected process in Mega version X (Kumar et al. 2018). GTR + G + I were selected by the Akaike Information Criterion. The maximum-likelihood method was used to infer the phylogenetic relationship, and the phylogenetic tree was constructed with Mega version X using 1000 bootstrap (Minh et al. 2013). The result shows that O. sativa Temperate Japonica was clustered with other species from genus Oryza (Figure 1).

Figure 1.

Figure 1.

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A maximum-likelihood tree illustrates the phylogenetic position of O. sativa Temperate Japonica among other species. The number on each node indicates bootstrap support value. After species is the chloroplast genome sequence accession numbers used by GenBank.

Funding Statement

This work was supported by the National Natural Science Foundation of China [No. 31701090].

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/nuccore/1929697386) under the accession no. MW001303. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA692344, SRR13447968, and SAMN17320349, respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/nuccore/1929697386) under the accession no. MW001303. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA692344, SRR13447968, and SAMN17320349, respectively.

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