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. 2021 Mar 24;6(3):1231–1232. doi: 10.1080/23802359.2021.1875926

The complete chloroplast genome sequences and phylogenetic analysis of Crotalaria pallida (Leguminosae)

Nong Zhou a,b,*, Hai-Ling Li a, You Zhou a,b, Dong-Qin Guo a,b,*,✉
PMCID: PMC7995896  PMID: 33796789

Abstract

The complete chloroplast genome of Crotalaria pallida was obtained using the high-throughput sequencing technology in this article. The complete chloroplast genomes of this species were 152,658 bp in length, consisting of a large single-copy region (LSC) of 83,652 bp and a small single-copy region (SSC) of 18,028 bp, which were separated by a pair of inverted repeat (IRs) regions of 25,489 bp. The chloroplast genome contained 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenomic relationship analysis suggested that C. pallida was closely related to Lupinus in the family of Leguminosae.

Keywords: Crotalaria pallida, complete chloroplast genome, Illumina sequencing, phylogeny

Crotalaria pallida, also named ‘Zhu-Shi-Dou’, is a species of genus Crotalaria, family Leguminosae, which is widely distributed in the tropical and subtropical regions of China, India as well as Africa and America countries (Editorial Committee of Flora of China 1998). Crotalaria pallida is used as folk medicine to treat scrofula, mastitis, and dysentery with stems and leaves, and to treat neurasthenia, dizziness, leucorrhea, and cancers with seeds in China (Lian 1986; Hu et al. 2017). Researches about bioactive constituents in C. pallida have been carried out, such as flavonoids, alkaloids, unexplored proteins, and anti-tyrosinase compounds (Weng et al. 2003; Ko et al. 2004; Ukil et al. 2017; Cheng et al. 2020). In the previous study, the analysis based on its complete chloroplast genome is still lack. Here, to provide a solid foundation for further phylogenetic studies, we assembled and characterized the complete plastome of C. pallida.

In this study, the sample of C. pallida was collected from Dali, Yunnan province, China (100°15′42.75′′E, 25°31′33.38′′N). The voucher specimen (NO. ZSY109) was preserved at the Herbarium of Medicinal Plants and Crude Drugs of the College of Pharmacy, Dali University. We used the modified CTAB method (Doyle 1987; Yang et al. 2014) to extract the total genomic DNA from the dry and healthy leaves. A pair-end (2 × 300 bp) library was constructed and sequenced via the Illumina Hiseq 2500 (Novogene, Tianjing, China) platform. After the sequencing, the raw data were filtered via Trimmomatic version 0.32 with default settings (Bolger et al. 2014). Subsequently, the filtered sequences were assembled into circular contigs utilizing GetOrganelle (Jin et al. 2020) with the cp genome of closely related species Lupinus atlanticus (KU726827) as the reference. Finally, the assembled genome was annotated and corrected manually using Geneious R version 11.0.2 (Kearse et al. 2012). The annotated complete chloroplast genome of C. pallida was submitted to GenBank under the accession number of MT920364.

The complete chloroplast genomes of C. pallida were 152,658 bp in length. The typical quadripartite structure consisted of a pair of inverted repeat regions (IRa and IRb, 25,489 bp), a large single-copy region (LSC, 83,652 bp), and a small single-copy region (SSC, 18,028 bp). The total GC content was 36.7%, while those of IR regions (42.9%) were higher than LSC (34.3%) and SSC (30.6%) regions. A total of 111 genes was successfully annotated, containing 77 coding protein genes, 30 tRNA genes, and four rRNA genes.

To further ascertain the phylogenetic position of C. pallida, a phylogenetic analysis was carried out among 23 complete chloroplast genomes in Leguminosae with Eriobotrya malipoensis (Rosaceae) as an outgroup. The genome sequences were aligned with MAFFT version 7.427 (Katoh and Standley 2013) and then the maximum-likelihood (ML) tree was conducted by RAxML (Stamatakis 2014) program with 1000 bootstrap replicates and the GTRGAMMAI model. The result showed that C. pallida was closely related to Lupinus in the family of Leguminosae (Figure 1).

Figure 1.

Figure 1.

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ML phylogenetic tree based on the complete chloroplast genome sequences of 24 species with Eriobotrya malipoensis as an outgroup. Bootstrap support values (1000 replicates) are shown next to the nodes.

Acknowledgments

We thank Dequan Zhang in Dali University for affording plant material of molecular experiments.

Funding Statement

This study was supported by the science and technology research program of Chongqing Education Commission of China [grant number KJQN202001242 and KJQN201801210].

Disclosure statement

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

Data availability statement

The data supporting the finding of this study is available in GenBank. The accession number is MT920364: https://www.ncbi.nlm.nih.gov/nuccore/MT920364.

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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 data supporting the finding of this study is available in GenBank. The accession number is MT920364: https://www.ncbi.nlm.nih.gov/nuccore/MT920364.

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