Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Mar 1;9(3):296.
doi: 10.3390/plants9030296.

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

Jacinta N Munyao  1   2   3 , Xiang Dong  1   2   3 , Jia-Xin Yang  1   2 , Elijah M Mbandi  1   2   3 , Vincent O Wanga  1   2   3 , Millicent A Oulo  1   2   3 , Josphat K Saina  1   2   3 , Paul M Musili  4 , Guang-Wan Hu  1   2   3
Affiliations

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

Jacinta N Munyao et al. Plants (Basel). .

Abstract

The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.

Keywords: C. comosum; C. gallabatense; chloroplast genome; phylogenetic analysis.

PubMed Disclaimer

Conflict of interest statement

The authors affirm no conflict of interest.

Figures

Figure 1
Figure 1
Gene map of the C. comosum and C. gallabatense complete cp genomes. Genes drawn within the circle are transcribed in the clockwise direction, and genes drawn out are transcribed in the counterclockwise direction. Genes are color-filled, basing on different functions. Inverted repeat (IR), small single-copy (SSC), and large single-copy (LSC) regions are indicated.
Figure 2
Figure 2
Amino acid proportion in C. comosum and C. gallabatense protein-coding sequences.
Figure 3
Figure 3
Number of different types of SSRs.
Figure 4
Figure 4
Number of different repeat units of SSRs.
Figure 5
Figure 5
Comparison of the junctions of LSC, SSC, and IR regions among seven chloroplast genomes.
Figure 6
Figure 6
Nucleotide diversity of different regions of Asparagales chloroplast genomes.
Figure 7
Figure 7
Comparison of seven cp genomes using mVISTA alignment program. Genome regions are color-coded as protein-coding, rRNA coding, tRNA coding, or conserved non-coding sequences. The vertical scale shows the percentage of identity, varying from 50% to 100%.
Figure 8
Figure 8
Comparison of the genome structure of seven Asparagales species using Mauve program. The DNA sequences above the line are presented in a clockwise direction, and those below the line in a counterclockwise direction.
Figure 9
Figure 9
Phylogenetic trees of Asparagales species based on whole chloroplast genome sequences, with two species from family Iridaceae used as outgroup.
See this image and copyright information in PMC

References

    1. Basu S., Jha T.B. Cytogenetic studies in four species of Chlorophytum Ker-Gawl. (Liliaceae) The Nucleus. 2011;54:123–132. doi: 10.1007/s13237-011-0039-8. - DOI
    1. Govaerts R., Zonneveld B., Zona S. World Checklist of Asparagaceae. Facilitated by the Royal Botanic Gardens; Kew, UK: 2012. [(accessed on 26 February 2020)]. Available online: http://apps.kew.org/wcsp/
    1. Malpure N.V., Yadav S. Chlorophytum gothanense, a new species of Anthericaceae from the Western Ghats of India. Kew Bull. 2009;64:739–741. doi: 10.1007/s12225-009-9165-8. - DOI
    1. Govaerts R. World Checklist of Selected Plant Families Asparagaceae. Royal Botanic Gardens; Kew, UK: 2015.
    1. Lekhak M., Adsul A., Yadav S. Cytotaxonomical investigations into the genus Chlorophytum from India. Kew Bull. 2012;67:285–292. doi: 10.1007/s12225-012-9355-7. - DOI

LinkOut - more resources