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The complete chloroplast genome of Medicago arabica (Fabaceae)

April 2022
7(4):689-691

DOI:10.1080/23802359.2022.2067498

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Medicago arabica (Linnaeus, 1762) Huds. is an important annual legume forage that grows in a wide range of climates, from subtropical to temperate. This study aimed to sequence the chloroplast genome of M. arabica and compare it with other legumes. In this study, we sequenced the entire chloroplast genome of M. arabica, which has 125,056 base pairs. The total GC content of the chloroplast genome of M. arabica was 34.4%. From the 110 unique genes of the circular genome, 30 tRNA genes, four rRNA genes, and 76 protein-coding genes were successfully annotated. A maximum likelihood (ML) tree was constructed using the model species and 17 species of the Medicago genus. M. arabica was shown to be phylogenetically closely related to M. polymorpha. The nucleotide diversity of the chloroplast genome may provide valuable molecular markers to study chloroplast, genetic breeding, and plant molecular evolution. These findings provide a solid foundation for future research on the molecular biology of the chloroplast.

A phylogenetic tree was reconstructed using the maximum likelihood (ML) method based on shared protein-coding genes of 17 species of the Medicago genus. Melilotus albus and Trifolium repens, both members of sister groups of Medicago in Fabaceae, served as outgroups. The numbers above the lines represent ML bootstrap values (>70%).

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PLASTOME ANNOUNCEMENT

The complete chloroplast genome of Medicago arabica (Fabaceae)

Yingxue Jiao

, Xiaofan He

, Yuhua Shen

, Yuehui Chao

and Tiejun Zhang

School of Grassland Science, Beijing Forestry University, Beijing, China;

College of Chemistry and Life Sciences, Chifeng University,

Chifeng, China

ABSTRACT

Medicago arabica (Linnaeus, 1762) Huds. is an important annual legume forage that grows in a wide

range of climates, from subtropical to temperate. This study aimed to sequence the chloroplast gen-

ome of M. arabica and compare it with other legumes. In this study, we sequenced the entire chloro-

plast genome of M. arabica, which has 125,056 base pairs. The total GC content of the chloroplast

genome of M. arabica was 34.4%. From the 110 unique genes of the circular genome, 30 tRNA genes,

four rRNA genes, and 76 protein-coding genes were successfully annotated. A maximum likelihood

(ML) tree was constructed using the model species and 17 species of the Medicago genus. M. arabica

was shown to be phylogenetically closely related to M. polymorpha. The nucleotide diversity of the

chloroplast genome may provide valuable molecular markers to study chloroplast, genetic breeding,

and plant molecular evolution. These findings provide a solid foundation for future research on the

molecular biology of the chloroplast.

ARTICLE HISTORY

Received 31 October 2021

Accepted 11 April 2022

KEYWORDS

Chloroplast genome;

Medicago arabica; Fabaceae

Medicago arabica (Linnaeus, 1762) Huds., also known as spot-

ted medic, is a flowering plant that belongs to the Fabaceae

family. It is native to the Mediterranean basin and has since

spread throughout the world, where it can be found growing

on cliff tops and in different types of grasslands. M. arabica is

one of the essential leguminous forages found worldwide,

especially in subtropical and temperate climates (Nair

et al. 2006).

According to the USDA, M. arabica has greater adaptability

than other annual legumes and is used to improve soil prop-

erties and grazing productivity (Bialy et al. 2004). It has a

symbiotic relationship with Sinorhizobium medicae, a bacter-

ium capable of fixing nitrogen present in the soil. It is consid-

ered essential for pasture improvement because of its short

vegetative period, flat or sub-flat stem type, sclerotized seeds,

and ability to adapt to a wide range of environmental condi-

tions (Tava et al. 2009). The aerial parts of M. arabica contain

high concentrations of saponins that have solid fungicidal

activity against several pathogenic fungi and have the poten-

tial to be developed as a natural source of fungicides

(Saniewska et al. 2005).

The chloroplast is involved in photosynthesis, and the syn-

thesis of key phytohormones is involved in defence

responses and inter-organelle signaling (Bhattacharyya and

Chakraborty 2018). This organelle also regulates starch stor-

age, sugar synthesis, and critical cellular components, includ-

ing amino acids, vitamins, pigments, lipids, and metabolic

pathways for sulfur and nitrogen (Martin et al. 2013).

The chloroplast is a vital organelle in plants that contains

genes and components specific to the chloroplast. In this

evolutionary context, the arrangement of the chloroplast

genome is remarkably conserved. The availability of complete

chloroplast genome sequences can provide essential informa-

tion for plant breeding, chloroplast genetic engineering, the

development of valuable molecular markers, and phylogen-

etic analysis (Tao et al. 2017). The chloroplast genome of M.

arabica will be a valuable source of genetic markers for

determining evolutionary linkage as well as a robust platform

for studying the evolution and genetic breeding of this crop.

The chloroplast genome sequence of M. arabica has not

yet been reported, and further research into its chloroplast

genomes is important and urgent. This study aimed to

sequence and annotate the chloroplast genome of M. arabica

and compare it with that of other legumes. In the present

study, the chloroplast genome of M. arabica was sequenced

and structurally characterized, providing an invaluable

resource for future studies in the Fabaceae family, especially

in the genetic evolution and genetic development of feed

crops and other plant species.

Samples of M.arabica were collected from the Bajia

Botanical Garden in Beijing, China (E116290, N40030). The

seeds of M.arabica were deposited in the forage germplasm

bank of the School of Grassland Science, Beijing Forestry

University (Beijing, China; E116290, N40030). One specimen

was deposited at the Herbarium of the School of Grassland

Science, Beijing Forestry University (http://cxy.bjfu.edu.cn/,

Tiejun Zhang, tiejunzhang@126.com) with the voucher

CONTACT Tiejun Zhang tiejunzhang@126.com School of Grassland Science, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing

100083, China

ß2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,

distribution, and reproduction in any medium, provided the original work is properly cited.

MITOCHONDRIAL DNA PART B

2022, VOL. 7, NO. 4, 689–691

https://doi.org/10.1080/23802359.2022.2067498

number PI495212. Genomic DNA from post-emergence

shoots was extracted using a DNA extraction kit from

Shanghai Limin Industries Co., Ltd. (Shanghai, China).

Sequencing was performed using the Illumina Novaseq

PE150 platform (Illumina Inc., San Diego, USA), which gener-

ated 150 bp paired-end reads. The complete chloroplast gen-

ome was assembled from the cleaned reads using

GetOrganelle v1.5 (Jin et al. 2020), which used the chloroplast

genome of Medicago truncatula (GenBank accession number:

NC 003119) as a reference. The chloroplast genome was

annotated using CPGAVAS2 (Shi et al. 2019) and GeSeq

(Tillich et al. 2017) and subsequently performed manually.

The annotated chloroplast genome sequences are registered

in GenBank with an accession number (MZ905469). The study

of M. arabica, including collecting plant material, followed

the standards established by the School of Grassland Science,

Beijing Forestry University, and Chinese and international reg-

ulations. Field research adhered to Beijing legislation and fol-

lowed all research protocols.

Our study revealed that the entire chloroplast genome of

M.arabica is 125,056 base pairs long. The GC content of the

entire chloroplast genome was 34.4%. The chloroplast gen-

ome of M.arabica consists of 110 different genes, including

76 protein-coding genes, 30 tRNA genes, and four rRNA

genes. There are 30 genes encoding amino acid transfer

proteins, 15 genes encoding light-harvesting structural pro-

teins (PSII), 11 genes encoding NADH dehydrogenase pro-

teins, and 11 genes encoding small subunit ribosomal

proteins, which are found in the chloroplast genome of

M.arabica.

To determine the phylogenetic relationships of M. arabica,

the chloroplast genomes of 17 species of the Medicago

genus, as well as Melilotus albus and Trifolium repens from sis-

ter groups of Medicago in Fabaceae as outgroup species,

were downloaded from the GenBank database of the

National Center for Biotechnology Information (NCBI). These

sequences were aligned with the help of MAFFT v7 (Katoh

et al. 2019). A maximum likelihood (ML) tree was also gener-

ated using the raxmlGUI 1.5 b programme (v8.2.10), which is

based on the common protein-coding genes of 19 species

and is based on the results of this study (Silvestro and

Michalak 2012). The nucleotide sequences of 69 common

genes were used to construct the ML tree. According to the

results of the phylogenetic survey, M. polymorpha is closely

related to M. arabica (Figure 1). This study provides valuable

information for species identification and phylogenetic rela-

tionships within the Fabaceae family, mainly legume forage.

It will provide a solid foundation for future research into the

molecular biology of chloroplast, genetic breeding, and the

molecular evolution of M. arabica.

Figure 1. A phylogenetic tree was reconstructed using the maximum likelihood (ML) method based on shared protein-coding genes of 17 species of the Medicago

genus. Melilotus albus and Trifolium repens, both members of sister groups of Medicago in Fabaceae, served as outgroups. The numbers above the lines represent

ML bootstrap values (>70%).

690 Y. JIAO ET AL.

Author contributions

YJ and XH both analyzed and interpreted the data, and YJ drafted the

paper. YS and YC critically reviewed the intellectual content and col-

lected samples. TZ was involved in the conception, design, and final

approval of the published version of the article. All authors agreed to

assume responsibility for all aspects of the work.

Disclosure statement

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

Funding

This work was supported by the Fundamental Research Funds for the

Central Universities [No.2021ZY81] and the National Natural Science

Foundation of China [Nos. 31772656 and 31402123].

Data availability statement

The genomic sequence data supporting the findings of this study are

publicly available in NCBI GenBank (https://www.ncbi.nlm.nih.gov/) under

the accession number MZ905469. The associated BioProject, SRA, and

Bio-Sample numbers are PRJNA750257, SRR15275748, and

SAMN20447317, respectively.

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MITOCHONDRIAL DNA PART B 691

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