Characterizing the chloroplast genome of Mammillaria elongata DC. 1828 in the Cactaceae family and unveiling its phylogenetic affinities within the genus Mammillaria

Abstract

With its nearly 200 species, the Mammillaria genus is the most species-rich within the Cactaceae family, yet surprisingly, few of its chloroplast genomes have been studied. We focused on the species Mammillaria elongata DC. 1828, a petite cactus native to Mexico and favored by horticulturists, yet whose phylogenetic relationships remain uncertain due to a lack of genomic data. We extracted the DNA from a sample obtained in China, sequenced it using the NovaSeq 6000 platform, and assembled the chloroplast genome using GetOrganelle software. Our assembly resulted in a chloroplast genome of 110,981 base pairs with an overall GC content of 36.28%, which included 100 genes (95 unique). Notably, several protein-coding genes were absent. Phylogenetic analysis using 59 shared genes across nine Mammillaria species and one Obregonia species revealed that M. elongata and M. gracilis are closely related, suggesting a recent common ancestor and possible shared evolutionary pressures or ecological niches. This study provides crucial genomic data for M. elongata and hints at intriguing phylogenetic relationships within the Mammillaria genus.

Keywords:

• Chloroplast genome
• gene loss
• genome size variation
• Mammillaria elongata
• phylogenetic analysis

Ethical approval

The manuscript does not encompass any research conducted on human subjects or animals by the authors. The flora explored in this study is not classified as endangered, protected, or privately owned. The plant samples were collected in strict adherence to the regulations put forth by the national authorities. Furthermore, guidelines established by our affiliated institution, the College of Horticulture and Landscape Architecture at Southwest University, were meticulously followed. The university is at No. 2 Tiansheng Road, Chongqing, China, 400716.

Author contributions

This study was conceptualized and structured by Haimei Chen and Jingling Li. Yang Ni and Jingling Li assemble and annotate the chloroplast genome. Qiqian Lu undertook the task of conducting the phylogenetic analysis. Yang Ni wrote the manuscript. Haimei Chen and Yang Ni reviewed the manuscript critically. All authors have perused and consented to the published iteration of the manuscript.

Disclosure statement

The authors reported no potential conflict of interest.\

Data availability statement

The genome sequence data supporting this study’s findings have been deposited in the NCBI GenBank and can be accessed at https://www.ncbi.nlm.nih.gov/ with the accession number MW553058.1. Corresponding BioProject, Sequence Read Archive (SRA), and BioSample entries are available under the identifiers PRJNA995908, SRR25317666, and SAMN36509928, respectively.

Additional information

Funding

This research was made possible through funding provided by the National Natural Science Foundation of China [81872966], the CAMS Innovation Fund for Medical Sciences (CIFMS) [2021-I2M-1-022], and the National Science & Technology Fundamental Resources Investigation Program of China [2018FY100705]. The funding bodies played no part in the formulation of the study design, the gathering and analysis of data, the decision to publish, or the preparation of the manuscript.