, Volume 147, Issue 5–6, pp 381–390 | Cite as

The complete chloroplast genomes of two species in threatened monocot genus Caldesia in China

  • Virginia M. Mwanzia
  • John M. Nzei
  • Dong-Ying Yan
  • Peris W. Kamau
  • Jin-Ming Chen
  • Zhi-Zhong LiEmail author
Original Paper


Caldesia is a genus in the family Alismataceae mainly found in the tropical and temperate regions of the Northern hemisphere. In China, two species, Caldesia parnassifolia, and Caldesia grandis are recorded as critically endangered in sporadic regions. Available protection of the genetic resource of these threatened species has been impeded due to limited genomic information. Here, we sequence the whole chloroplast (cp) genome of the two Caldesia species using high throughput sequencing technology. The whole cp genomes of C. parnassifolia and C. grandis were 167,647 bp and 168,500 bp, respectively with a typical quadripartite structure. There were 115 unique genes with 81 protein-coding genes, 31 tRNA genes, and four rRNA genes. Both species showed a GC content of 37.1%. A duplication of two tRNA genes and a ~ 6 kb inversion region in the LSC was noted in both species. Mononucleotide simple sequence repeats (SSRs) A/T were most abundant for both Caldesia species. High nucleotide variability was recorded in ycf1 gene and trnK-UUU/rps16 intergenic spacer region. All RNA editing conversions were C–U in 23 and 24 protein-coding genes for C. parnassifolia and C. grandis, respectively. Phylogenetic analysis placed both Caldesia species as sister to Sagittaria lichuanensis. This study will be useful for further evolutionary, systematic researches and conservation of the genus Caldesia.


Chloroplast genome Phylogenetic analysis Alismataceae Caldesia 



The authors thank Andrew Gichira for useful comments on the manuscript. This work was supported by the Special Foundation for State Basic Working Program of China: 2013FY112300 and Wuhan Botanical Garden (CAS): Y655261W03.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10709_2019_79_MOESM1_ESM.docx (398 kb)
Supplementary material 1 (DOCX 480 kb)
10709_2019_79_MOESM2_ESM.docx (46 kb)
Supplementary material 2 (DOCX 38 kb)


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Virginia M. Mwanzia
    • 1
    • 2
    • 3
  • John M. Nzei
    • 1
    • 2
    • 3
  • Dong-Ying Yan
    • 1
    • 2
    • 5
    • 6
  • Peris W. Kamau
    • 4
  • Jin-Ming Chen
    • 1
    • 2
  • Zhi-Zhong Li
    • 1
    • 2
    Email author
  1. 1.CAS Key Laboratory of Aquatic Botany and Watershed EcologyWuhan Botanical Garden, Chinese Academy of SciencesWuhanChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.Sino-African Joint Research Center, Chinese Academy of SciencesWuhanChina
  4. 4.The National Museums of KenyaNairobiKenya
  5. 5.Research Center for Ecology and Environment of Qinghai-Tibetan PlateauTibet UniversityTibetChina
  6. 6.College of ScienceTibet UniversityTibetChina

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