Abstract
Zostera marina a kind of seagrass with high wildlife value, is threatened by human activities in the coastal area of China and Indonesia. In this study, we obtained the complete chloroplast genome sequence of Zostera marina, of which the length is 143,877 bp. It contained a pair of IR regions (25,915 bp) separated by a small single copy region (8823 bp) and a large single copy region (83,224 bp). The overall GC contents of the chloroplast genome were 35.5%. This circular genome contains 116 annotated genes, including 78 protein-coding genes, 30 tRNAs and 8 rRNA. By phylogenetic analysis using maximum likelihood (ML) and neighbor-joining (NJ) method, Z. marina showed the closest relationship with Elodea canadensis and Potamogeton perfoliatus. This complete chloroplast genomes can be subsequently used for population genomic studies of Z. marina and provide valuable insight into in situ and ex situ conservation for this valuable species.
References
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Institute, Cambridge, UK
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput. Biol. 19(5):455–477
Han Q, Huang X, Shi P, Zhang J (2007) Effects of human activities on seagrass bed ecosystem services value in Hepu of Guangxi Province. Chin J Ecol 26(4):544–548
Kato Y, Aioi K, Omori Y, Takahata N, Satta Y (2003) Phylogenetic analyses of Zostera species based on rbcL and matK nucleotide sequences: implications for the origin and diversification of seagrasses in Japanese waters. Genes Genet Syst 78(5):329–342
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874
Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucl Acids Res 32(1):11–16
Ogden J (2006) Seagrasses: biology, ecology and conservation. Mar Ecol 27(4):431–432
Riani E, Djuwita I, Budiharsono S, Purbayanto A, Asmus H (2012) Challenging for seagrass management in Indonesia. J Coast Dev 15(3):234–242
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313
Unsworth RK, Cullen LC (2010) Recognising the necessity for Indo-Pacific seagrass conservation. Conserv Lett 3(2):63–73
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors have declared that no competing interests exist.
Rights and permissions
About this article
Cite this article
Xing, Q., Guo, J. Characterization of the complete chloroplast genome of the seagrass Zostera marina using Illumina sequencing technology. Conservation Genet Resour 10, 419–422 (2018). https://doi.org/10.1007/s12686-017-0839-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-017-0839-5