The genus Halophila (Hydrocharitaceae) has the greatest diversity of seagrass species, and distributed along the coastlines worldwide (Short et al. 2007). The taxonomy of this genus has long been confused due to its high plasticity in morphology (Kuo et al. 2006). So far, 17 Halophila species have been reported (Short et al. 2011). Halophila beccarii, a small seagrass species, is characterized by distinct erect lateral shoots with a pseudo-whorl of 4–10 sheathing petiolate tiny leaves (den Hartog and Kuo 2006). This species exhibits both clonal and sexual reproduction, and mainly occurs along the coasts of south-east Asia. However, its distribution area has experienced a rapid decline due to anthropogenic disturbances (Jiang et al. 2014). Now this species has been listed as a vulnerable species on the IUCN Red List of threatened seagrass species (Short et al. 2011). In this study, we sequenced the complete plastid genome of H. beccarii using next-generation technology. Information about this genome will be very useful in taxonomy and phylogenetic studies for Halophia.

Fresh plant of H. beccarii was collected from Chengmai, Hainan Province, China (19.93°N, 109.98°E), and the specimen was stored at Fourth Institute of Oceanography Herbarium (CM201908-1). After cleaning the attached epiphytes with fresh water, and then the genomic DNA was extracted using Plant Genomic DNA kit (Tiangen, Beijing, China), and sequenced using the Illumina Novaseq platform. Low-quality reads and adapters were removed by the FastQC software (Andrews 2010). De novo genome assembly was conducted by SPAdes v3.9 (Bankevich et al. 2012). The complete plastid genome was annotated using GeSeq (Tillich et al. 2017) with default sets. The annotations of tRNA genes were performed by ARAGORN (Laslett and Canback 2004). The complete plastid genome of H. beccarii was submitted to GenBank database (Accession Number: MN736637).

In H. beccarii, the complete plastid genome is 168,585 bp in length with a typical structure including one large single-copy region (80,881 bp), one small single-copy region (4730 bp) and a pair of inverted repeats (IRs) (41,487 bp). The guanine-cytosine (GC)-content is 38.5%. A total of 132 genes in this genome consisted of 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There are 29 duplicated genes in the IR regions including 18 protein-coding genes (infA, ndhF, rpl2, rpl14, rpl16, rpl22, rpl23, rpl32, rpl36, rpoA, rps3, rps7, rps8, rps11, rps12, rps19, ycf15 and ycf2), 7 tRNA genes (trnA-UGC, trnH-GUG, trnI-CAU, trnI-GAU, trnL-CAA, trnR-CCG and trnV-GAC), and 4 rRNA genes (rrn16, rrn23, rrn4.5 and rrn5).

To clarify the phylogenetic position of H. beccarii, we then downloaded 24 completed plastid genomes from GenBank database. The phylogenetic tree was reconstructed with MEGA6 software (Tamura et al. 2013) using the maximum likelihood (ML) method (Figure 1). Bootstrap values were calculated using 1000 replicates. The phylogenetic analysis indicated that H. beccarii and Thalassia hemprichii formed a distinct clade.

Characteristics of the complete chloroplast genome of Halophila beccarii

All authors

Shuo Yu, Xiaojuan Li, Kai Jiang, Xuyang Chen & Xiangping Wang

https://doi.org/10.1080/23802359.2020.1715879

Published online:

22 January 2020

Figure 1. Phylogenetic relationship of 25 species based on the plastid genome sequences with maximum likelihood (ML) analysis.

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Geolocation information

Chengmai, Hainan Province, China (19.93°N, 109.98°).