Complete chloroplast genome of Ulva meridionalis (Ulvales: Ulvaceae): an extremely fast-growing green macroalgae

Abstract

Ulva meridionalis is one of the causal green macroalgae for green tides in Japan and exists in coastal areas of China. In the present study, complete chloroplast (cp) genome sequence of Ulva meridionalis was reported, and the total length of this species was 88,653 bp (GenBank accession number MN889540). The overall base composition of cp genome was A (37.1%), T (39.0%), C (11.4%) and G (12.5%), similar to other Ulva macroalgae within cp genome, and the percentage of A + T (76.1%) was higher than C + G (23.9%). U. meridionalis cp genome encoded 113 genes, including 80 protein-coding genes, 27 transfer RNAs genes and 6 ribosomal RNAs genes. The maximum likelihood phylogenetic analysis shows that Ulva linza is the closest sister species of U. meridionalis.

Keywords:

• Ulva meridionalis
• Ulva
• macroalgae
• chloroplast genome
• phylogenetic analysis

Ulva species widely exist in the world, and there are more than 80 species of Ulva counted (Blomster et al. 1998; Guiry and Nic 2003; Hayden et al. 2003). On the one hand, Ulva species are important economic macroalgae (Vesty et al. 2015), such as Ulva linza and Ulva fasciata (Sivaprakash et al. 2019), which have the potential development value. On the other hand, the proliferation of Ulva species may cause green tides, such as Ulva prolifera, which causes challenges to the prevention of ecological disasters around the world (Huo et al. 2014; Zhang et al. 2014; Zhang, Shi, et al. 2019; Liu et al. 2019). China has the high frequency outbreak of green tides (Smetacek and Zingone 2013; Wang et al. 2018). In fact, green tides have erupted in the East Sea, Yellow Sea and Bohai Sea of China over the past years (Zhang et al. 2015; Cai et al. 2018; Zhao et al. 2019; Song et al. 2019), resulting in serious damage to the marine environment (Zhang, He, et al. 2019).

Ulva meridionalis is a marine tropical macroalgae that mainly distributed in southern Japan (Shimada et al. 2008). This species has not been collected from the Yellow Sea before. However, in August 2019, we found that U. meridionalis widely distributed in crab aquaculture ponds near the estuary of Qingdao, China (36°12′26.316″N, 120°06′37.756″E), and the specimen was stored in the herbarium of Shanghai Ocean University Museum (SHOU2019QD082001). According to reported researches, this species has a strong ecological adaptability, the maximum growth rate can reach up to 0.796 d⁻¹ under the conditions that organic phosphorus and nitrogen concentrations are 0.125 mg/L and 4.02 mg/L (Yang 2018; Kang et al. 2020), which has a high risk to become new green tides in China. So it is of great significance to sequence the chloroplast (cp) genome of U. meridionalis for further research of evolutionary relationships. Here, we reported the complete cp genome of U. meridionalis first time, in order to effectively record genetic resources of this species and provide references for subsequent researches. Additionally, the phylogenetic status of U. meridionalis was analyzed.

We sent the specimen to Sangon Biotech (Shanghai) Co., Ltd. for high-throughput sequencing. The genomic shotgun library was prepared by using the TruSeq DNA Sample Prep Kit (Illumina, USA), paired-end sequences were obtained through the Illumina HiSeq 2500 platform later. Ulva flexuosa (Cai et al. 2017) and U. prolifera (Jiang et al. 2019) were taken as models for sequence splicing about the cp genome of U. meridionalis. Complete cp genome of U. meridionalis was 88,653 bp in length and was annotated in GenBank with the accession number MN889540. The overall base composition of cp genome was A (37.1%), T (39.0%), C (11.4%), G (12.5%), similar to other Ulva macroalgae in cp genome, and the percentage of A + T (76.1%) was higher than C + G (23.9%). The U. meridionalis cp genome encoded 113 genes, including 80 protein-coding genes, 27 transfer RNAs genes and 6 ribosomal RNAs genes.

Our laboratory had studied the cp genome of U. flexuosa (NC035823, KX579943), U. linza (NC030312; KX058323) (Wang et al. 2017) and U. prolifera (NC036137, KX342867) before. In addition, we downloaded sequences from the NCBI database: Ulva mutabilis (MK069584, NC043860), Ulva ohnoi (AP018696), Ulva sp. (KP720616), Ulva fasciata (KT882614, NC029040), Ulva lactuca (MH730972, NC042255), Ulva pertusa (MN853875) and Ulva compressa (MK069585). A Maximum-likelihood (ML) phylogenetic tree with 17 complete cp genome of Ulva and 1 outgroup called Pseudendoclonium akinetum (NC008114) was constructed by using the MEGA 7 software (Figure 1) (Kumar et al. 2016), which showed U. meridionalis is closely related to U. linza.

Figure 1. Maximum likelihood phylogenetic tree for U. meridionalis based on the chloroplast genomes. Numbers above each node indicate the bootstrap support value.

In this thesis, we reported a complete cp genome of U. meridionalis and provided detailed genetic information about this species, which will be useful for studying the genetic diversity and phylogenetic history of U. meridionalis and its related species.

Acknowledgments

We thank North China Sea Environmental Monitoring Center for providing personnel assistance and vehicle transportation service.

Disclosure statement

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

Additional information

Funding

This study was financially supported by National Key R&D Program of China [2018YFD0901500], National Natural Science Foundation of China [41576163], Shanghai Sailing Program [17YF1407900], Luo Zhaorao Science and Innovation Fund [A1200400201307, A1200400201328] and Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A. [MATHAB201817].