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. 2021 Mar 11;6(3):720–722. doi: 10.1080/23802359.2020.1860696

Complete chloroplast genome of Ulva compressa (Ulvales: Ulvaceae)

Lihua Xia a,b,✉, Yutao Qin a,b, Jinlin Liu a,c, Haofei Zhang a,b, Lingjuan Wu d, Song Gao d, Minmin Zhuang c, Jing Xia c, Shuang Zhao c, Yang Xu c, Meilin Fu c, Yuqing Sun c, Yichao Tong c, Jianheng Zhang c,✉, Peimin He c
PMCID: PMC7954497  PMID: 33763560

Abstract

Ulva compressa is one of the causal green macroalgae in many countries. In this study, complete chloroplast genome sequence of U. compressa was reported, and the total length of this species was 94,226 bp (GenBank accession number MT916929). The overall base composition of chloroplast genome was A (37.2%), T (37.0%), C (12.7%) and G (13.1%), and the percentage of A + T (74.2%) was higher than C + G (25.8%). U. compressa chloroplast genome encoded 90 genes, including 63 protein-coding genes, 23 transfer RNAs genes, and 4 ribosomal RNAs genes. The maximum likelihood phylogenetic analysis showed that U. compressa is the closest sister species of U. linza. This study will be helpful to understand the genetic diversity of Ulva species.

Keywords: Ulva compressa, green tide macroalgae chloroplast genome phylogenetic analysis

China has the high-frequency outbreak of the green tides (Smetacek and Zingone 2013; Hu et al. 2014; Zhang et al. 2014; Zhang et al. 2015; Cui et al. 2019; Liu, Zhao et al. 2020; Liu, Zhuang, et al. 2020; Kang et al. 2020; Xiao et al. 2020). The formation of the green tide in the Southern Yellow Sea of China is complicated. Many researches demonstrated that the significant amount of attached Ulva species on the Pyropia aquaculture rafts were considered as the main source of the blooms in the Yellow Sea (Liu et al. 2009; Hu et al. 2010; Huo et al. 2015; Zhang et al. 2017; Zhang et al. 2019; Shan et al. 2019; Wang et al. 2018; Zhao et al. 2019; Zhao et al. 2020). The attached Ulva species consisted of four species which were Ulva compressa, Ulva linza, Ulva flexuosa and Ulva prolifera.

Our laboratory had studied the chloroplast genome of U. flexuosa (NC035823) (Cai et al. 2017), U. linza (KX058323) (Wang et al. 2017) and U. prolifera (KX342867) (Jiang et al. 2019) before. In order to study the chloroplast genome of U. compressa, we collected U. compressa from the estuary of Nantong, China (32°49′42″N, 121°19′05″E). The specimen was stored in the herbarium of Shanghai Ocean University Museum (SHOU2020NT032202). We sent the specimen to Sangon Biotech (Shanghai) Co., Ltd. for high-throughput sequencing.

DNA of the sample was extracted by using the Dzup (Plant) Genomic DNA Isolation Reagent. 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. U. flexuosa, U. linza and U. prolifera were taken as models for sequence splicing about the complete chloroplast genome of U. compressa. We used GeSeq software and Plastid Genome Annotator (PGA) software for annotation (Qu et al. 2019), and used homology comparison for correction, the chloroplast genome was perfectly assembled. Complete chloroplast genome of U. compressa was 94,226 bp in length and was annotated in GenBank with the accession number MT916929. The percentage of A + T (74.2%) was higher than C + G (25.8%). The overall base composition of chloroplast genome was A (37.2%), T (37.0%), C (12.7%), G (13.1%), similar to other Ulva macroalgae in chloroplast genome. The U. compressa chloroplast genome encoded 90 genes, including 63 protein-coding genes, 23 transfer RNAs genes and 4 ribosomal RNAs genes.

In addition, we downloaded sequences from the NCBI database: Ulva mutabilis (MK069584), Ulva ohnoi (AP018696) (Suzuki et al. 2018), Ulva sp. (KP720616) (Melton et al. 2015), Ulva fasciata (KT882614) (Melton and Lopez-Bautista 2016), Ulva lactuca (MH730972) (Hughey et al. 2019) and Ulva pertusa (MN853875) (Han et al. 2020). A Maximum-likelihood (ML) phylogenetic tree with 10 complete chloroplast genome of Ulva and 1 outgroup called Pseudendoclonium akinetum (NC008114) (Pombert et al. 2006) was constructed by using the MEGA 7 software based on Kimura-2-parameter model (K2P) (Figure 1) (Kumar et al. 2016). This phylogenetic analysis used 1,000 bootstrap replicates to verify the support rate of each node in the tree, and the result showed U. compressa was closely related to U. linza.

Figure 1.

Figure 1.

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

In this thesis, we analyzed complete chloroplast genome of U. compressa (GenBank accession number MT916929) from the Southern Yellow Sea, which will be useful for studying the genetic diversity of Ulva species.

Acknowledgements

Jinlin Liu thanks Wei Liu from Shanghai Ocean University for his support.

Funding Statement

This study was financially supported by National Key R&D Program of China [2016YFC1402103], the Project of Key Laboratory of Marine Ecological Monitoring and Restoration Technologies, M.N.R. [202008], National Natural Science Foundation of China [41576163], Shanghai Sailing Program [17YF1407900], Luo Zhaorao Science and Innovation Fund [A1200400201328].

Disclosure statement

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

Data availability statement

The data that support the findings of this study are openly available in National Center for Biotechnology Information (GenBank accession number MT916929) at https://www.ncbi.nlm.nih.gov and ResearchGate at https://doi.org/10.13140/RG.2.2.30130.43200.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The data that support the findings of this study are openly available in National Center for Biotechnology Information (GenBank accession number MT916929) at https://www.ncbi.nlm.nih.gov and ResearchGate at https://doi.org/10.13140/RG.2.2.30130.43200.

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