Chloroplast genome data sequence of the stuarine Ulva sp. GE257 from Ecuador: genome features and phylogenetic relevance

Abstract

Objectives

Ulva species are ecologically important components of coastal and estuarine systems and are increasingly recognized as candidates for biomass production and other applied uses. However, genomic resources for Ecuadorian Ulva remain scarce. Here, we report the complete chloroplast genome of Ulva sp. GE257, an estuarine macroalga from Ecuador, and provide a description of its genome features and phylogenetic position as a baseline resource for future taxonomic, ecological, and cultivation-related studies.

Data description

We present the complete chloroplast genome of Ulva sp. GE257 from Puerto El Morro, Ecuador. The genome is a circular DNA molecule of 92,301 bp with a GC content of 24.42% and encodes a total of 98 genes, 67 protein-coding genes, 26 transfer RNA genes, and three ribosomal RNA genes. Four introns were annotated, including one in the rrn23 gene and three in the psbB gene, which contains five exons. No inverted repeat regions were identified in the genome. In addition, the majority of the ORFs are located on the light strand.

Objective

The estuarine region of Puerto El Morro, in the province of Guayas, Ecuador, offers favorable conditions for exploring native species with ecological and biotechnological relevance. Among these, the genus Ulva is of particular interest because species of this group are widely distributed in the coastal and stuarine habitats, where they contribute to primary production [1]. This genus includes green seaweed with rapid growth rates, high environmental tolerance, and the ability to accumulate bioactive compounds with applications in animal nutrition, bioremediation, and high-value bioproducts [2, 3]. This alternative is particularly valuable for mangrove ecosystems, as it offers opportunities for bioremediation by improving water quality and represents a potential new source of income for local fishers, who could integrate Ulva cultivation into their traditional fishing activities, promoting a more sustainable and diversified livelihood. In addition, Ulva sp. has been reported to produce bioactive compounds with activity against pathogenic Vibrio and Photobacterium species affecting farmed oysters and shrimp [4–7].

This study aims to explore the chloroplast genome of an Ulva species collected from this region (Fig. 1), a valuable resource for molecular characterization, evolutionary studies, and conservation strategies, thereby facilitating more informed management and sustainable use of Ulva sp. GE257.

Fig. 1.

A circular map of the chloroplast genome of a specimen of Ulva sp. GE257 collected in Ecuador

Data description

Specimen sampling and sample processing

Specimens of Ulva sp. (Fig. 2) were collected at low tide in Puerto Morro, Guayas Province, Ecuador (0°40’39.5” S; 80°21’39.6” W) and then transported in a plastic container to the Molecular Biology Laboratory of the National Center for Aquaculture and Marine Research (CENAIM) of the Littoral Polytechnic Higher School (ESPOL). The measurement of key parameters, including salinity (24.00 g/L), dissolved oxygen concentration (6.59 mg·L − 1), and pH (7.10) were measured using a portable multi-meter (Hach HQ Series, Hach, Germany). In addition, the concentrations of total nitrogen (4.10 mg·L − 1), and total phosphorus (1.52 mg·L ⁻¹) were determined according to a published protocol [8]. At the laboratory, the sample was externally cleaned from external contamination. Fresh algal tissue was preserved in DNA/RNA Shield (Zymo Research, USA) at -20 °C until DNA extraction. A portion of the tissue was flash-frozen in liquid nitrogen and ground until pulverized. Afterward, Ulva DNA was isolated using the EZNA HP Plant DNA Mini Kit (Omega Bio-tek, USA) according to the manufacturer’s instructions. DNA quality and concentration were checked using a Dnovix DS-11 spectrophotometer (Dnovix, USA) and 2% (w/v) agarose horizontal gel electrophoresis.

Fig. 2.

Specimens of Ulva sp. GE257 collected from coastal environments in Ecuador. A Occurrence of Ulva sp. GE257 in its stuarine habitat. B Cultivation of Ulva sp. on cane mesh structures used for biomass production and harvesting

Sequencing and genome assembly

The library construction (~ 100ng DNA was fragmented to 350 bp followed by NEBNext Ultra and sequencing were performed by Novogene Inc. (Sacramento, USA) using the Illumina NovaSeq 6000 PE150 (paired end, 2 × 150 bp). A total of 41,473,142 raw reads (6.2 Gb) with a GC content of 52.94% were obtained. The chloroplast genome was generated in a single contig using the GetOrganelle pipeline v1.7.7.1 [9] with default software and parameters over the raw data. The assembly was performed using SPAdes v3.15.5 [10] and visualized with Bandage v0.9.0 [11]. Genome annotation was performed using the GeSeq web interface [12]. Furthermore, all genes in the assembled chloroplast genome were identified by sequence alignment against the chloroplast genomes of Ulva sp. KP720616 and U. meridionalis NC077591 using Geneious v2024.0. A circular genome map (Fig. 1) was generated using the OGDRAW web tool [13]. All data related to the cpDNA genome, including sequence data, genome assembly, and associated figures, have been deposited in their respective public repositories. Detailed information, including file types, DOIs, and accession numbers, is provided in Table 1 to ensure transparency and accessibility of the datasets.

Table 1.

Overview of data files/data sets

Label	Name of data file/data set	File types (file extension)	Data repository and identifier (DOI or accession number)
Data file 1	Figure 1. A circular map of the chloroplast genome of a specimen of Ulva sp. GE257 collected in Ecuador.	Picture file (.tiff)	Figshare 10.6084/m9.figshare.28451480.v1 [19]
Data file 2	Figure 2. Specimens of Ulva sp. GE257 collected from coastal environments in Ecuador. (A) Occurrence of Ulva sp. GE257 in its stuarine habitat. (B) Cultivation of Ulva sp. on cane mesh structures used for biomass production and harvesting.	Picture file (.tiff)	Figshare 10.6084/m9.figshare.31968348 [20]
Data file 3	Figure 3. Phylogenetic position of Ulva sp. GE257 based on a comparison with the complete chloroplast genome sequences of 24 other Ulva species.	Picture file (.tiff)	Figshare 10.6084/m9.figshare.28451543.v1 [21]
Data set 1	Whole genome assembly and annotation of Ulva sp. GE257	Fasta file (.fasta)	GenBank from NCBI repository under accession number PV138240 https://identifiers.org/ncbi/insdc:PV138240 [22]

Genome analysis

The chloroplast genome of Ulva sp. GE257 showed ATG as the start codon for all coding sequences (CDSs). TAA was the predominant stop codon for most CDSs, except for ChIl, rpl2, and cemA, where TAG served as the stop codon. In addition, TGA was identified as the stop codon for the rpoA gene. The rbcL and tufA genes were analyzed by BLAST against the NCBI database and showed 99.4% and 99.5% identity with U. meridionalis. In addition, the 67 CDS of the chloroplast genome of GE257 showed 98.47% identity and 100% coverage with U. meridionalis. Among all species analyzed, U. meridionalis showed the highest sequence identity and coverage, while the remaining species exhibited lower similarity. Consistently, the overall genome features of GE257 (92,301 bp; 24% GC; 98 total genes including 67 CDSs, 26 tRNAs, and 3 rRNAs) fall within the range reported for other species of the genus Ulva (Table 2), which exhibit genome sizes between ~ 79 kb and 122 kb, GC contents of 24–26%, and relatively conserved numbers of tRNA genes but variable coding capacity. However, the morphology of our seaweed is not clearly consistent with U. meridionalis, and this species has not been previously reported in Ecuador. Tandem Repeats Finder [14] revealed notable differences between the chloroplast genomes of Ulva sp. GE257 and U. meridionalis. While Ulva sp. GE257 (92,301 bp) contained 64 tandem repeats, U. meridionalis (122,172 bp) exhibited a higher number of repeats (95), consistent with its larger genome size. In both genomes, repeats were predominantly short, with period sizes commonly ranging from ~ 10 to 30 bp; however, U. meridionalis displayed a broader range, including longer repeats up to 48 bp and higher copy numbers reaching 6.6–7.0, compared to a maximum of 6.6 in GE257. Percent similarity among repeats was comparable between the two species (approximately 69–100%), as were indel levels, which reached up to ~ 22% in both cases. Overlapping and nested repeats were frequently observed in both genomes. Overall, U. meridionalis shows a greater abundance and slightly wider diversity of tandem repeat features relative to Ulva sp. GE257.

Table 2.

Comparative genomic features of chloroplast genomes from species of the genus Ulva. Data were retrieved from GenBank using the accession numbers indicated

Ulvophyceae	GenBank accession	Genome Size (bp)	CG (%)	Total genes	Coding sequences	tRNA genes	rRNA genes
Ulva sp. GE257	PV138240	92,301	24	98	67	26	3
Ulva prolifera	MN853879	88,801	24	99	71	26	2
Ulva tepita	NC067776	94,449	24	106	77	26	3
Ulva sp. UNA00071828	KP720616	99,983	25	102	71	28	3
Ulva meridionalis	NC077591	122,172	25	129	99	27	3
Ulva gigantea	NC053613	117,606	26	97	67	28	2
Ulva laetevirens	MT179351	103,444	26	103	66	34	2
Ulva lacinulata	MT179357	79,723	26	65	26	37	1
Ulva taeniata	NC086797	100,923	26	101	72	26	3
Ulva dactylifera	NC086808	93,205	25	102	73	26	3
Ulva ohnoi	AP018696	103,313	25	107	78	26	3
Ulva lactuca	PQ824971	96,008	25	104	76	26	2
Ulva fasciata	NC029040	96,005	25	106	77	27	2
Ulva linza	NC030312	86,726	25	96	67	26	3
Ulva torta	NC067777	112,034	25	120	90	27	3
Ulva californica	MZ561475	92,126	25	96	68	26	2
Ulva flexuosa	NC035823	89,414	25	99	71	26	2
Ulva aragoensis	NC077590	87,172	25	102	73	26	3
Ulva intestinalis	MZ158703	99,041	25	112	83	26	3
Ulva mutabilis	NC043860	119,866	26	92	64	26	2
Ulva compressa	MW344287	91,189	26	101	73	25	3
Ulva rigida	MW543060	117,995	26	115	86	26	3
Ulva fenestrata	NC053612	94,654	25	98	65	31	2
Ulva pertusa	MN853875	104,380	26	99	71	26	2
Ulva australis	NC053611	109,820	26	95	62	31	2

Phylogenetic analysis

The protein-coding genes of the chloroplast genomes of 24 species of Ulva sp. were obtained from GenBank (Fig. 3) and processed in PhyloSuite v1.2.3 [15]. These sequences were aligned using MACSE [16], and ambiguous sites and gaps were removed using trimAI v1.5.0. The concatenated dataset was then subjected to model selection and phylogenetic inference using IQ-TREE v3.1.1. The best-fit nucleotide substitution model (GTR + F+I+R2) was selected according to the Bayesian Information Criterion (BIC) using ModelFinder [17]. Phylogenetic relationships were reconstructed using the maximum likelihood (ML) method with 1,000 ultrafast bootstrap replicates and 1,000 SH-like approximate likelihood ratio test (aLRT) replicates to assess branch support. The resulting consensus tree was uploaded to iTOL for visualization and editing [18], with Tupiella akineta used as the outgroup. Ulva sp. GE257 formed a distinct branch with U. meridionalis and clusters with U. tepida and Ulva sp. UNA00071828 in a well-supported clade, suggesting a close evolutionary relationship and a recent common ancestor. This clade is clearly separated from other lineages, such as those including U. australis and U. pertusa, highlighting the distinct phylogenetic position of Ulva sp. GE257 within the genus.

Fig. 3.

Phylogenetic position of Ulva sp. GE257 inferred from concatenated protein-coding genes (PCGs) of chloroplast genomes from 24 Ulva species. The phylogenetic analysis was performed using the maximum likelihood (ML) method implemented in IQ-TREE under the best-fit substitution model (GTR + F+I+R2). Branch support values are indicated as ultrafast bootstrap (UFBoot) and SH-like approximate likelihood ratio test (aLRT) values. Tupiella akineta was used as the outgroup. Accession numbers are shown alongside species names

Abbreviations

BLAST

Basic local alignment search tool

BP

Base pair

CDS

Coding sequence

CENAIM

Centro Nacional de Acuicultura e Investigaciones Marinas

DNA

Deoxyribonucleic acid

GC

Guanine, Cytosine

gDNA

Genomic DNA

GB

Gigabase

MACSE

Multiple alignment of coding sequences

ORF

Open reading frame

PCG

Protein-coding genes

PE

Paired-end

RNA

Ribonucleic acid

Author contributions

GR: Formal analysis, Methodology, Investigation, Data curation, Writing – Original draft, Visualization and Software. A.A: Methodology, and Review. S.S: Methodology, Conceptualization and Review. A.M: Supervision, Resources, Methodology, Conceptualization, and Funding Acquisition.

Funding

This research was founded by the Secretaría de Educación Superior, Ciencia, Tecnología e Innovación (SENESCYT) of Ecuador in the framework of the Inédita project N° PIC-21-INE-ESPOL-005, “Desarrollo de la bioeconomía de macroalgas: Estrategia sostenible para mitigar enfermedades emergentes del camarón”.

Data availability

The whole genome assembly and annotation described here have been uploaded to the GenBank database under the accession number PV138240 (https://identifiers.org/ncbi/insdc: PV138240).

Declarations

Ethics approval and consent to participate

Sampling was conducted on private land with the explicit consent of the landowner. The sampling process adhered to national legislation and was conducted under the authorization granted by permit MAE-DNB-CM-2018-0103.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.