De novo sequencing and analysis of the Ulva linza transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems
© Zhang et al.; licensee BioMed Central Ltd. 2012
Received: 11 December 2011
Accepted: 20 October 2012
Published: 25 October 2012
The green algal genus Ulva Linnaeus (Ulvaceae, Ulvales, Chlorophyta) is well known for its wide distribution in marine, freshwater, and brackish environments throughout the world. The Ulva species are also highly tolerant of variations in salinity, temperature, and irradiance and are the main cause of green tides, which can have deleterious ecological effects. However, limited genomic information is currently available in this non-model and ecologically important species. Ulva linza is a species that inhabits bedrock in the mid to low intertidal zone, and it is a major contributor to biofouling. Here, we presented the global characterization of the U. linza transcriptome using the Roche GS FLX Titanium platform, with the aim of uncovering the genomic mechanisms underlying rapid and successful colonization of the coastal ecosystems.
De novo assembly of 382,884 reads generated 13,426 contigs with an average length of 1,000 bases. Contiguous sequences were further assembled into 10,784 isotigs with an average length of 1,515 bases. A total of 304,101 reads were nominally identified by BLAST; 4,368 isotigs were functionally annotated with 13,550 GO terms, and 2,404 isotigs having enzyme commission (EC) numbers were assigned to 262 KEGG pathways. When compared with four other full sequenced green algae, 3,457 unique isotigs were found in U. linza and 18 conserved in land plants. In addition, a specific photoprotective mechanism based on both Lhc SR and Psb S proteins and a C4-like carbon-concentrating mechanism were found, which may help U. linza survive stress conditions. At least 19 transporters for essential inorganic nutrients (i.e., nitrogen, phosphorus, and sulphur) were responsible for its ability to take up inorganic nutrients, and at least 25 eukaryotic cytochrome P450s, which is a higher number than that found in other algae, may be related to their strong allelopathy. Multi-origination of the stress related proteins, such as glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase and heat-shock proteins, may also contribute to colonization of U. linza under stress conditions.
The transcriptome of U. linza uncovers some potential genomic mechanisms that might explain its ability to rapidly and successfully colonize coastal ecosystems, including the land-specific genes; special photoprotective mechanism based on both Lhc SR and Psb S; development of C4-like carbon-concentrating mechanisms; muti-origin transporters for essential inorganic nutrients; multiple and complex P450s; and glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase, and heat-shock proteins that are related to stress resistance.
Green algae originated as much as 1500 million years ago, evolving shortly after the endosymbiotic event that gave rise to early photosynthetic eukaryotes . During the evolutionary history of Earth, green algae have become major players in global energy/biomass production and biogeochemical recycling . The green algal genus Ulva Linnaeus (Ulvaceae, Ulvales, Chlorophyta), which includes the genus formerly known as Enteromorpha, is a cosmopolitan intertidal macroalga and includes more than 100 species . It is well known for its distribution in all aquatic habitats including freshwater, brackish environments, marine and fully saline environments throughout the warm temperate and tropical regions of the world [5–7]. This group also possesses features that provide them with a competitive edge for rapid and successful colonization in eutrophic conditions, namely a copious production of reproductive spore bodies; the ability to rapidly take up and store high amounts of inorganic nitrogen; and a wide tolerance to adverse environmental conditions such as temperature, light intensity, salinity, and anoxia [8, 9]. In addition, when these algae grow under eutrophic conditions, they have the competitive advantage of rapid and successful colonization, resulting in a “green tide” [8, 10, 11], which has the following deleterious ecological effects: the uncoupling of biogeochemical cycles in sediments from those in the water column , a negative effect on seagrass beds due to shading, disruption of feeding by wading birds , the development of a lethal environment due to oxygen deficiency  and a shift from a high diversity mixture to low-diversity assemblages of fast growing annuals . Because of their ecological effects, green tides have drawn considerable attention from scientists and governments [8, 9, 12].
Whole genome or transcriptome sequencing could elucidate the genetic basis for this physiological characteristic or exploit this group’s unique genetic resources based on global gene expression [15–17]. Over the last few years, the application of newly developed high-throughput sequencing technologies has allowed hundreds of thousands of high-quality sequence reads to be produced de novo from whole genome or transcriptome templates, thus enabling immediate inroads to genetic studies of organisms for which little or no sequence data exist . For non-model organisms, sequencing and assembling of genomes remains challenging and costly, even when considering high throughput sequencing technology . As an alternative, sequencing transcriptomes is less complex and provides fast and cost-effective access to the gene expression profile of an organism [16, 20]. Transcriptomes present a valuable resource for accelerating gene discovery by expanding gene families [21, 22], improving genome annotation , elucidating phylogenetic relationships , facilitating breeding programs for both plants and animals by providing SSR and SNP markers [25, 26], and allowing large-scale expression analysis [27, 28] and rapid identification of transcripts involved in specific biological processes . Recent studies have demonstrated the success of 454 de novo sequencing, assembly and analysis of transcriptomes in non-model organisms with no prior genomic resources [30–33]. The generation of such large-scale sequence data will enable functional analyses that were previously limited to model organisms and their rapid application in ecologically important taxa .
To date, genomic information about algae is still limited compared to land plants. Moreover, algae are generally far more diverse and evolutionarily divergent than land plants . Currently, nearly complete genomic information is available publicly for only five green microalgae species: Chlamydomonas reinhardtti (Chlorophyceae) , Chlorella variabilis (Trebouxiophyceae) , Ostreococcus tauri (Prasinophyceae) , Micromonas (Prasinophyceae)  and Volvox carteri (Chlorophyceae) . To date, there is little genomic data available for the Ulvophyceae, a group that is diverse and evolutionarily divergent from all of the currently sequenced genomes of green microalgae. For the Ulvophyceae group, EST resources have been developed using Sanger sequencing in three species, Acetabularia acetabulum, Ulva linza and Ulva prolifera. A comprehensive description of the full complement of genes as a transcriptome, however, is still unavailable. Ulva linza is one of the species found in the mid to low intertidal on bedrock, and it is also a major contributor to biofouling . It must cope with more dramatic changes than land plants because of tidal changes in light intensity, temperature, salinity, and wave action and with the biotic stresses characteristic of dense coastal ecosystems. In this study, we sequenced the transcriptome of U. linza under a wide variety of environmental stress conditions with the aim of uncovering some of potential genomic mechanisms that might explain its ability to rapidly and successfully colonize the coastal ecosystems and form green tides.
Results and Discussion
454 sequencing and de novo assembly of the transcriptome
Summary of the sequencing and assembly
Average read length
Reads used in assembly
Average read length after trimming
Reads assembled as contigs
Number of contigs
Average length of contigs
Range of contig length
Depth on contigs
Number of isotigs
Average length of isotigs
Range of isotig length
Depth on isotigs
Comparison to other proteomes of green algae
All sequences were aligned against the local non-redundant (nr) protein database downloaded from the National Center for Biotechnology Information (NCBI) using the BLASTx algorithm. When the E-value cutoff was set at 10-2, a total of 304,101 reads (72.2% of total) had significant BLAST matches. According to the scores obtained by the BLASTX, the high quality reads were assigned to the taxonomic tree that was representative of Bacteria (10,685; 3.5%) and Eukaryota (218,725; 71.9%). As expected, the taxonomic assignment was well represented by Chlorophyta (90,074; 29.6%) and Embryophyta (11,229; 3.7%) within the Viridiplantae group. Within Chlorophyta, the top four assignments were assigned to Chlorella, Ulva, Volvox and Chlamydomonas.
Photoprotection mechanisms in U. linza
In taxa of photosynthetic eukaryotes, the thylakoid membrane-integral light-harvesting complex (LHC) antenna systems, especially LHCII in Photosystem II, play important roles in regulating energy flow to reaction centers . The LHC systems are generally used to harvest and transfer excitation energy into the reaction centers to drive photosynthesis. However, under excess light conditions, they undergo a conformational change and activate a quenching state for energy dissipation, termed non-photochemical quenching (NPQ) [46, 47].
The light-harvesting antenna complex in PSII consists of two types of proteins: major trimer-forming LHCII antenna proteins and minor LHCII proteins. In land plants, major LHCII proteins are encoded by multiple Lhcb1, Lhcb2 and Lhcb3 genes , but in green algae, the major LHCII proteins encoded by Lhcbm genes showed great diversity [48–51]. Nineteen Lhcbm-encoding genes have been found in the transcripome of U. linza, and of these, the five genes that had full-length sequences were selected for phylogenetic tree construction. The phylogenetic tree shows that the major LHCII genes have undergone significant divergence in different organisms; this may be an adaptation mechanism to optimize light-harvesting capacity and acclimation to environmental conditions. Three minor PSII antenna have been found in land plants, namely CP26 (Lhcb5), CP29 (Lhcb4), and CP24 (Lhcb6); all of these are located at the interface between the major LHCII proteins and PSII [52, 53]. The minor proteins CP26 and CP29 have been shown to play direct roles in NPQ in land plants . The CP24 protein evolved differently and more recently in land plants as it is absent in all green algae [49, 50]. In U. linza, only the CP26 and CP29 proteins were found as expected. From the phylogenetic tree, it can be seen that CP26 and CP29 are found in all green plant groups examined and evolved distinctly to the major LHCII proteins, which were present prior to diversification of the major lineages (Additional file 4: Figure S1). The conserved nature and distribution of the minor LHCII proteins suggests that they have a significant function.
Carbon fixation pathway
Besides photoprotection mechanisms, efficient carbon fixation is essential for photosynthesis, and as such likely to facilitate the colonization of coastal ecosystems and the accumulation of high U. linza biomass. Aquatic photosynthetic organisms are exposed to dramatic changes in the supply of dissolved inorganic carbon (Ci; CO2 and/or HCO3-). To acclimate to the Ci-limiting environmental conditions, they have developed a carbon concentrating mechanisms (CCM) to optimize the photosynthesis rate under the CO2-limiting condition [66, 67]. At least one α-carbonic anhydrase (CA) with targeting signals for the chloroplast lumen was found in U. linza. Lumenal-targeted αCAs are well known from C. reinhardtii and higher plants and are essential for growth under ambient CO2 concentrations . Thus, we predicted that the α-CA-based CCM type found in U. linza would show a strong similarity to the CCM in C. reinhardtii. Few genes common to organisms that actively or passively enhance Ci influx in CCMs were found in U. linza. Only a putative soluble protein, LciB, was identified as a candidate for a chloroplast Ci transporter, and no Ci membrane transporter candidate was found. Five low/limited CO2-induced proteins were identified, including two regulatory factors (CCM1 and LCR1) that control the expression of the CO2-related genes.
C4-photosynthesis is an important feature in some higher plants in tropical environments, as it helps them cope well with high light intensities, high temperatures, and dryness [70, 71]. Some intermediate products of the C4 carbon-fixation pathway have been detected in diatoms, brown algae, green algae and red algae [72–77]. The C4-like CCM mechanism in green algae of O. tauri and Micromonas may provide them an ecological advantage in the CO2-limiting conditions of phytoplankton blooms. In Ulva prolifera, coexistence of C3 and C4-like pathway may contribute to its wide distribution and forming blooms . In U. linza, genes encoding all of the enzymes required for C4 photosynthesis were identified implying a putative C4-like CCM mechanism (Additional file 5: Table S4).
Transporters are mainly responsible for the acquisition, redistribution and compartmentalization of organic nutrients and inorganic ions, as well as for the efflux of toxic compounds and metabolic end products. A total of 114 transport members were found in the U. linza transcriptome, and the complement resembles that of both green algae and land plants. The ATP-binding cassette (ABC) family (36 members) and the P-type adenosine triphosphatase (ATPase) family (12 members) are large compared to other transporters. One homologue of a plant-specific peroxisomal ABC transporter was found in Ulva, but is absent in the genomes of other green algae. Ulva is known for its ability to take up inorganic nutrients and use them to grow rapidly, which allows it to be successful in nitrogen-rich areas and form the green tides [8, 11]. The transcriptome encodes at least 19 transporters for essential inorganic nutrients (i.e., nitrogen, phosphorus, and sulphur). U. linza obtains nitrogen in at least three different ways, and ammonium is the best nitrogen source for Ulva growth, followed by urea and nitrate . The complete set of genes allowing transport and assimilation of these substrates include six ammonium transporters, three high-affinity nitrate transporters, and two urea transporters. The high number of ammonium transporters indicates that Ulva is a strong competitor for this resource, which is very efficiently pumped from surrounding seawater and is probably the privileged nitrogen source for Ulva. The inorganic nutrient transporters found in Ulva showed multiple origins. The unicellular green algae O. tauri has two prokaryote-like ammonium transporters, and one was found in U. linza (Additional file 6: Figure S2). All of the three phosphate transporters found in U. linza are absent in higher land plants, two occur only in green algae, and the third one is present in moss (Additional file 7: Figure S3). These results suggest that the phosphate transporting mechanism in Ulva may be old and associated with aquatic environments and that it was lost during adaptation to land. Of the three sulfate transporters, two are in the Na+/SO42--family; neither of these is present in higher land plants but one is present in moss. The third one is conserved in both green algae and high plants (Additional file 8: Figure S4).
Cytochrome P450 oxidoreductases
Eukaryotic cytochrome P450s are oxidoreductases, most of which catalyze NADPH- and O2-dependent hydroxylation reactions . Plant P450s participate in a myriad of biochemical pathways, including those devoted to the synthesis of plant products and plant growth regulators . The complexity of the P450 family is reflected in the evolution of the metabolic complexity of organisms. U. linza has at least 25 cytochrome P450s, which is a higher number than that found in other algae (eg. the unicellular green alga Chlamydomonas (13) and brown alga Ectocarpus (12)), but a lower number than that found in land plants (e.g., Physcomitrella (71) and Arabidopsis (286)). Nearly half of the P450s in U. linza are conserved in algae (even cyanobacteria) (Additional file 9: Figure S5). These P450s likely originated in algae and may be related to acclimatization to the aquatic environment. The role of these conserved P450s is poorly understood. A few of members of the CYP97 family are known to be involved in accumulating secondary ketocarotenoids in response to stress in terrestrial plants [82, 83]. Some P450s genes in U. linza are homologous to those in fungus, land plants, and even animals but are absent in unicellular green algae. We predicted that these genes may function in allelopathy in U. linza, thus allowing it to produce toxic substances for defense against herbivory or other phototrophic organisms that compete for light and nutrients [84–86]. U. linza is known to exhibit strong allelopathy: as one of the most common green tide macroalgal species, it has to outcompete other coastal primary producers and establish dominant populations in a short time .
Glutamate dehydrogenase (GDH) catalyzes the reversible oxidative deamination of glutamate to α-ketoglutarate and ammonia. In plants, the enzyme can work in either direction depending on environment and stress [88, 89]. It links the two fundamental metabolic processes involving carbon and nitrogen within a cell, and transgenic plants expressing microbial GDHs exhibit improved tolerance to herbicides, water deficits, and pathogen infections [89, 90]. Two GDH genes were found in Arabidopsis, and only one was found in Chlamydomonas. In contrast, eight putative GDH genes were found in U. linza. Seven of these GDH genes have similarities to those found in bacteria, fungus, and even animals (Additional file 10: Figure S6). Lateral gene transfer has been shown to play a significant role in the evolution of the GDH genes . Thus, we predicted that the diverse GDH genes in Ulva may have been obtained recently by gene transfer and function in maintaining a balance between carbon and nitrogen metabolites and enhancing the stress tolerance.
Reactive oxygen species generated during photosynthesis are scavenged by superoxide dismutases (SODs), ascorbate peroxidase (APX), and catalase (CAT) in plants [92–94]. Four putative APX genes were found in U. linza, which is more than has been found in C. reinhardtii (2), V. carteri (3), and P. patens (3) but less than in A. thaliana (6). All four APX genes are conserved in green algae and land plants (Additional file 11: Figure S7). In contrast, the two CAT genes in U. linza show higher similarities to those in fungi and bacteria than to those in green algae, and they have no homologous genes in land plants (Additional file 12: Figure S8). The APX and CAT genes, which are involved in scavenging reactive oxygen, may have evolved in different ways. Two Fe-type and one Mn-type SODs were found in U. linza, but no Cu/Zn-type or Ni-containing SOD was found. However, a Cu/Zn-type SOD was found to be expressed in Ulva fasciata in response to copper stress . We predicted that Fe-type and Mn-type SODs may play dominant roles in response to broad stress conditions, such as high salt, high light, and high temperature conditions. In contrast, the Cu/Zn-type SOD may be related only to heavy metal stresses.
Heat-shock proteins (Hsps) constitute a major class of stress-response proteins that mainly assist in protein refolding under stress conditions. Thirty-two Hsp genes were found in U. linza from four conserved families: Hsp70, Hsp90, Hsp100, and low-molecular-mass Hsps (sHsps). In U. linza, 8 sHsps belong to the Hsp20 family, and these Hsp20 proteins show high similarities to prokaryotes as to green algae and plants (Additional file 13: Table S5; Additional file 14: Figure S9). Similar observations were also made in terrestrial plants, where the sHsps are highly diverse, such as in Arabidopsis, 13 different sHsps are grouped into six classes . In contrast to Hsp20 proteins, most members of the Hsp70, Hsp90 and Hsp100 families found in U. linza were conserved well in eukaryotic algae and plants, with the exception of only three (Additional file 13: Table S5). Compared to other unicellular green algae, number of Hsp90 and Hsp100 proteins was increased in U. linza, especially members of the Hsp90 family (Additional file 15: Table S6). The Hsp90 family is distinct in that most of its known substrates are signal transduction proteins, such as steroid hormone receptors and signaling kinases , which may play a key role in signal transduction networks, protein degradation and protein trafficking. Thus, the increasing number of Hsp90 members indicates that U. linza may possess a Hsp/chaperone network that is more complicated than that found in unicellular algae, and it may be related to the acclimation of U. linza to the intricate environment of the intertidal zone.
The green algal genus Ulva Linnaeus (Ulvaceae, Ulvales, Chlorophyta) is well known for its wide distribution in marine, freshwater, and brackish environments throughout the world. The Ulva species are also highly tolerant of variations in salinity, temperature, and irradiance and are the main cause of green tides, which can have deleterious ecological effects. However, only limited genomic information is currently available in this non-model and ecologically important species. The transcriptome of U. linza uncovers some of potential genomic mechanisms that might explain its ability to rapidly and successfully colonize the coastal ecosystems, including the specific photoprotective mechanism based on both Lhc SR and Psb S; development of C4-like carbon-concentrating mechanisms; muti-origin transporters for essential inorganic nutrients; multiple and complex P450s, glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase and heat-shock proteins that are related to stress resistance.
Sampling and culture conditions
The Ulva linza samples were collected in May of 2010 from intertidal zone 20 (35°35´N, 119°30´E) of Zhanqiao Wharf, Qingdao, China. In the laboratory, the intact 21 samples were washed several times with sterile seawater, sterilized with 1% sodium hypochlorite for 2 min, and then rinsed with autoclaved seawater. The sterilized material was then placed into an aquarium containing enriched seawater and which was aerated and maintained at 15°C under a 12:12 h LD photoperiod with 120 μmol photons m−2 s−1 provided by cool white fluorescent tubes.
Library preparation and 454 sequencing
The samples of Ulva linza were subjected to different stress conditions: low temperature (6°C, 2 h), high temperature (42°C, 1 h), high light (400 μmol photons m−2 s−1, 1 h), high salt (93‰, 3 h) and UV-B stress (60 μw cm-2, 3 h). All the treated samples were frozen in liquid nitrogen, and total RNA was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s recommendations. The mRNA was purified from the total RNA using the Oligotex mRNA Midi Kit (QIAGEN, Germany). Double-stranded cDNA was then synthesized using the SMART cDNA Library Construction kit (Clontech, USA) by following the manufacturer’s protocol. The cDNA was purified using Qiagen QIAquick PCR purification spin columns. Normalization was performed using the TRIMMER cDNA normalization kit (Evrogen) to decrease the prevalence of abundant transcripts before sequencing, and the quality of cDNA was checked using the Agilent 2100 Bioanalyzer. A half-plate sequencing run was performed at the Tianjin Biochip Corporation following the manufacturer’s protocols. Raw data has been submitted to the Status of the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra_sub/sub.cgi?).
De novo assembly
The “-cdna” option of the latest release of Roche 454’s Newbler (version 2.5p1) was used to assemble transcriptome. Newbler creates isotigs out of contigs that are consistently connected by a subset of reads. Each isotig corresponds to an alternative transcript, and any contigs or isotigs that share any read overlaps are put into the same isogroup.
We used local BLASTX to align 454 reads to the GenBank nonredundant protein (nr) database using an E value threshold of 10-2. The unigene sequences were also translated into proteins using ESTScan and the translated protein sequences were then compared to InterPro and pfam domain databases. The gene ontology (GO) terms were assigned to each unigene based on the GO terms annotated to its corresponding homologues in the UniProt database, and based on the InterPro and Pfam domains using interpro2go and pfam2go mapping files provided by the GO website, respectively . Then, the MEGAN v4.0 software  was used to assign the annotated reads to KEGG pathways . The number of reads assigned to each KEGG functional category can be used to evaluate gene quantities and expression levels.
Real-time RT-PCR analysis
Real-time RT-PCR approach was employed to analyze the expression of lhc SR and psb S genes under different stress conditions. The primers for real-time RT-PCR analysis in this experiment are shown in Additional file 16: Table S7. The different light intensity treatments were provided at 120, 240, 400, 500, and 600 μmol photons m−2 s−1 and lasted 1 h at 15°C. For each condition, three biological replicates were conducted. The expression of the genes under different conditions was measured by real-time PCR. The qPCR was performed with the ABI StepOne plus Real-Time PCR System (Applied Biosystems, USA) and performed using SYBR Green fluorescence (Takara) according to the manufacturer’s instructions. The RNA levels were expressed relative to those of the 18S rDNA sequence. The thermal profile for real-time PCR was 30 s followed by 40 cycles at 95°C for 5 s, 55°C for 10 s and 72°C for 30 s. Dissociation curve analysis of the amplification products was performed at the end of each PCR reaction to confirm that only one specific PCR product was amplified and detected. The qPCRs were performed in triplicate for each sample. The 2-ΔΔCT method  was used to analyze the quantitative real-time PCR data.
We acknowledge the supercomputing support for the genomics analysis by Beijing Institutes of Life Science, Chinese Academy of Sciences (BIOLS). We appreciate the reviewers very much for their positive and constructive comments and suggestions on our manuscript. This work was supported by the National Natural Science Foundation of China (41176153, 31200187), Hi-Tech Research and Development Program (863) of China (2012AA052103), Shandong Science and Technology plan project (2011GHY11528).
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