Characterization of prognosis and immune infiltration by a novel glutamine metabolism-related model in cutaneous melanoma

Glutamine metabolism(GM)plays an important role in tumor growth and proliferation.Skin cutaneous melanoma(SKCM)is a glutamine-dependent cancer.However,the molecular characteristics and action mechanism of GM on SKCM remain unclear.Therefore,we aimed to explore the effects of GM-related genes on survival,clinicopathological characteristics,and the tumor microenvironment in SKCM.In this study,682 SKCM samples were obtained from the Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)databases.Consensus clustering was used to classify SKCM samples into distinct subtypes based on 41 GM-related genes.Differences in survival,immune infiltration,clinical characteristics,and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways as well as differentially expressed genes(DEGs)between subgroups were evaluated.A prognostic model was constructed according to prognostic DEGs.Differential analyses in survival,immune infiltration,tumor microenvironment(TME),tumor mutation burden(TMB),stemness,and drug sensitivity between risk groups were conducted.We identified two distinct GM-related subtypes on SKCM and found that GM-related gene alterations were associated with survival probability,clinical features,biological function,and immune infiltration.Then a risk model based on six DEGs(IL18,SEMA6A,PAEP,TNFRSF17,AIM2,and CXCL10)was constructed and validated for predicting overall survival in SKCM patients.The results showed that the risk score was negatively correlated with CD8+T cells,activated CD4+memory T cells,M1 macrophages,andγδT cells.The group with a low-risk score was accompanied by a better survival rate with higher TME scores and lower stemness index.Moreover,the group with high-and low-risk score had a significant difference with the sensitivity of 75 drugs(p<0.001).Overall,distinct subtypes in SKCM patients based on GM-related genes were identified and the risk model was constructed,which might contribute to prognosis prediction,guide clinical therapy,and develop novel therapeutic strategies.

Magnetic resonance imaging-based radiomics model for preoperative assessment of risk stratification in endometrial cancer

BACKGROUND Preoperative risk stratification is significant for the management of endometrial cancer(EC)patients.Radiomics based on magnetic resonance imaging(MRI)in combination with clinical features may be useful to predict the risk grade of EC.AIM To construct machine learning models to predict preoperative risk stratification of patients with EC based on radiomics features extracted from MRI.METHODS The study comprised 112 EC patients.The participants were randomly separated into training and validation groups with a 7:3 ratio.Logistic regression analysis was applied to uncover independent clinical predictors.These predictors were then used to create a clinical nomogram.Extracted radiomics features from the T2-weighted imaging and diffusion weighted imaging sequences of MRI images,the Mann-Whitney U test,Pearson test,and least absolute shrinkage and selection operator analysis were employed to evaluate the relevant radiomic features,which were subsequently utilized to generate a radiomic signature.Seven machine learning strategies were used to construct radiomic models that relied on the screening features.The logistic regression method was used to construct a composite nomogram that incorporated both the radiomic signature and clinical independent risk indicators.RESULTS Having an accuracy of 0.82 along with an area under the curve(AUC)of 0.915[95%confidence interval(CI):0.806-0.986],the random forest method trained on radiomics characteristics performed better than expected.The predictive accuracy of radiomics prediction models surpassed that of both the clinical nomogram(AUC:0.75,95%CI:0.611-0.899)and the combined nomogram(AUC:0.869,95%CI:0.702-0.986)that integrated clinical parameters and radiomic signature.CONCLUSION The MRI-based radiomics model may be an effective tool for preoperative risk grade prediction in EC patients.

CpG Island Definition and Methylation Mapping of the T2T-YAO Genome

Precisely defining and mapping all cytosine(C)positions and their clusters,known as CpG islands(CGIs),as well as their methylation status,are pivotal for genome-wide epigenetic studies,especially when population-centric reference genomes are ready for timely application.Here,we first align the two high-quality reference genomes,T2T-YAO and T2T-CHM13,from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs.Second,by mapping some representative genome-wide methylation data from selected organs onto the two genomes,we find that there are about 4.7%–5.8%sequence divergency of variable categories depending on quality cutoffs.Genes among the divergent sequences are mostly associated with neurological functions.Moreover,CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG(O/E)ratio between the two genomes.Finally,we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing(WGBS)data from the European and American populations are mapped to each reference,but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 genome.Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.

The apricot(Prunus armeniaca L.)genome elucidates Rosaceae evolution and beta-carotenoid synthesis

Apricots,scientifically known as Prunus armeniaca L,are drupes that resemble and are closely related to peaches or plums.As one of the top consumed fruits,apricots are widely grown worldwide except in Antarctica.A high-quality reference genome for apricot is still unavailable,which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background,evolutionary diversity,and population diversity in apricot.DNA from P.armeniaca was used to generate a standard,size-selected library with an average DNA fragment size of~20 kb.The library was run on Sequel SMRT Cells,generating a total of 16.54 Gb of PacBio subreads(N50=13.55 kb).The high-quality P.armeniaca reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70×coverage and 171×Illumina reads(40.46 Gb),combined with a genetic map for chromosome scaffolding.The assembled genome size was 221.9 Mb,with a contig NG50 size of 1.02 Mb.Scaffolds covering 92.88%of the assembled genome were anchored on eight chromosomes.Benchmarking Universal Single-Copy Orthologs analysis showed 98.0%complete genes.We predicted 30,436 protein-coding genes,and 38.28%of the genome was predicted to be repetitive.We found 981 contracted gene families,1324 expanded gene families and 2300 apricot-specific genes.The differentially expressed gene(DEG)analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase(NCED)gene but not lycopene beta-cyclase(LcyB)gene results in a lowβ-carotenoid content in the white cultivar“Dabaixing”.This complete and highly contiguous P.armeniaca reference genome will be of help for future studies of resistance to plum pox virus(PPV)and the identification and characterization of important agronomic genes and breeding strategies in apricot.

Incidence,predictors,and prognosis of thrombocytopenia among patients undergoing intra-aortic balloon pumping in the intensive care unit:a propensity score analysis

OBJECTIVE To explore the incidence,predictors,and prognosis of intra-aortic balloon pumping(IABP)-related thrombocytopenia in critically ill patients.METHODS This multi-center study used the eICU Collaborative Research Database V1.2,comprising data on>130,000 patients from multiple intensive care units(ICUs)in America between 2014 and 2015.A total of 710 patients undergoing IABP were included.Thrombocytopenia was defined as a drop in platelet count>50%from baseline.From the cohort,167 patients who developed thrombocytopenia were matched 1:1 with 167 patients who did not,after propensity score(PS)matching.The associations between IABP-related thrombocytopenia and clinical outcomes were examined by multivariable logistic regression.RESULTS Among 710 patients undergoing IABP,249 patients(35.07%)developed thrombocytopenia.The APACHE IVa score was a predictor of thrombocytopenia[adjusted odds ratio(OR)=1.09,95%confidence interval(CI):1.02−1.15].After 1:1 PS matching,in-hospital mortality(adjusted OR=0.76,95%CI:0.37−1.56)and in-ICU mortality(adjusted OR=0.74,95%CI:0.34−1.63)were similar between the thrombocytopenia and non-thrombocytopenia groups.However,major bleeding occurred more frequently in the thrombocytopenia group(adjusted OR=2.54,95%CI:1.54−4.17).In-hospital length of stay(LOS)and in-ICU LOS were significantly longer in patients who developed thrombocytopenia than in those who did not(9.71 vs.7.36,P<0.001;5.13 vs.2.83,P<0.001).CONCLUSIONS Among patients undergoing IABP in the ICUs,thrombocytopenia was not associated with a difference in inhospital mortality or in-ICU mortality;however,thrombocytopenia was significantly associated with a greater risk of major bleeding and increased in-ICU and in-hospital LOS.

De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes associated with carrageenan biosysthesis

Betaphycus gelatinus, Kappaphycus alvarezii and Eucheuma denticulatum of Family Solieriaceae, Order Gi-gartinales, Class Rhodophyceae are three important carrageenan-producing red algal species, which pro-duce different types of carrageenans, beta （β）-carrageenan, kappa （κ）-carrageenan and iota （ι）-carrageenan. So far the carrageenan biosynthesis pathway is not fully understood and few information is about the So-lieriaceae genome and transcriptome sequence. Here, we performed the de novo transcriptome sequencing, assembly, functional annotation and comparative analysis of these three commercial-valuable species using an Illumina short-sequencing platform Hiseq 2000 and bioinformatic software. Furthermore, we compared the different expression of some unigenes involved in some pathways relevant to carrageenan biosynthe-sis. We finally found 861 different expressed KEGG orthologs which contained a glycolysis/gluconeogenesis pathway （21 orthologs）, carbon fixation in photosynthetic organisms （16 orthologs）, galactose metabolism （5 orthologs）, and fructose and mannose metabolism （9 orthologs） which are parts of the carbohydrate me-tabolism. We also found 8 different expressed KEGG orthologs for sulfur metabolism which might be impor-tantly related to biosynthesis of different types of carrageenans. The results presented in this study provided valuable resources for functional genomics annotation and investigation of mechanisms underlying the biosynthesis of carrageenan in Family Solieriaceae.

Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts of essential brown algae(Phaeophyceae)in China

The chloroplast and mitochondrion of brown algae （Class Phaeophyceae of Phylum Ochrophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lineages by using algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Kingdom Chromista. We have found that there is a split between Class Phaeophyceae of Phylum Ochrophyta and the others （Phylum Cryptophyta and Haptophyta） in Kingdom Chromista, and identified more diversity in chloroplast genes than mitochondrial ones in their phylogenetic trees. Taxonomy resolution for Class Phaeophyceae showed that it was divided into Laminariales-Ectocarpales clade and Fucales clade, and phylogenetic positions of Kjellmaniella crassi-folia, Hizikia fusifrome and Ishige okamurai were confirmed. Our analysis provided the basic phylogenetic relationships of Chromista algae, and demonstrated their potential ability to study endosymbiotic events.

Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts for marine red algae(Rhodophyta)in China

The chloroplast and mitochondrion of red algae （Phylum Rhodophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lin-eages by using red algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta. We have found that red algae were divided into three clades of orders, Florideophyceae, Bangiophyceae and Cyanidiophyceae. Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales, while Order Graci-lariales was in a clade of Order Ceramials. We confirmed Prionitis divaricata （Family Halymeniaceae） was closely related to the clade of Order Gracilariales, rather than to genus Grateloupia of Order Halymeniales as reported before. Furthermore, we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection （Ka/Ks〈1）, suggesting that red algae, as one primitive group of eukaryotic algae, might share joint evolutionary history with these two organelles for a long time, although we identified some dif-ferences in their phylogenetic trees. Our analysis provided the basic phylogenetic relationships of red algae, and demonstrated their potential ability to study endosymbiotic events.

Origin and evolution of alginate-c5-mannuronan-epimerase gene based on transcriptomic analysis of brown algae

The coding product of alginate-c5-mannuronan-epimerase gene （algG gene） can catalyze the conversion of mannuronate to guluronate and determine the M/G ratio of alginate. Most of the current knowledge about genes involved in the alginate biosynthesis comes from bacterial systems. In this article, based on some algal and bacterial algG genes registered on GenBank and EMBL databases, we predicted 94 algG genes open reading frame （ORF） sequences of brown algae from the 1 000 Plant Transcriptome Sequencing Project （OneKP）. By method of transcriptomic sequence analysis, gene structure and gene localization analysis, multiple sequence alignment and phylogenetic tree construction, we studied the algal algG gene family characteristics, the structure modeling and conserved motifs of AlgG protein, the origin of alginate biosyn-thesis and the variation incidents that might have happened during evolution in algae. Although there are different members in the algal algG gene family, almost all of them harbor the conserved epimerase region. Based on the phylogenetic analysis of algG genes, we proposed that brown algae acquired the alginate bio-synthesis pathway from an ancient bacterium by horizontal gene transfer （HGT）. Afterwards, followed by duplications, chromosome disorder, mutation or recombination during evolution, brown algal algG genes were divided into different types.

Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene

Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.

Effect of peroxiredoxin 6 on total and progressive motility of human spermatozoa after cryopreservation

Sperm cryopreservation is useful in assisted reproductive technology and male fertility preservation.However,freezing and thawing significantly reduces the total and progressive motility of human spermatozoa.In the present study,we explored the effects of peroxiredoxin 6(PRDX6)on total and progressive motility of human spermatozoa after cryopreservation.Semen samples of 20 males with normal parameters were collected and frozen in media supplemented with different concentrations of PRDX6(0 mM,10−5 mM,10−7 mM,and 10−9 mM,respectively).Postthaw total and progressive motility of sperms were measured.The results showed that in comparison with 0 mM,the concentrations of 10−5 mM,10−7 mM,and 10−9 mM of PRDX6 all significantly improved total motility and progressive motility of sperms(p<0.05).The 10−7 mM of PRDX6 showed the best performance.In conclusion,the supplementation of PRDX6 helps to maintain the total and progressive motility of human spermatozoa.

Comparative gene expression analysis in stems of <i>Dolichos purpureus</i>and <i>Arabidopsis thaliana</i>

The outermost layer epidermis of a plant stem plays an important role in protection and environment-sensing. The mechanisms of sensing and response to the environment through the stem epidermis remain unclear. Here we report enriched expression of genes involved in stress resistance and signal transduction functions in the stem epidermis of both D. purpureus and A. thaliana by cDNA cloning and QPCR in D. purpureus and by analysis using dataset from a genome-wide comparison with cDNAs differentially expressed between the epidermis and inner parts of top and base stem in A. thaliana. Among 188 cDNAs from the stem epidermis of D. purpureus, 13% and 17% were related to signal transduction and defense respectively. Most of them were up-regulated more in the stem epidermis than the inner stem, as well as in A. thaliana. Also, the distribution of the numbers and specificities of up-regulated genes related to signal transduction and regulatory networks in the epidermis and inner stem revealed the possibility of positional differences in regulation. The results revealed the importance of the epidermis in signal transduction and plant defence.

Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny

Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.

Phylogeny of genera Laminaria and Saccharina(Laminariales, Phaeophyceae) based on three molecular markers

In the past two decades, many studies have focused on the classification within genus Laminaria, ultimately trying to divide it into two subgroups or genera： Laminaria and Saccharina. A significant debate still surrounds the question of its division, as the conflicting phylogenetic hypotheses that have resulted from the classification studies are based on different taxon sampling, molecular markers, or analysis methods. It is aimed at elucidate the molecular phylogeny within Laminaria and Saccharina. The nine species of Lami- nariales are sampled from northern Asia and Europe, and 23 new sequences in the nuclear, plastid, and mitochondrial genomes are determined to identify their taxonomic status. The phylogenetic analyses of 71 species are performed, including representatives from six of the seven families of the order Laminariales, based on three separate data sets. An evidence is provided to strongly support a clear split that maintains the two recognized genera, Laminaria and Saccharina, with Laminaria appearing to be the ancestor group. Further, analyses indicate that all taxa in Saccharina and Laminaria did not form a monophyletic lineage, instead Laminariaceae and Lessoniaceae grouped together interlacedly, and Costariaceae appeared as the sister taxon of the Lessoniaceae-Laminariaceae clade. In the phylogenetic analysis, mitochondrial c oxi- dase I （COI） sequences appeared to be the most credible molecular marker which was more befitting than nuclear encoded internal transcribed spacer （ITS） and plastid encoded rbcL for establishment of Laminariales systematics. It is the most comprehensive phylogeny of the order Laminariales, and contributes to an enhanced understanding and estimation of the phylogenetic relationships for the economically important seaweeds, Laminaria and Saccharina.

Phylogeny of Saccharina and Laminaria(Laminariaceae, Laminariales, Phaeophyta) in sequence-tagged-site markers

Laminaria and Saccharina have recently been recognized as two independent clades from the former genus Laminaria. Traditional morphological taxonomy is being challenged by molecular evidence from both nucleus and plastid. Intensive work is in great demand from the perspective of genome colinearity. In this study, 118 sequence-tagged site(STS) markers were screened for phylogenetic analyses, 29 based on genome sequences, while 89 were based on expressed sequence tag(EST) sequences. EST-based STS marker development(29.37%) had an effi ciency twice as high as genome-sequence-based development(9.48%) as a result of high conservation of gene transcripts among the relative species. S. ochotensis, S. religiosa, S. japonica, and L. hyperborea showed great homogeneity in all 118 STS markers. Our result supports the view that the diversifi cation between the genera Saccharina and Laminaria was a more recent event and that Saccharina and Laminaria shared high phylogenetic affi nity. However, when it came to the single nucleotide polymorphism(SNP) level among the 41 SNPs, L. hyperborea owned 29 unique SNPs against 12 within the left three Saccharina species and 12 of the 13 indels were supposedly unique for L. hyperborea, indicated by its high variability. Originating from homologous ancestors, species between the recently diverged genera Laminaria and Saccharina may have taken in enough mutations at the SNP level only, in spite of different evolutionary strategies for better adaptation to the environment. Our study lays a solid foundation from a new perspective, although more accurate phylogenetic analysis is still needed to clarify the evolutionary traces between the genera Saccharina and Laminaria.

Label-Free and Real-Time Monitor of Binding and Dissociation Processes between Protein A and Swine IgG by Oblique-Incidence Reflectivity Difference Method

Life science has a need for detection methods that are label-free and real-time. In this paper, we have selected staphylococcal protein A （SPA） and swine immunoglobulin G （IgG）, and monitor the bindings between SPA and swine IgG with different concentrations, as well as the dissociations of SPA-swine IgG complex in different pH values of phosphate buffer by oblique-incidence reflectivity difference （OIRD） in a label-free and real-time fashion. We obtain the ON and OFF reaction dynamic curves corresponding to the bindings and dissociations of SPA and swine IgG. Through our analysis of the experimental results, we have been able to obtain the damping coefficients and the dissociation time of SPA and swine IgG for different pH values of the phosphate buffer. The results prove that the OIRD technique is a competing method for monitoring the dynamic processes of biomolecule interaction and achieving the quantitative information of reaction kinetics.

A brief review on the evolution of GPCR: conservation and diversification

G-protein couple receptors (GPCR) possess diversified functions and they comprise a large protein superfamily in cellular signaling. Numerous identification methods for GPCR have been employed and versatile GPCR types are discussed. Although they share conserved transmembrane structural topology, alignment results of all GPCR show no significant sequence similarities. Each GPCR type distributes diversely in different evolutionary hierarchies of eukaryotes, but it has a distinctive boundary in the era of metazoan. The common ancestor of GPCR metabotropic glutamate receptor includes 7-transmembrane structure and venus flytrap module, which is probably evolved from a compound of bacteriorhodopsin and periplasmic binding protein. Many investigations focus on fine structure shaping and GPCR classification. Here, we briefly discuss evolutionary dynamic mechanism of GPCR from the perspective of classification, diversification and conservation.

On the collection and integration of SARS-CoV-2 genome data

Genome data of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)is essential for virus diagnosis,vaccine development,and variant surveillance.To archive and integrate worldwide SARS-CoV-2 genome data,a series of resources have been constructed,serving as a fundamental infrastructure for SARS-CoV-2 research,pandemic prevention and control,and coronavirus disease 2019(COVID-19)therapy.Here we present an over-view of extant SARS-CoV-2 resources that are devoted to genome data deposition and integration.We review deposition resources in data accessibility,metadata standardization,data curation and annotation;review integrative resources in data source,de-redundancy processing,data curation and quality assessment,and variant annotation.Moreover,we address issues that impede SARS-CoV-2 genome data integration,including low-complexity,inconsistency and absence of isolate name,sequence inconsistency,asynchronous update of genome data,and mismatched metadata.We finally provide insights into data standardization consensus and data submission guidelines,to promote SARS-CoV-2 genome data sharing and integration.

Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta)

In 2008, a green tide broke out before the sailing competition of the 29th Olympic Games in Qingdao. The causative species was determined to be Enteromorpha prolifera （Ulva prolifera O. F. Miiller）, a familiar green macroalga along the coastline of China. Rapid accumulation of a large biomass of floating U. prolifera prompted research on different aspects of this species. In this study, we constructed a nonnormalized cDNA library from the thalli of U. prolifera and acquired 10072 high-quality expressed sequence tags （ESTs）. These ESTs were assembled into 3 519 nonredundant gene groups, including 1 446 clusters and 2 073 singletons. After annotation with the nr database, a large number of genes were found to be related with chloroplast and ribosomal protein, GO functional classification showed 1 418 ESTs participated in photosynthesis and 1 359 ESTs were responsible for the generation of precursor metabolites and energy. In addition, rather comprehensive carbon fixation pathways were found in U. prolifera using KEGG. Some stress-related and signal transduction-related genes were also found in this study. All the evidences displayed that U. prolifera had substance and energy foundation for the intense photosynthesis and the rapid proliferation. Phylogenetic analysis of cytochrome c oxidase subunit I revealed that this green-tide causative species is most closely affiliated to Pseudendoclonium akinetum （Ulvophyceae）.

Comparative analysis of four essential Gracilariaceae species in China based on whole transcriptomic sequencing

Three Gracilaria species, G. chouae, G. blodgettii, G. vermiculophylla and a close relative species, Gracilari-opsis lemaneiformis which is now nominated as Gracilaria lemaneiformis, are the typically indigenous spe-cies which are important resources for the production of special proteins, phycobilisomes, special carbo-hydrates, and agar in China. In this study, de novo transcriptome sequencing on these four species using the next generation sequencing technology was performed for the first time. Functional annotations on assembled sequencing reads showed that the transcriptomic profiles were quite different between G. lema-neiformis and other three Gracilaria species. Comparative analysis of differential gene expression related to carbohydrate and phycobiliprotein metabolisms also showed that the expression profiles of these essential genes were different in four species. The genes encoding allophycocyanin, phycocyanin and phycoerythrin were further examined in four species and their deduced amino acid sequences were used for phylogenetic analysis to confirm that G. lemaneiformis had close relationship to genus Gracilaria, as well as that within genus Gracilaria, G. chouae had closer relationship to G. vermiculophylla rather than to G. blodgettii. The de novo transcriptome study on four species provided a valuable genomic resource for further understanding and analysis on biological and evolutionary study among marine algae.