NCBI Nr Research Articles

The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea.

The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome showed little similarity (BLASTn) to known viruses. Only twenty-two of the 53 (41%) predicted proteins were significantly similar to sequences in the NCBI nr protein database (E-value ≤ 10−15). Six caudovirus-like proteins were encoded, including large subunit terminase (TerL), major capsid protein (Mcp) and tape measure protein (Tmp). Hardycor1 was predicted to be a siphovirus (VIRFAM). No close relationship to other viruses was found using phylogenetic tree reconstructions based on TerL and Mcp. Unexpectedly, the sequenced virus stock HC1 also revealed two induced proviruses of the host: a siphovirus (Humcor1) and a pleolipovirus (Humcor2). A re-examination of other similarly sequenced, archival virus stocks revealed induced proviruses of Haloferax volcanii, Haloferax gibbonsii and Haloarcula hispanica, three of which were pleolipoviruses. One provirus (Halfvol2) of Hfx. volcanii showed little similarity (BLASTn) to known viruses and probably represents a novel virus group. The attP sequences of many pleolipoproviruses were found to be embedded in a newly detected coding sequence, split in the provirus state, that spans between genes for integrase and a downstream CxxC-motif protein. This gene might play an important role in regulation of the temperate state.

Metagenomic discovery and functional validation of L-asparaginases with anti-leukemic effect from the Caspian Sea.

SummaryBy screening 27,000 publicly available prokaryotic genomes, we recovered ca. 6300 type I and ca. 5200 type II putative L-asparaginase highlighting the vast potential of prokaryotes. Caspian water with similar salt composition to the human serum was targeted for in silico L-asparaginase screening. We screened ca. three million predicted genes of its assembled metagenomes that resulted in annotation of 87 putative L-asparaginase genes. The L-asparagine hydrolysis was experimentally confirmed by synthesizing and cloning three selected genes in E. coli. Catalytic parameters of the purified enzymes were determined to be among the most desirable reported values. Two recombinant enzymes represented remarkable anti-proliferative activity (IC50 <1IU/ml) against leukemia cell line Jurkat while no cytotoxic effect on human erythrocytes or human umbilical vein endothelial cells was detected. Similar salinity and ionic concentration of the Caspian water to the human serum highlights the potential of secretory L-asparaginases recovered from these metagenomes as potential treatment agents.

The transcriptome of anterior regeneration in earthworm Eudrilus eugeniae.

The oligochaete earthworm, Eudrilus eugeniae is capable of regenerating both anterior and posterior segments. The present study focuses on the transcriptome analysis of earthworm E. eugeniae to identify and functionally annotate the key genes supporting the anterior blastema formation and regulating the anterior regeneration of the worm. The Illumina sequencing generated a total of 91,593,182 raw reads which were assembled into 105,193 contigs using CLC genomics workbench. In total, 40,946 contigs were annotated against the NCBI nr and SwissProt database and among them, 15,702 contigs were assigned to 14,575 GO terms. Besides a total of 9389 contigs were mapped to 416 KEGG biological pathways. The RNA-Seq comparison study identified 10,868 differentially expressed genes (DEGs) and of them, 3986 genes were significantly upregulated in the anterior regenerated blastema tissue samples of the worm. The GO enrichment analysis showed angiogenesis and unfolded protein binding as the top enriched functions and the pathway enrichment analysis denoted TCA cycle as the most significantly enriched pathway associated with the upregulated gene dataset of the worm. The identified DEGs and their function and pathway information can be effectively utilized further to interpret the key cellular, genetic and molecular events associated with the regeneration of the worm.

First Report of Fusarium armeniacum Causing Fusarium Head Blight on Soft Red Winter Wheat in Illinois.

In the summer of 2016, while surveying the diversity of the Fusarium head blight (FHB) causal agent on soft red winter wheat (Triticum aestivum) in Illinois, we identified hundreds of naturally infected plants in five locations. Samples with characteristic symptoms of FHB (bleaching, accompanied by pink/white mycelium) were collected one to three weeks after anthesis. The collected glumes and developing kernels were surface sterilized and plated on sterile media. Single conidia isolates were derived for further work. All isolates were deposited to the USDA-ARS Mycotoxin Prevention and Applied Microbiology Research Unit in Peoria, IL. Among the collection, isolate CMR105 showed characteristics of F. armeniacum growing on PDA with abundant white mycelia and pigments of orange to pink (Suppl. Figure 1B). The CMR105 macroconidia were prominently curved, long, and tapering with a distinct foot shape typical of F. armeniacum (Leslie and Summerell, 2006). CMR105 conidia were produced quickly and abundantly compared to typical isolates such as BMR001, which were rare and slow-growing. The translation elongation factor 1-alpha (EF1-α), RNA polymerase 2 (RPB2), β-tubulin, and the internal transcribed spacer (ITS) genes were sequenced from selected isolates, including CMR105. The resulting DNA sequences were trimmed and aligned using blast on the Fusarium ID database and NCBI's nr database. For all the genes, isolate CMR105 had a 99% or higher similarity to multiple F. armeniacum accessions (Suppl. Table 1). We then conducted a phylogenetic analysis using the DNA sequences of three concatenated genes (RPB2, β-tubulin, and ITS). A maximum likelihood tree supported that isolate CMR105 is F. armeniacum (Suppl. Figure 1E). Koch's postulates were carried out in greenhouse experiments on spring wheat cultivar 'Norm'. At anthesis, a spore suspension of 5 x 104 spores per ml was injected into the central spikelet of wheat heads. Three plants were inoculated per isolate and a mock control consisting of water. The inoculated plants were placed into a mist chamber for 48 hours. Symptoms consisting of premature bleaching of multiple spikelets and pink/white coloration were observed one-week post-inoculation. No symptoms were observed on the control. Two weeks post-inoculation, kernels from the wheat heads were collected, surface sterilized with 10% bleach, and plated on PDA. The recovered isolates showed similar colony morphology to the inoculum. Similar results were obtained on field inoculations on soft red winter wheat. F. armeniacum has been reported from the United States, Australia, South Africa, China, and Argentina (Kommedahl et al., 1979; Nichea et al., 2015). To date, F. armeniacum has been reported to cause seed and root rot on soybeans, has been recovered from asymptomatic corn, and more commonly found as a soil saprophyte (Ellis et al., 2012; Leslie and Summerell, 2006; Nichea et al., 2015). We have shown here for the first time that F. armeniacum also causes FHB on wheat in Illinois. In both field and greenhouse assays, our F. armeniacum strain was less aggressive than F. graminearum strains. Recently, F. armeniacum was reported to cause FHB on emmer and spring wheat in New York (Fulcher and Bergstrom, 2020). It is important to note that many species of the genus Fusarium cause FHB. In this report, we show evidence that F. armeniacum is another causal agent of FHB in Illinois and warrants further study and surveillance.

Transcriptome Sequencing of the Striped Cucumber Beetle, Acalymma vittatum (F.), Reveals Numerous Sex-Specific Transcripts and Xenobiotic Detoxification Genes.

Acalymma vittatum (F.), the striped cucumber beetle, is an important pest of cucurbit crops in the contintental United States, damaging plants through both direct feeding and vectoring of a bacterial wilt pathogen. Besides providing basic biological knowledge, biosequence data for A. vittatum would be useful towards the development of molecular biopesticides to complement existing population control methods. However, no such datasets currently exist. In this study, three biological replicates apiece of male and female adult insects were sequenced and assembled into a set of 630,139 transcripts (of which 232,899 exhibited hits to one or more sequences in NCBI NR). Quantitative analyses identified 2898 genes differentially expressed across the male–female divide, and qualitative analyses characterized the insect’s resistome, comprising the glutathione S-transferase, carboxylesterase, and cytochrome P450 monooxygenase families of xenobiotic detoxification genes. In summary, these data provide useful insights into genes associated with sex differentiation and this beetle’s innate genetic capacity to develop resistance to synthetic pesticides; furthermore, these genes may serve as useful targets for potential use in molecular-based biocontrol technologies.

De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba

Gloriosa superba is an economical source of pharmaceutical colchicine, which is a mitotic poison used to treat gout, cancer and inflammatory diseases. It is important to study the genetic variations in this plant, but the progress is impeded due to limited number of molecular markers. In this study, we developed the expressed sequence tag-derived simple sequence repeat (EST-SSR) markers from the transcriptome sequence of the leaf samples of three different ecotypes of G. superba. De novo assembly was performed on these sequencing data to generate a total of 65,579 unigenes and 38,200 coding sequences (CDSs). These CDSs were annotated using NCBI Nr protein database, gene ontology terms and KEGG pathways. Differential gene expression was studied to yield differences in these ecotypes at the molecular level. Finally, a total of 14,672 potential EST-SSRs were identified from these unigenes, among which the dinucleotide (5754, 39.22%) and trinucleotide (5421, 36.95%) repeats were most abundant types followed by mononucleotides (3213, 21.83%). The most frequent motifs were CT/GA (1392, 9.48%), AG/TC (1219, 8.31%), and GA/CT (1146, 7.82%) among the dinucleotide repeats and CCG/ CGG (1487, 10.13%), AGG/CCT (1421, 9.68%), AGC/CTG (697, 4.75%) and AAG/CTT (621, 4.23%) among the trinucleotide repeats. Polymorphism study using a random set of 20 newly developed EST-SSRs revealed polymorphic information content value ranging from 0 to 0.5926 with an average of 0.4021. The large-scale ESTs developed in the current study will be useful as a genomic resource for further investigation of the genetic variations in this species.

First Report of Mume Virus A Infection of Prunus persica in China

Mume virus A, belonging to Capillovirus in the family Betaflexiviridae, was discovered recently from Japanese apricot (Prunus mume) and exhibited diffuse chlorotic spots on leaves (Marais et al. 2018). To date, Japanese apricot is the only known host of Mume virus A (MuVA) (Maliogka et al. 2018). Peach (Prunus persica) is a delicious and healthy summer fruit grown in most temperate regions of the world. More than 20 different viruses infecting peach trees have been reported (Jo et al. 2018). In April 2019, the leaves from four peach trees showing severe yellow mosaic and leaf curling were collected from peach orchards in Xinjiang, China. The pooled total RNA was extracted from these four trees leaves with TRIzol reagent (Life Technologies Corporation, Carlsbad, CA) and subjected to high-throughput sequencing (HTS) using a PE150 sequence strategy on an Illumina HiSeq2000 (Novogene Corporation, Tianjin, China). Approximately 39.3 million of 150-bp paired-end reads were obtained and used for de novo transcriptome assembly by SPAdes Genome Assembler (Bankevich et al. 2012). A total of 89,163 contigs with N50 of 866 bp were obtained and then were annotated by BLASTX analysis against the NCBI nr virus database (Altschul et al. 1997). Six known viruses (apple chlorotic leaf spot virus, Asian prunus virus 2, cherry green ring mottle virus, nectarine stem pitting-associated virus, peach associated luteovirus, and plum bark necrosis stem pitting-associated virus) and one known viroid (hop stunt viroid) were identified. Moreover, a 7,623-bp contig with a coverage of 84.4-fold was identified as capillovirus-related sequence. To classify the capillovirus accurately, pairwise genome alignments analysis was performed between all members of the Capillovirus genus using PASC online tool (Bao et al. 2014). The closest match was the genome of MuVA (NC_040568.1), sharing 78.36% nucleotide identity, followed by those of some isolates of cherry virus A, sharing less than 58.5% nucleotide identity. This result suggests that the capillovirus from peach belongs to the same species with the MuVA from apricot but should be a different isolate. We designated it as isolate pp, and its HTS-derived viral genome sequence was deposited in GenBank (accession no. MN412555). To confirm the HTS experiment results, from the same peach orchards, 23 peach leaf samples from different trees were collected, and total RNA was extracted with TRIzol reagent with standard procedures following the instructions. The RNA was subsequently used to test for pp isolate by reverse transcription polymerase chain reaction (PCR) using specific primers DT-MVAF5716 (5′-CTTCACATCGGAGCTGTCCT-3′) and DT-MVAR6277 (5′-TGCTGATTGCTTCAGACCCT-3′), targeting a portion of the open reading frame 2 (putative movement protein). Eleven samples produced the expected 560-bp PCR fragment. Three PCR products randomly selected were cloned into pMD19-T Vector (TaKaRa) for Sanger sequencing. All sequences of amplicons shared nearly 100% sequence identity with the corresponding region of the HTS-derived viral genome sequence. However, at least the other two viruses and viroid had been detected in all 11 MuVA-positive samples, so the symptoms of the initial sample cannot be explained by MuVA infection. To our knowledge, this is the first report of MuVA infecting peach trees. This report suggests that MuVA may have a broad host range in the genus Prunus.

Comparative transcriptome analysis of high-growth and wild-type strains of Pyropia yezoensis

Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi is a popular edible macro-alga that is found mostly in intertidal zones. It is one of the most economically important seaweed species and has been cultivated extensively in the cold waters of East Asia. Various reports have been published on the isolation and characterization of improved strains of Pyropia. However, there are few studies focusing on the molecular basis underlying these mutant strains. In this study, we performed a comparative analysis of whole transcriptomes of wild-type (PyWT) and high-growth (Py500G) strains of P. yezoensis using next generation RNA sequencing (RNA-seq). After sequencing, a total of 167,110,896 paired-end reads with a length of 151 nucleotides, were obtained. De novo transcriptome assembly and redundancy removal generated 19,441 transcripts. The assembly was annotated in NCBI nr, Swiss-Prot, Pfam, KEGG, GO and KOG databases. To unravel the differences in Py500G and PyWT, we mapped Py500G and PyWT reads to the assembly and calculated the expression levels. In total, there were 454 transcripts that were differentially expressed. Among the differentially expressed transcripts, candidate genes were identified with well-known growth and development functions. This study not only identifies candidate genes responsible for the high-growth phenotype of Py500G, but it also provides more comprehensive genomic data for future research on P. yezoensis.

Transcriptome profiling of two Dactylis glomerata L. cultivars with different tolerance in response to submergence stress

Submergence is one of the environmental stresses that limit plant growth and development. Dactylis glomerata L. is an important cool-season forage grass globally. To investigate the genes related to submergence response and the molecular mechanism associated with submergence tolerance, the transcriptome of D. glomerata in response to waterlogging treatment was analyzed. RNA-sequencing was performed in two D. glomerata cultivars, submergence tolerant ‘Dianbei’ and submergence sensitive ‘Anba’. A total of 50,045 unique genes matched the known proteins in the NCBI nr database by BLAST searches and 60.8% (30,418) of these genes were annotated with GO terms. Among these, 1395 genes only differentially expressed in ‘Dianbei’ and 18 genes shown different expression all the time were detected between the submergence tolerant ‘Dianbei’ and sensitive ‘Anba’. Gene ontology (GO) and KEGG pathway enrichment analyses demonstrated that the DEGs were mainly implicated in oxidation-reduction system, nucleic acid binding transcription factor activity, and glycerol kinase activity. The D. glomerata assembled transcriptome provided substantial molecular resource for further genomic analysis of forage grasses in response to submergence stress. The significant difference in expression of specific unigenes may account for waterlogging tolerance or acclimation in the two different D. glomerata cultivars. This study provided new insights into the molecular basis of submergence tolerance in D. glomerata.

High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii).

The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions.

De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway

Gymnema sylvestre is a highly valuable medicinal plant in traditional Indian system of medicine and used in many polyherbal formulations especially in treating diabetes. However, the lack of genomic resources has impeded its research at molecular level. The present study investigated functional gene profile of G. sylvestre via RNA sequencing technology. The de novo assembly of 88.9 million high quality reads yielded 23,126 unigenes, of which 18116 were annotated against databases such as NCBI nr database, gene ontology (GO), KEGG, Pfam, CDD, PlantTFcat, UniProt & GreeNC. Total 808 unigenes mapped to 78 different Transcription Factor families, whereas 39 unigenes assigned to CYP450 and 111 unigenes coding for enzymes involved in the biosynthesis of terpenoids including transcripts for synthesis of important compounds like Vitamin E, beta-amyrin and squalene. Among them, presence of six important enzyme coding transcripts were validated using qRT-PCR, which showed high expression of enzymes involved in methyl-erythritol phosphate (MEP) pathway. This study also revealed 1428 simple sequence repeats (SSRs), which may aid in molecular breeding studies. Besides this, 8 putative long non-coding RNAs (lncRNAs) were predicted from un-annotated sequences, which may hold key role in regulation of essential biological processes in G. sylvestre. The study provides an opportunity for future functional genomic studies and to uncover functions of the lncRNAs in G. sylvestre.

Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.

Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value < 10−5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of a discussion meeting issue ‘Single cell ecology’.

Using de novo transcriptome assembly and analysis to study RNAi in Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae)

Phenacoccus solenopsis is one of the major polyphagous crop pests in India. Inadequate genomic or transcriptomic resources have limited the molecular studies in this insect despite its huge economic importance. The existing molecular sequence resources of this insect were supplemented through RNA sequencing, de novo transcriptome assembly and analysis, which generated 12, 925 CDS from 23,643 contigs with an average size of 1077.5 bp per CDS and 85.1% positive BLAST hits with NCBI Non redundant (nr) database. Twenty three genes involved in RNAi machinery identified through BLASTx search against NCBI nr database suggested the existence of robust RNAi in mealybug. RNAi in P. solenopsis was demonstrated through knockdown of IAP (Inhibitor of Apoptosis), AQP (Aquaporin), CAL (Calcitonin), VATPase (V-type proton ATPase subunit F 1), bursicon, chitin synthase, SNF7 and α-amylase by injecting sequence specific dsRNA of respective genes in adult female. Additionally, feeding RNAi has been demonstrated in 2nd instar nymph through dsRNA uptake in plant. The knockdown of core RNAi machinery genes such as Dicer, Argonaute and Staufen significantly hampered RNAi efficiency in this insect. However, downregulation of dsRNases improved RNAi efficiency. Sequential studies for understanding RNAi in P. solenopsis using transcriptome sequences have also been reported. The present study provides a base for future research on developing RNAi as strategy for management of this pest.

Identification of microsatellite loci, gene ontology and functional gene annotations in Indian salmon (Eleutheronema tetradactylum) through next-generation sequencing technology using illumina platform

Abstract Whole genome sequencing was performed on three samples of four finger threadfin Eleutheronema tetradactylum (KET25, KET29 and KET30) using illumina NextSeq500 platform using 2 × 150 bp chemistry. 8,390,317, 7,085,775 and 8,461,589 high quality reads were obtained after trimming low quality reads and adapter sequence. These high quality reads obtained were used for de novo assembly and obtained a number of scaffolds. From these scaffolds of vast sequenced data, we were able to identify 60246, 46107 and 60907 Simple Sequence Repeats (SSR) markers in KET25, KET29 and KET30 respectively, which will be useful in population genetic analysis and other diversity studies in Indian salmon. The gene prediction on assembled scaffolds predicted 31,943 genes for KET25; 26,487 genes for KET29 and 31,654 genes for KET30 with average gene size of 458bp, 424bp and 459bp respectively. A total of 30,209, 25,107 and 29,943 genes were annotated against the NCBI Nr database for the samples respectively. E. tetradactylum is a commercially important fish species for many countries. This is the first report on the identification of genomic SSR markers in E. tetradactylum using NGS technology. This study provides an insight of baseline knowledge of the genome sequence of Indian salmon for future studies.

Characterization and complete genomic analysis of two Salmonella phages, SenALZ1 and SenASZ3, new members of the genus Cba120virus.

Salmonella phages SenALZ1 and SenASZ3, two novel phages infecting Salmonella enterica, were isolated and analyzed. The genomes of these two phages consist of 154,811 and 157,630 base pairs (bp), with G+C contents of 44.56% and 44.74%, respectively. Fifty-nine of 199 open reading frames (ORFs) in the SenALZ1 genome, and 60 of the 204 in the SenASZ3 genome show similarity to reference sequences in the NCBI nr database that encode putative phage proteins with predicted functions. Based on the results of transmission electron microscopy (TEM) examination, complete genome sequence alignment, phylogenetic analysis, and gene annotation, we propose that these two phages are representative isolates of two new species of the genus Cba120virus, subfamily Cvivirinae, family Ackermannviridae.

Circatidal gene expression in the mangrove cricket Apteronemobius asahinai

The mangrove cricket Apteronemobius asahinai is endemic to mangrove forest floors. It shows circatidal rhythmicity, with a 12.6-h period of locomotor activity under constant conditions. Its free-running activity also has a circadian component; i.e. it is more active during the subjective night than during the day. In this study, we investigated rhythmic gene expression under constant darkness by RNA sequencing to identify genes controlled by the biological clock. Samples collected every 3 h for 48 h were analysed (one cricket per time-point). We identified 284 significant circatidal cycling transcripts (period length 12–15 h). Almost half of them were annotated with known genes in the NCBI nr database, including enzymes related to metabolic processes and molecular chaperones. There were less transcripts with circadian rhythmicity than with circatidal rhythmicity, and the expression of core circadian clock genes did not show significant rhythmicity. This may reflect the nature of the mangrove cricket or may be due to the paucity of the sampling repeats: only two periods for circadian cycle with no replications. We evaluated for the first time the rhythmic transcriptome of an insect that shows circatidal rhythmic activity; our findings will contribute to future studies of circatidal clock genes.

Comparative transcriptome profiling of Kappaphycus alvarezii (Rhodophyta, Gigartinales) in response to two extreme temperature treatments: an RNA-seq-based resource for photosynthesis research

ABSTRACTKappaphycus alvarezii provides an important raw material for the extraction of κ-carrageenan. Comparative transcriptome analysis of K. alvarezii after 24 h extreme temperature treatments (17°C and 34°C) was performed to uncover the molecular mechanisms controlling temperature-related photosynthesis regulation. Optimum temperature (28°C) was employed as the control. After de novo assembly of these three transcriptome samples and searching the assembled transcripts by BLAST against the NCBI nr databases, 11,537 top-hit transcripts were assigned as unigenes. Through comparisons, 302 significantly differentially expressed genes were identified. Twenty-three of the differentially expressed unigenes encoded photosystem antenna protein subunits and a further 25 were associated more broadly with photosynthesis functions. Compared to the light-harvesting complex (LHC) protein, the expression of phycobiliproteins (PBPs) was stable after extreme low and high temperature (ELT/EHT) treatments. Both ELT and EHT were found to inhibit the expression of subunits of photosystem II (PsbA, PsbC, Psb27, PsbW, PsbS), photosystem I (PsaF, PsaG, PsaK) and photosynthetic electron transport (PetE). These results were confirmed through targeted analysis of the mRNA and protein abundance of individual proteins, and were congruent with the results of chlorophyll a fluorescence (OJIP) measurements performed with temperature-stressed lines. In conclusion, similarities and differences in the behaviours of photosynthesis-related genes were summarized to provide opportunities for understanding the responses of K. alvarezii after extreme temperature treatments.

Comparative Proteomic Analysis of Wheat Carrying Pm40 Response to Blumeria graminis f. sp. tritici Using Two-Dimensional Electrophoresis.

Wheat powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is considered a major wheat leaf disease in the main wheat producing regions of the world. Although many resistant wheat cultivars to this disease have been developed, little is known about their resistance mechanisms. Pm40 is a broad, effective resistance gene against powdery mildew in wheat line L699. The aim of this study was to investigate the resistance proteins after Bgt inoculation in wheat lines L699, Neimai836, and Chuannong26. Neimai836 with Pm21 was used as the resistant control, and Chuannong26 without any effective Pm genes was the susceptible control. Proteins were extracted from wheat leaves sampled 2, 4, 8, 12, and 24 h after Bgt inoculation, separated by two-dimensional electrophoresis, and stained with Coomassie brilliant blue G-250. The results showed that different proteins were upregulated and downregulated in three wheat cultivars at different time points. For the wheat cultivar L699, a total of 62 proteins were upregulated and 71 proteins were downregulated after Bgt inoculation. Among these, 46 upregulated proteins were identified by mass spectrometry analysis using the NCBI nr database of Triticum. The identified proteins were predicted to be associated with the defense response, photosynthesis, signal transduction, carbohydrate metabolism, energy pathway, protein turnover, and cell structure functions. It is inferred that the proteins are not only involved in defense response, but also other physiological and cellular processes to confer wheat resistance against Bgt. Therefore, the resistance products potentially mediate the immune response and coordinate other physiological and cellular processes during the resistance response to Bgt. The lipoxygenase, glucan exohydrolase, glucose adenylyltransferasesmall, phosphoribulokinase, and phosphoglucomutase are first reported to be involved in the interactions of wheat-Bgt at early stage. The further study of these proteins will deepen our understanding of their detailed functions and potentially develop more efficient disease control strategies.

Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes.

In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization.

Near-complete genome assembly and annotation of the yellow drum (Nibea albiflora) provide insights into population and evolutionary characteristics of this species.

Yellow drum (Nibea albiflora) is an important fish species in capture fishery and aquaculture in East Asia. We herein report the first and near‐complete genome assembly of an ultra‐homologous gynogenic female yellow drum using Illumina short sequencing reads. In summary, a total of 154.2 Gb of raw reads were generated via whole‐genome sequencing and were assembled to 565.3 Mb genome with a contig N50 size of 50.3 kb and scaffold N50 size of 2.2 Mb (BUSCO completeness of 97.7%), accounting for 97.3%–98.6% of the estimated genome size of this fish. We further identified 22,448 genes using combined methods of ab initio prediction, RNAseq annotation, and protein homology searching, of which 21,614 (96.3%) were functionally annotated in NCBI nr, trEMBL, SwissProt, and KOG databases. We also investigated the nucleotide diversity (around 1/390) of aquacultured individuals and found the genetic diversity of the aquacultured population decreased due to inbreeding. Evolutionary analyses illustrated significantly expanded and extracted gene families, such as myosin and sodium: neurotransmitter symporter (SNF), could help explain swimming motility of yellow drum. The presented genome will be an important resource for future studies on population genetics, conservation, understanding of evolutionary history and genetic breeding of the yellow drum and other Nibea species.