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This study intends to assess miRNA-326’s effect on the immune-inflammatory microenvironment and its mechanism in gastric cancer (GC). GC adjacent tissues and tumor tissues were collected to analyze inflammatory factors by immunohistochemistry and ELISA, Est-1 and miRNA-326 level by Western blot or PCR, Th17 cells by flow cytometry. CD4+ T cells were transfected with Est-1 inhibitor, Est-1 mimics, or miR-326 mimics followed by measurement of Th17 differentiation-related genes via gene chips and inflammatory factor release. Inflammatory factors in serum of GC patients were significantly increased and miR-326 was upregulated with decreased Est-1 and unbalanced Th17/Treg cell ratio. miR-326 targeted Est-1 to inhibit its expression. After transfection with Est-1 inhibitor, Th17 differentiation-related genes were upregulated. After transfection with miR-326 mimics, Est-1 level was reduced and inflammation was enhanced with maturation of Th17 cells. In conclusion, miRNA-326 induces Th17 cell differentiation by targeting Est-1, thereby promoting the release of inflammatory factors and inducing immune inflammatory microenvironment.

The aim of this study was to identify genes that are specifically expressed in pancreatic islet β-cells (hereafter referred to as β-cells). Large-scale complementary DNA-sequencing analysis was performed for 3,429 expressed sequence tags derived from murine MIN6 β-cells, through homology comparisons using the GenBank database. Three individual ESTs were found to code for protease serine S1 family member 53 (Prss53). Prss53 mRNA is processed into both a short and long form, which encode 482 and 552 amino acids, respectively. Transient overexpression of myc-tagged Prss53 in COS-7 cells showed that Prss53 was strongly associated with the luminal surfaces of organellar membranes and that it underwent signal peptide cleavage and N-glycosylation. Immunoelectron microscopy and western blotting revealed that Prss53 localized to mitochondria in MIN6 cells. Short hairpin RNA-mediated Prss53 knockdown resulted in Ppargc1a downregulation and Ucp2 and Glut2 upregulation. JC-1 staining revealed that the mitochondria were depolarized in Prss53-knockdown MIN6 cells; however, no change was observed in glucose-stimulated insulin secretion. Our results suggest that mitochondrial Prss53 expression plays an important role in maintaining the health of β-cells.

Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification. The increasing numbers of available genomic sequences of ectomycorrhizal (ECM) fungi enable deeper insights into the characteristics of MT genes in these fungi that form the most important symbiosis with the host trees in forest ecosystems. The aim of this study was to establish a comprehensive, genome-wide inventory of MT genes from the ECM fungus Laccaria bicolor. Eight MT genes in L. bicolor were cloned, and the expression patterns of their transcripts at various developmental stages based on expressed sequence tag (EST) counts were analyzed. The expression levels of four MTs were significantly increased during symbiosis stages. Quantitative real-time PCR (qRT-PCR) analysis revealed that transcripts of LbMT1 were dominant in free-living mycelia and strongly induced by excessive copper (Cu), cadmium (Cd), and hydrogen peroxide (H2O2). To determine whether these eight MTs functioned as metal chelators, we expressed them in the Cu- and Cd-sensitive yeast mutants, cup1∆ and yap1∆, respectively. All LbMT proteins provided similar levels of Cu(II) or Cd(II) tolerance, but did not affect by H2O2. Our findings provide novel data on the evolution and diversification of fungal MT gene duplicates, a valuable resource for understanding the vast array of biological processes in which these proteins are involved.

application/pdf, Objectives:Haemaphysalis longicornis is the most important tick species in Japan and has a wide range of vector capacity. Due to its veterinary and medical importance, this tick species has been used as a model for tick/vector biological studies. To identify the key molecules associated with physiological processes during blood feeding and embryogenesis, full‑length cDNA libraries were constructed using the fat body, hemocytes‑containing hemolymph, midgut, ovary and salivary glands of fed females and embryos of the laboratory colony of parthenogenetic H. longi-cornis. The sequences of cDNA from the salivary glands had been already released. However, the related information is still poor, and the other expressed sequence tags have not yet been deposited.Data description:A total of 39,113 expressed sequence tags were obtained and deposited at the DNA DataBank of Japan. There were 7745 sequences from embryos, 7385 from the fat body, 8303 from the hemolymph including hemocytes, 7385 from the midgut, and 8295 from the ovary. The data, including expressed sequence tags from the salivary glands was summarized into Microsoft Excel files. Sharing this data resource with the tick research community will be valuable for the identification of novel genes and advance the progress of tick research., Explanation of these data Data file 1_ESTs_Hl_Fat Body (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004700) Data file 2_ESTs_Hl_Hemolymph (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004701) Data file 3_ESTs_Hl_Midgut (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004702) Data file 4_ESTs_Hl_Ovary (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004703) Data file 5_ESTs_Hl_Salivary glands (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004704) Data file 6_ESTs_Hl_Embryo (Umemiya-Shirafuji et al.) (http://doi.org/10.24556/00004705)

Wild edible plants are often found to be rich sources of nutrients and medicinally beneficial compounds with pharmacological activities. Gnetum gnemon is a nutritionally important plant and a popular food source in parts of Assam and North-East India. Various microRNAs (miRNAs) have been recently identified in many plants; how ever, there are no records of identification of miRNAs in any species of Gnetum. The prediction of miRNA-target associations in G. gnemon is an important step to facilitate functional genomics studies in this species. In the present study, all known miRNAs from plants available in public domain were used to search for the conserved G. gnemon miRNA homologues in publicly accessible expressed sequence tags (ESTs) in NCBI database. An aggregate of 20 new potential miRNAs belonging to two diverse miRNA families (miR399 and miR5021) were identified through a homology-based search by following stringent filtering criteria. To investigate the potential cross-king dom effects of the identified miRNAs, we further identified the putative target genes of G. gnemon miRNAs in hu man transcriptome and analyzed them against the NCBI non-redundant protein database. The KEGG analysis of the target genes indicated that these genes were involved in different metabolic pathways such as caffeine meta bolism, drug metabolism, and nitrotoluene degradation. The target genes of G. gnemon miRNAs in humans were found to be associated with various disorders of both hereditary and non-hereditary origin. These results could help to shed new light on understanding of miRNA-mRNAs functional networks in this species and its po tential use as a small RNA-based therapy against some human diseases.

Background: Japanese hop is an important cause of weed pollinosis in East Asia. Its pollen is abundant in autumn. This pollen is known to be the cause of many allergic diseases. However, molecular characteristics of its allergens have not been elucidated. Objective: In this study, we produced recombinant proteins of allergen homologues from Japanese hop by the analysis of expressed sequence tags (EST), and evaluated its allergenicity. Methods: cDNA library was constructed using as little as 50 ng of total RNA from Japanese hop pollen. Allergen homologues were identified by the initial screening of 963 EST clones. Recombinant proteins were overexpressed in the E. coli expression system and purified using Ni-nitrilotriacetic acid-agarose. Purified proteins were analyzed by ELISA. Results: Japanese hop pathogenesis-related 1 protein (PR-1) shares 37.0 to 44.4% of amino acid sequence identity with Art v 2, Cuc m 3, and Cyn d 24. Pectin methyl esterase (PME) shows 23.2 to 50.2% of identities to Act d 7, Ole e 11, and Sal k 1. Polygalacturonase (PGs) shows 16.7 to 19.3% of identities to Phl p 13, Cry j 2, Cha o 2, Jun a 2, Pla a 2, and Pla or 2. IgE antibodies from Japanese hop allergy patients’ sera recognized PR-1 (3.4%), PME (13.8%), PGs (3.7%), and profilin (13.8%), respectively. Conclusion: Novel allergenic components were identified, even though low IgE reactivity was displayed reflecting the low degree of cross-reactivity with other pollen allergens. We believe that these molecules have worth further studies.

Platycodon grandiflorum is a perennial plant that has been used for medicinal purposes. Specifically, it is widely used in Northern China and Korea for the treatment of various diseases. Terpenoids belong to a group called secondary metabolites and have attracted a wide range of interest. Here, we determined the expressed sequence tag (EST) library of the methyl jasmonate (MeJA)-treated hairy root of P. grandiflorum. In total, 5760 ESTs were obtained, but after deleting the vector sequences and removing poor-quality sequences, a total of 2536 ESTs were attained. Of these, 811 contigs and 1725 singletons were annotated. The data were further analyzed with a focus on the gene families of the terpenoid biosynthetic pathway (TBP). We identified and characterized four TBP genes; among these were three full-length cDNAs encoding PgHMGS, PgMK, and PgMVD, whereas PgHMGR had a partial sequence based on the EST library database. Phylogenetic analysis and a pairwise identity matrix showed that these identified genes were closely related to those of other higher plants. Moreover, the tertiary structure and multiple alignment analysis showed that several distinct conserved motifs were present. Quantitative reverse transcription-polymerase chain reaction results revealed that TBP genes were constitutively expressed in all organs of P. grandiflorum, while the expression of transcript levels of these genes varied distinctly among the organs. Additionally, the total amount of platycosides was highly detected in the root, accumulating in concentrations 7.8 and 2.6 times higher than in the hairy root and stem, respectively, and 1.4 times higher than in the leaf and flower. The highest amount of total phytosterols was found to accumulate in the leaves at 9.3, 9.1, 1.8, and 1.6 times higher than that of the stem, root, hairy root, and flower, respectively. After the hairy root was exposed to the MeJA treatment, the transcript levels of PgHMGS, PgHMGR, PgMK, and PgMVD had significantly increased. The highest level of transcript accumulation occurred at 3 h after initial exposure for most of the genes. Meanwhile, triterpene saponin accumulation increased with the increase in the time of exposure, and at 48 h after initial exposure, the total saponin content was the highest recorded.

MicroRNAs (miRNA) are recently discovered endogenous, small noncoding RNAs (of 22 nucleotides) that play pivotal roles in gene regulation. They are involved in post-transcriptional control of gene expression. miRNAs are emerging as important regulators of cell proliferation, development, cancer formation, stress responses, cell death and physiological conditions. Increasing evidence has demonstrated the human miRNAs bind to their target mRNA sequences with perfect or near-perfect sequence complementarily. This provides a powerful strategy for discovering potential type 2 diabetes mellitus (T2DM) targets and gives the probability to exploit them for diagnostic and therapeutic causes. About 6% of the world population is affected by T2DM, and it is recognized as a global epidemic by the World Health Organization. At present there is no valid biomarker to control or manage T2DM. Therefore, the present study applied a mature sequence of miRNAs from publicly accessible databases to identify the miRNA from T2DM expressed sequence tags, and the results are detailed and discussed below.

Genetic improvement in coconut relies on exploiting the vast existing diversity among coconut accessions. Robust molecular markers are a pre-requisite for efficient characterization of genetic diversity. Microsatellites or simple sequence repeats (SSRs), mined from expressed sequence tags (ESTs), constitute an important resource for analysis of genetic diversity as they are abundant, polymorphic and represent function regions of the genome. We have identified a total of 318,528 putative EST-SSRs from 130,942 unigenes utilizing a leaf transcriptome dataset of coconut. Among the EST-SSRs, dinucleotide repeats were abundant (219,912; 69.04%) followed by trinucleotide (70,722; 22.2%) and tetra-nucleotide repeats (6281; 1.9%). Among the dinucleotide repeat motifs, the dominant repeat was AG/CT (35.87%), followed by AT/AT (18.59%), while the dominant trinucleotide repeat was AAG/CTT (4.59%). One hundred and twenty EST-SSR primer pairs were designed and utilized to amplify six DNA samples of coconut accessions. Fifty primers (41.7%) produced reproducible polymorphic fragments of expected sizes, from which a total of 10 primers were selected for the diversity assessment in 186 palms of 50 coconut accessions, comprising of 25 each of tall and dwarf accessions. A total of 137 alleles were detected with an average of 13.7 alleles per SSR locus. The number of alleles observed at each locus in the data set ranged from 7 to 22. All the loci showed 100% polymorphism with respect to the samples screened. The average observed heterozygosity was 0.46. The PIC values ranged from 0.79 (CnKGDEST129 and CnKGDEST100) to 0.91 (CnKGDEST117 and CnKGDEST122) with a mean value of 0.85, indicating the capacity of the EST-SSR markers to detect high levels of polymorphism. The cluster analysis revealed that accessions were generally clustered based on their relative similarity and irrespective of their geographic origins. The present study demonstrates the usefulness of transcriptome sequencing as a rapid and cost-effective methodology for the development of molecular markers. The EST-SSR markers generated through this study constitute useful and reliable tools for assessment of genetic diversity and marker-assisted selection in coconut.

Sequence-based markers have added a new dimension in the efficiency of identifying alien introgressions in wheat. Expressed sequence tag-sequence tagged sites (EST-STS) markers have proved useful in tracing alien chromatin. In this study, we report the development of Thinopyrum bessarabicum- and Secale anatolicum-specific EST-STS markers and their application in tracing respective alien chromatin introgressions in wheat. The parental lines, Chinese Spring (CS), ISR991.1 (CS/Th. bessarabicum amphidiploid), and ISR1049.2 (CS/Secale anatolicum amphidiploid), were used as core experimental materials. Using comparative analysis of RNA-Seq data, 10 903 and 10 660 candidate sequences specific to Th. bessarabicum and S. anatolicum, respectively, were assembled and identified. To validate the genome specificity of these candidate sequences, 68 and 64 EST-STS markers were developed from randomly selected candidate sequences of Th. bessarabicum and S. anatolicum, respectively, and tested on sets of alien addition lines. Fifty-five and 53 markers for Th. bessarabicum and S. anatolicum chromatin, respectively, were assigned to chromosomal location(s), covering all seven chromosomes. Approximately 83% of S. anatolicum-specific markers were transferable to S. cereale. The genome-specific candidate sequences identified and the EST-STS markers developed will be valuable resources for exploitation of Th. bessarabicum and Secale species diversity in wheat and triticale breeding.

Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

Shaggy-related protein kinase (SK) plays important roles in the plant growth development, signal transduction, abiotic stress and biotic stress and substance metabolism regulation. In the present paper, a cDNA sequence encoding MmSK (GenBank accession No: KY348867) was cloned from the leaves of mulberry based on mulberry expressed sequence tags (EST) and homologous cloning technology using RT-PCR, which was 1705 bp in length with a full open reading frame (ORF) of 1236 bp encoding a protein of 411 amino acids. The estimated molecular weight and isoelectric point (pI) of the putative protein were 46.55 kDa and 8.61, respectively. Conservation domain structure analysis indicated that MmSK protein had typical structure of the protein kinase domain and belonged to GSK3/shaggy protein kinase family. Multiple sequence alignment and phylogenetic analysis showed that the homology between the amino acid sequences encoded by the MmSK gene and various species was more than 89%. Quantitative real-time PCR (qRT-PCR) analysis revealed that MmSK was expressed in all the tested tissues including leaf, bud, fruit, stem, phloem and xylem of the mulberry with the highest expression in the phloem. The expression level of the mRNA has changed significantly under salt, drought, cold and ABA stress treatments compared to the normal growth environment. Overall, these results showed a better understanding of the molecular basis for the signal transduction mechanism during the stress responses in mulberry trees.

To examine the genetic basis for the variable susceptibility of Striga hermonthica from differing zones of sub-Saharan Africa to Fusarium oxysporum f. sp. strigae (Fos) isolates Foxy-2 and FK3, 10 S. hermonthica populations from Eastern and Western Africa were phenotyped for their susceptibility response to Foxy-2 and FK3, and then genotyped with 22 simple sequence repeat (SSR) markers. There is low genetic differentiation between East African and West African S. hermonthica populations (i.e. the proportion of the total genetic variance contained in the subpopulation relative to the total genetic variance, FST = 0.012, P

Stevia rebaudiana, or stevia, is a perennial herb native to the northern region of South America. It is commercially important due to the high level of non-caloric sweetening compound, which has been consumed worldwide as food and medicine. Stevioside is considered as the most important compound of steviol glycosides that functions as the main sweetener. Exposure of the stevia plant to long-day conditions (increased exposure to light) will delay the flowering process, which led to an increase in glycoside accumulation. The bioinformatics analysis of 5548 expressed sequence tags (ESTs) obtained from dbEST (NCBI) using the Blast2GO software and manual curation identified 7 ESTs that contain domains involved in the flowering process. The domains were the heat shock protein (Hsp) domain, squamosa promoter-binding protein (SBP) domain, CONSTANS, CO-like, and TOC1 (CCT) domains; K homology (KH) domain; and ubiquitin-conjugating enzyme domain (UBC).

Bread wheat is a major food crop on a global scale. Stripe rust, caused by Puccinia striiformis f. sp. tritici, has become one of the largest biotic stresses and limitations for wheat production in the 21st century. Post 2000 races of the pathogen are more virulent and able to overcome the defense of previously resistant cultivars. Despite the availability of effective fungicides, genetic resistance is the most economical, effective, and environmentally friendly way to control the disease. There are two major types of resistance to stripe rust: all-stage seedling resistance (ASR) and adult-plant resistance (APR). Although both resistance types have negative and positive attributes, ASR generally is race-specific and frequently is defeated by new races, while APR has been shown to be race non-specific and durable over time. Finding genes with high levels of APR has been a major goal for wheat improvement over the past few decades. Recent advancements in molecular mapping and sequencing technologies provide a valuable framework for the discovery and validation of new sources of resistance. Here we report the discovery of a precise molecular marker for a highly durable type of APR – high-temperature adult-plant (HTAP) resistance locus in the wheat cultivar Louise. Using a Louise × Penawawa mapping population, coupled with data from survey sequences of the wheat genome, linkage mapping, and synteny analysis techniques, we developed an amplified polymorphic sequence (CAPS) marker LPHTAP2B on the short arm of wheat chromosome 2B, which cosegregates with the resistant phenotype. LPHTAP2B accounted for 62 and 58% of phenotypic variance of disease severity and infection type data, respectively. Although cloning of the LPHTAP2B region is needed to further understand its role in durable resistance, this marker will greatly facilitate incorporation of the HTAP gene into new wheat cultivars with durable resistance to stripe rust.

Sugarcane generates the vast majority of sugar consumed worldwide. The large-scale development of EST-SSR markers are crucial for the analysis of genetic mechanisms important in agronomic traits of sugarcane. In this study, based on published 107,598 full-length expressed sequence tags (ESTs) from 22 sugarcane cultivars, we identified a total of 46,043 loci of simple repeat sequences. The SSRs with di-nucleotide (8175 loci) and tri-nucleotide (10,709 loci) repeat motifs account for 40.96% (18,884) of the total SSR loci, with (AT/TA)n and (ACA/TGT)n being found to be the major repeat motifs. A total of 1070 pairs of primers were randomly selected to verify using 12 accessions including S. officinarum, S. robustum, S. spontaneum and cultivars. The results showed that 847 (79.1%) were successfully amplified, of which 349 (32.60%) were polymorphic in the analyzed samples. The polymorphic rates of EST-SSR markers with di-nucleotide, tri-nucleotide, tetra-nucleotide, penta-nucleotide and hexa-nucleotide repeat motifs were 36.82% (81), 49.40% (165), 43.04% (34), 30.19% (32) and 34.26% (37), respectively. Among them, the EST-SSRs comprising five types of repeat motifs (CA)n, (CCG)n, (CCGC)n, (CGGCG)n and (GCCGGC)n presented high degrees of polymorphism. Finally, 20 EST-SSR markers with polymorphisms were selected to perform a cluster analysis of 48 accessions from Saccharum and Erianthus genera. These results demonstrated that Chinese sugarcane cultivars from group IV (25/39) had a lower genetic divergence than cultivars from other countries and EST-SSR markers can also be used in determining the genetic diversity of Erianthus genus. This set of EST-SSR markers is an important molecular resource for analyzing genetic diversity, molecular fingerprinting and genetic mapping.

Chemokines are small cytokines that are classified into four groups, one of which is called CC chemokines. In the present study, the full-length cDNA of a CCL25 chemokine was identified from black rockfish, Sebastes schlegelii (named as SsCCL25) by EST (expressed sequence tag) analysis. The cDNA of SsCCL25 consisted of a 5-terminal untranslated region (UTR) of 74 bp, a 3-UTR of 882 bp with a poly (A) tail, and an open reading frame (ORF) of 303 bp encoding a polypeptide of 100 amino acids with the putative molecular mass of 11.5 kDa. There was a SCY domain in the deduced amino acid sequence of SsCCL25. The phylogenetic relationships and syntenic analyses provided evidences for the identities of SsCCL25 with CCL25 group. The mRNA transcripts of SsCCL25 were expressed in all detected tissues and dominantly in liver, muscle and gill. Moreover, after Vibrio anguillarum stimulation, the mRNA expression levels of SsCCL25 were significantly up-regulated at 24 h (p 0.05) in the liver and during 4-8 h (p 0.05) in the spleen. Recombinant SsCCL25 protein induced chemotaxis of both control and LPS-stimulated peripheral blood leukocytes (PBL) and enhanced their resistance to bacterial infection in a dose-dependent manner. Furthermore, rSsCCL25 showed significant inhibitory effect on V. anguillarum and Edwardsiella tarda growth. All these results collectively indicated that SsCCL25 might contribute to the defense against microbe infection and function as a chemoattractant in black rockfish.

Citrus limon (lemon) is an important fruit crop of Rutaceae family with high nutritive value. The microRNAs (miRNAs) are a class of small RNAs, approximately 22 nucleotides long. They are evolutionary conserved and function at post-transcriptional level to regulate the expressivity of genes in both plants and animals. They have crucial roles in different biological and metabolic processes like growth and development, pathogen defense, abiotic and biotic stress response in plants. Computational analysis of Citrus limon expressed sequence tags (ESTs) resulted in the identification of one conserved microRNA (clm-miR5658). The secondary structure of newly identified microRNA was generated based on minimal folding energy (MFE= −50.60 kcal/mol) and minimal folding energy index (MFEI= 0.81). Phylogenetic analysis of miR5658 family revealed a close association of clm-miR5658 with bra-miR5658. Further, a total of 14 potential target genes of the putative miRNA were identified and functionally annotated. The findings of this study will contribute to understand the role of miRNAs in lemon and expected to lay foundation for further research on lemon miRNAs.

Long non-coding RNAs (lncRNAs) is a class of eukaryotic transcripts with length of more than 200 bp. They contribute to the regulation of gene expressions involved in multiple processes including the skin cell proliferation, differentiation, and reconstruction of the secondary hair follicles (SHFs). In this study, firstly, we identified 16 putative lncRNAs from SHFs of cashmere goat based on the EST sequences from NCBI database. Secondly, we investigated their transcriptional pattern in SHFs of cashmere goat, and constructed their ceRNA regulatory networks. The RT-qPCR results showed four lncRNAs (lncRNA-475074, -052149, -052140, and -051789) were significantly up-regulated, and nine lncRNAs (lncRNA-711032, -475083, -475070, -052139, -052127, -052037, -051903, -051847, and -051804) were significantly down-regulatd in anagen SHFs of cashmere goat. CeRNA networks analysis revealed complex interactional relationship among lncRNAs, miRNAs and mRNAs. Further, the KEGG pathway enrichment was performed for the potential target genes of the identified lncRNAs based on bioinformatics technique, and the results indicated that differentially expressed lncRNAs directly or indirectly might regulate potential target genes. Our results from this study will provide a significant information for further exploring the functions and possible mechanisms of the identified lncRNAs in SHFs of cashmere goat.

Calotropis procera (Aiton) Dryand is a medicinally and economically important woody shrub used to cure various diseases. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from C. procera and studied the cross-species transferability of the selected markers. We have identified 34,355 potential EST-SSRs from C. procera and classified them based on the type of repeat motifs and Gene Ontology (GO) annotation. Virtual primers for 17,036 EST-SSRs were designed, and 55 primer pairs representing di-, tri-, tetra-, penta-, and hexa-nucleotide repeats were used for the validation of the EST-SSRs. A total of 48 out of 55 EST-SSR primers showed clear amplification in Calotropis procera. To validate EST-SSRs at the nucleotide level, four randomly selected EST-SSR primer sets were amplified and sequenced. Sequence alignment confirmed the presence of SSRs in the amplified primers. The polymorphisms of the 16 primer pairs were studied, and it was observed that 15 primer sets produced polymorphic bands. Out of these 15 pairs of primers, we identified 141 alleles with an average of 2.56 alleles per locus. The allelic diversity was estimated for 15 EST-SSR markers using three accessions of Calotropis. The study has succeeded in the development of novel EST-SSR markers from Calotropis procera and establishment of the molecular marker resources that can serve as a useful genomic tool for further development of germplasm resources and effective marker-assisted breeding and domestication programs for Calotropis procera.

The filamentous fungus Aspergillus terreus has been successfully used for industrial production of itaconic acid (IA) for many years. The IA biosynthesis pathway has recently been characterized at a molecular genetic level as an IA gene cluster by a clone-based transcriptomic approach. The cluster consists of four genes, including genes for cis-aconitic acid decarboxylase (cadA), a predicted transcription factor (tf), a mitochondrial organic acid transporter (mttA) and an MFS (major facilitator superfamily) type transporter (mfsA). In this research, we performed expressed sequence tag (EST) analysis and systematic gene deletions to further investigate the role of those genes during IA biosynthesis in A. pseudoterreus ATCC32359. EST analysis showed a similar expression pattern among those four genes that were distinct from neighboring genes and further confirmed that they belong to the same biosynthesis cluster. Systematic gene deletion analysis demonstrated that tf, cadA, mttA and mfsA genes in the cluster are essential for IA production; deletion of any of them will either completely abolish the IA production or dramatically decrease the amount of IA produced. The tf gene plays a regulatory role in this cluster. Deletion of tf led to decreased expression levels of cadA, mttA and mfsA. More importantly, a significant amount of aconitic acid was detected in the cadA deletion strain but not in the other deletion strains. Therefore, by deleting only one gene, the cadA, we established a novel microbial host for the production of aconitic acid and other value-added chemicals from sugars in lignocellulosic biomass.