Expressed Sequence Tags Research Articles

Drivers of population divergence and genetic variation in Elymus breviaristatus (Keng) Keng f. (Poaceae: Triticeae), an endemic perennial herb of the Qinghai-Tibet plateau

Elymus breviaristatus, a rare grass species with excellent resistance and ecological importance, is narrowly distributed on the Qinghai-Tibet plateau. Populations of E. breviaristatus are declining due to habitat fragmentation, and thus far, characteristics of genetic differentiation and adaptive responses to climate change remain poorly understood in this species. Here, we explored the genetic structure of 18 natural populations (269 individuals) in the transition zone between Tibet and the Hengduan Mountains using 15 expressed sequence tag (EST)-SSR primer pairs and identified possible barriers to gene flow that might have caused genetic discontinuities. Additional analyses were performed to identify the environmental factors affecting genetic diversity and to test whether the patterns of genetic variation among populations were more consistent with the isolation by distance (IBD) or isolation by environment (IBE) model. Multiple measures of genetic diversity revealed that intra-population genetic variation was low, while inter-population genetic variation was high. Clustering, structure, and principal coordinate analyses identified three genetic groups: (a) Eastern Qamdo, (b) Nagqu and Western Qamdo, and (c) Lhasa and Nyingchi. A clear physical barrier to gene flow was formed by the Yarlung Zangbo Grand Canyon and the Tanggula Mountains. We found that both IBD and IBE contributed to the observed patterns of genetic variation, and the IBE model played a leading role. In addition, precipitation-related variables, soil phosphorus content and soil K:P ratio significantly affected population genetic variation. Overall, our results emphasized the genetic fragility of E. breviaristatus populations and showed that this species requires attention, as future climate changes and human activities may further threaten its survival. In addition, the genetic differences among E. breviaristatus populations should be considered when formulating conservation measures for E. breviaristatus populations in the study area.

Differential expression of iron transporters in Amaranthus cruentus roots when are subjected to salt stress: The influence of root endophytes

Salt-stress is one the main abiotic factors that negatively affect plant growth leading to crop losses throughout the world. Amaranth (Amaranthus L.) is a plant with outstanding agronomic properties and can grow under several environmental stresses including salinity. But, despite its agronomic qualities, molecular changes in plants subjected to salt stress are not well studied. Plant roots are the primary sensors responsible for sensing the rhizosphere conditions to adjust the adequate nutrient uptake for plant growth, and they also house endophytic microbes that play important roles in plant growth promotion. In this work, suppression subtractive hybridization libraries from amaranth roots growing under control conditions and in plants exposed to 150 mM NaCl were constructed. Identified differential expressed sequences tags (EST) were related with Fe, Mo, and amino acids transport, interestingly those EST showed high homology with bacterial sequences. Bacterial endophytes were isolated and identified by 16S ARNr gene sequencing. Under control conditions culturable diazotrophic endophytes were mainly composed by Pseudomonas and Variovorax, while under salt stress were Pseudomonas, Kosakonia, and Enterobacter. Most of the isolated bacteria were able to produce siderophores, solubilize phosphates, and showed the ability to grow under high NaCl conditions. These results open new venues on the relevance of amaranth endophytes on salt-stress tolerance.

Computational Approach for Mining Simple Sequence Repeats in Expressed Sequence Tags

Expressed sequence tags, the short sequences of cDNA are mined for identifying and characterizing simple sequence repeats for studying genetic variations. Web-based tools due to lack of server maintenance, become unusable; also few available stand-alone tools lack processing adequateness. Therefore with the intent to process multiple expressed sequence tag files without size limitations, proper validations, and the ability to retrieve more genome-related features; a simple to use, speed efficient portable standalone tool has been developed. The algorithm is implemented in Java using microsatellite search algorithm, with dictionary-based approach MISA – Perl script, called via command line for data mining. Another parallel module retrieves additional information from GenBank files. In the pipeline primer 3 was invoked for designing batch primers. This algorithm with an extended interface in Java Net Beans provides naïve users with a simple interactive tool for mining microsatellites, statistical analysis, and primer designing on one platform in the form of a stand-alone application. The number of repeats/ interruptions parameters can be reset through the graphical interface. This tool has interactive modules with proper validations; batch processing and cost-effective analysis of tandem repeats as compared to peers, the source code can be upgraded in the future.

IN SILICO EST DATA ANALYSIS OF CURCUMA LONGA: A CROSS KINGDOM APPROACH

MicroRNAs are a newly discovered class of non-coding small RNAs with 22–24 nucleotides. They play multiple roles in biological processes including development, cell proliferation, apoptosis, stress responses and many other cell functions. In this research, several approaches were combined to make a computational prediction of potential miRNAs and their targets in Curcuma longa. The already available information of the plant miRNAs present in miRbase v21 was used against expressed sequence tags (ESTs). A total of 89 uniq miRNA were detected following a range of strict filtering criteria. The target prediction was carried out for this miRNA having various targets. These targets were functionally annotated and GO terms were assigned. To study the conserved nature of the miRNAs, predicted phylogeny analysis was carried out. These findings will significantly provide the broader picture for understanding the functions of Curcuma longa in Anti-cancer and Anti-Immunosuppressor activity.

MicroRNA miR1118 contributes to wheat (Triticum aestivum L.) salinity tolerance by regulating the Plasma Membrane Intrinsic Proteins1;5 (PIP1;5) gene

microRNAs (miRNAs) are important regulators of various adaptive stress responses in crops; however, many details about associations among miRNAs, their target genes and physiochemical responses of crops under salinity stress remain poorly understood. We designed this study in a systems biology context and used a collection of computational, experimental and statistical procedures to uncover some regulatory functions of miRNAs in the response of the important crop, wheat, to salinity stress. Accordingly, under salinity conditions, wheat roots' Expressed Sequence Tag (EST) libraries were computationally mined to identify the most reliable differentially expressed miRNA and its related target gene(s). Then, molecular and physiochemical evaluations were carried out in a separate salinity experiment using two contrasting wheat genotypes. Finally, the association between changes in measured characteristics and wheat salinity tolerance was determined. From the results, miR1118 was assigned as a reliable salinity-responsive miRNA in wheat roots. The expression profiles of miR1118 and its predicted target gene, Plasma Membrane Intrinsic Proteins1,5 (PIP1;5), significantly differed between wheat genotypes. Moreover, results revealed that expression profiles of miR1118 and PIP1;5 significantly correlate to Relative Water Content (RWC), root hydraulic conductance (Lp), photosynthetic activities, plasma membrane damages, osmolyte accumulation and ion homeostasis of wheat. Our results suggest a plausible regulatory node through miR1118 adjusting the wheat water status, maintaining ion homeostasis and mitigating membrane damages, mainly through the PIP1;5 gene, under salinity conditions. To our knowledge, this is the first report on the role of miR1118 and PIP1;5 in wheat salinity response.

Genetic diversity analysis of Capsicum annuum L. cultivars from Bosnia and Herzegovina using EST-SSR markers

With a significant economic value, pepper (Capsicum annuum L., Solanaceae) represents a major vegetable crop worldwide. Simple sequence repeats (SSR) markers and expressed sequence tags (EST-SSR) are powerful tools for genetic studies and the breeding of pepper. In this study, the genetic variability among local pepper species was assessed by using 8 EST/SSR markers. The pepper varieties were collected locally, based on old sorts, hybrids, and sorts found in markets, with a total of 14 pepper varieties. Mean expected heterozygosity (He) ranged from s 0.30 to 0.83 in the populations studied, whereas the mean polymorphic information content (PIC) was 0.62. The average polymorphic number of alleles per primer was 2.5 per locus. The genetic relationships among the populations revealed by Neighbor-Joining dendrogram showed a clear clustering to three sub-populations making distinct clusters. As expected, all local varieties make up one cluster, together with the hybrid Istra, concluding that this hybrid evolved from the cross-breeding of local varieties. These results indicate and confirm the regional and physiological differences between the pepper sorts.

Comparative transcriptome profiling and molecular marker development for oil palm fruit color

Oil palm harvesting is normally determined by fruit exocarp color. To detect expressed sequence tag (EST)-simple sequence repeat (SSR) markers in oil palm hybrid populations, de novo transcriptomic profiling of Nigeria black and Suratthani 1 (Deli × Calabar) plants was performed. More than 46 million high-quality clean reads with a mean length of 1117 bp were generated. Functional annotation and gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs) revealed that the genes were involved in fruit color development and pigment synthesis. Comparison of immature/mature DEGs indicated that nigrescent fruit color was driven by the anthocyanin biosynthesis pathway (ABP); however, the carotenoid biosynthesis pathway (CBP) was involved in the color development of both fruit types. The transcripts of both unique and different genes involved in the ABP and CBP in higher plants were highlighted for further study, especially 3GT, downstream genes in the ABP, and DEARF27 in the CBP. Additionally, SSR primer motifs, namely, 9949, discovered from the DEGs upregulated in the virescent type that encode vacuolar iron transporter (VIT), could separate the nigrescence and virescence traits of Nigeria hybrids. This novel primer has potential to be used as a molecular for further selection in breeding programs especially involving the specific genetic backgrounds described in this study.

Common and novel metabolic pathways related ESTs were upregulated in three date palm cultivars to ameliorate drought stress

Date palm is an important staple crop in Saudi Arabia, and about 400 different date palm cultivars grown here, only 50–60 of them are used commercially. The most popular and commercially consumed cultivars of these are Khalas, Reziz, and Sheshi, which are also widely cultivated across the country. Date palm is high water-demanding crop in oasis agriculture, with an inherent ability to tolerate drought stress. However, the mechanisms by which it tolerates drought stress, especially at the transcriptomic level, are still elusive. This study appraised the physiological and molecular response of three commercial date palm cultivars Khalas, Reziz, and Sheshi at two different field capacities (FC; 100% and 25%) levels. At 25% FC (drought stress), leaf relative water content, chlorophyll, photosynthesis, stomatal conductance, and transpiration were significantly reduced. However, leaf intercellular CO2 concentration and water use efficiency increased under drought stress. In comparison to cvs. Khalas and Reziz, date palm cv. Sheshi showed less tolerance to drought stress. A total of 1118 drought-responsive expressed sequence tags (ESTs) were sequenced, 345 from Khalas, 391 from Reziz, and 382 from Sheshi and subjected to functional characterization, gene ontology classification, KEGG pathways elucidation, and enzyme codes dissemination. Three date palm cultivars deployed a multivariate approach to ameliorate drought stress by leveraging common and indigenous molecular, cellular, biological, structural, transcriptional and reproductive mechanisms. Approximately 50% of the annotated ESTs were related to photosynthesis regulation, photosynthetic structure, signal transduction, auxin biosynthesis, osmoregulation, stomatal conductance, protein synthesis/turnover, active transport of solutes, and cell structure modulation. Along with the annotated ESTs, ca. 45% of ESTs were novel. Conclusively, the study provides novel clues and opens the myriads of genetic resources to understand the fine-tuned drought amelioration mechanisms in date palm.

Analysis of Polyadenylation Signal Usage with Full-Length Transcriptome in Spodoptera frugiperda (Lepidoptera: Noctuidae).

Simple SummaryRNA polyadenylation is an important process in mRNA maturation. The process is controlled by various cis-acting elements surrounding the cleavage site, and their binding factors. Recently high sequencing technology especially full-length transcriptome provides a large amount of sequencing data for us to explore the variations of poly(A) signals, alternative polyadenylation (APA) in Spodoptera frugiperda. We studied 50,616 polyadenylation signals using full-length transcriptome and EST data. These data show that 51.64% of the 50,616 pA sites had the conserved AAUAAA hexamers, while 10.13% of pA sites had none of the AAUAAA-like hexamers. Among these genes, more than 64.76% have more than one pA site. Our results also support that APA plays a significant role in increasing transcriptome diversity and gene expression regulation in Spodoptera frugiperda. Our dataset was the first polyadenylation signal analysis in the Lepidoptera and would provide a theoretical basis for pest control.During the messenger RNA (mRNA) maturation process, RNA polyadenylation is a key step, and is coupled to the termination of transcription. Various cis-acting elements near the cleavage site and their binding factors would affect the process of polyadenylation, and AAUAAA, a highly conserved hexamer, was the most important polyadenylation signal (PAS). PAS usage is one of the critical modification determinants targeted at mRNA post-transcription. The full-length transcriptome has recently generated a massive amount of sequencing data, revealing poly(A) variation and alternative polyadenylation (APA) in Spodoptera frugiperda. We identified 50,616 polyadenylation signals in Spodoptera frugiperda via analysis of full-length transcriptome combined with expression Sequence Tags Technology (EST). The polyadenylation signal usage in Spodoptera frugiperda is conserved, and it is similar to that of flies and other animals. AAUAAA and AUUAAA are the most highly conserved polyadenylation signals of all polyadenylation signals we identified. Additionally, we found the U/GU-rich downstream sequence element (DSE) in the cleavage site. These results demonstrate that APA in Spodoptera frugiperda plays a significant role in root growth and development. This is the first polyadenylation signal usage analysis in agricultural pests, which can deepen our understanding of Spodoptera frugiperda and provide a theoretical basis for pest control.

Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis.

Melatonin is a master regulator of diverse biological processes, including plant's abiotic stress responses and tolerance. Despite the extensive information on the role of melatonin in response to abiotic stress, how plants regulate endogenous melatonin content under stressful conditions remains largely unknown. In this study, we computationally mined Expressed Sequence Tag (EST) libraries of salinity-exposed Chinese cabbage (Brassica rapa) to identify the most reliable differentially expressed miRNA and its target gene(s). In light of these analyses, we found that miR168a potentially targets a key melatonin biosynthesis gene, namely O-METHYLTRANSFERASE 1 (OMT1). Accordingly, molecular and physiochemical evaluations were performed in a separate salinity experiment using contrasting B. rapa genotypes. Then, the association between B. rapa salinity tolerance and changes in measured molecular and physiochemical characteristics was determined. Results indicated that the expression profiles of miR168a and OMT1 significantly differed between B. rapa genotypes. Moreover, the expression profiles of miR168a and OMT1 significantly correlated with more melatonin content, robust antioxidant activities, and better ion homeostasis during salinity stress. Our results suggest that miR168a plausibly mediates melatonin biosynthesis, mainly through the OMT1 gene, under salinity conditions and thereby contributes to the salinity tolerance of B. rapa. To our knowledge, this is the first report on the role of miR168a and OMT1 in B. rapa salinity response.

Association mapping for abiotic stress tolerance using heat- and drought-related syntenic markers in okra.

Considerable production losses are caused by heat and drought stress in okra. Germplasm evaluation at genetic level is essential for the selection of promising genotypes. Lack of genomic information of okra limits the use of genetic markers. However, syntenic markers of some related family could be used for molecular characterization of major economic traits. Herein, 56 okra genotypes were evaluated for drought and heat tolerance. Sixty-one expressed sequence tags (ESTs) identified for heat and drought tolerance in cotton were searched from literature surveys and databases. The identified ESTs were BLAST searched into okra unigene database. Primers of selected okra unigenes were synthesized and amplified in all genotypes using standard polymerase chain reaction (PCR) protocol. Marker trait association (MTA) of the syntenic unigenes were identified between genotypic and phenotypic data on the basis of linkage disequilibrium Functional syntenic analysis revealed that out of these 61 cotton ESTs 55 had functional homology with okra unigenes. These 55 unigenes were used as markers for further analysis (amplification). Okra genotypes showed significance variations for all the physo-morphological parameters under heat and drought stress. Genotypes Perbhani Karanti, IQRA-III, Selection Super Green, Anmol and Line Bourd performed better under drought stress whereas genotypes Perbhani Karanti, IQRA-III, Green Gold, OK-1501 and Selection Super Green showed heat tolerance. Fifty markers showed amplification in okra. Fifty-six okra genotypes were clustered into three distinct populations. LD analysis has shown most significant linkage between markers Unigene43786 and Unigene3662. MTAs using MLM and GLM models revealed that 23 markers have significant associations (p < 0.05) with different traits under control and stressed conditions. Relative water content is associated with four markers (Unigene10673, Unigene99547, Unigene152901, and Unigene129684) under drought conditions. Whereas, Electrolyte leakage was associated with 3 markers (Unigene109922, Unigene28667 and Unigene146907) under heat stress. These identified unigenes may be helpful in the development of drought and heat tolerant genotypes in okra.

In-Silico Mining and Characterization of EST-SSRs for the Genetic Diversity Analysis of Lemon

One of the economically important plants of the family of Rutaceae, Citrus limon L. Osbeck also known as lemon exists as different varieties of which many are indigenous to our country. Therefore, to assess the diversity or the genetic variations among the lemon varieties, the development of molecular markers is necessitated. Expressed Sequence Tags (ESTs) are small region of expressed DNA sequences of a genome which are highly conserved across species and are co-dominant in nature by having Simple Sequence Repeats (SSRs) unlike RAPD and AFLP which are dominant. Hence, this study was taken up for mining and characterizing SSR markers from the publically available EST data. The ESTs downloaded from NCBI database were mined for SSRs using MISA followed by primer designing using Primer3. Functional domains and GO analysis were performed on Blast2GO and primer-BLAST was done to check the suitability of the primers flanking the SSR regions. Total 1505 sequences were retrieved from NCBI database which after initial clean up filtered 1406 sequences containing 59 contigs and 1347 singletons. Total 80 SSRs were identified with frequency of 1SSR/Kb to be 8.27 of the total sequences examined. The 76 SSR containing EST sequences were functionally annotated, which resulted in 20 annotated ESTs and 22 ESTs having IPR (PFAM) domains. Successful primer pairs were designed for these EST-SSRs and out of these, 33 sequences having &gt;200bp products were sorted of which 26 were optimised further and finally 12 primer pairs gave successful primer-BLAST results without any mismatch with two other citrus species. Thus, the findings gave an insight on the distribution and frequency of SSR in the ESTs of lemon. In the future, the usage of these functional molecular markers may further assist to explore the genetic diversity analysis of different lemon varieties.

The Etv1/Er81 transcription factor coordinates myelination-related genes to regulate Schwann cell differentiation and myelination.

BackgroundAxonal myelination is critical for the functioning of vertebrate nervous system. Myelin sheath malformation or degeneration can cause a variety of neurological diseases. Our previous study identified multiple potential myelination-related transcriptional factors (TFs), including expressed sequence tag (ETS) variant transcription factor 1 (Etv1)/Er81, via gene microarray analysis of Schwann cells (SCs) at various myelination stages. Etv1 is known to be involved in the regulation of neuronal specialization, muscle spindle differentiation, and sensorimotor connectivity. However, to our knowledge, to date, there are no relevant studies that Etv1 regulates SC myelination.MethodsTo investigate the roles of Etv1 in SC re-myelination, an in vivo mouse myelination model was used, in which the sciatic nerve is crushed. Etv1 in nerves was knocked down via in situ injection of cholesterol-modified Etv1-small interfering (si)RNA. The expression of myelin-associated glycoprotein (MAG) was evaluated by Western blotting (WB) and immunohistochemistry (IHC). Myelination was assessed by transmission electron microscopy (TEM). The effects of Etv1 on SC proliferation, migration, and differentiation were assessed in vitro using the EdU cell proliferation kit, a culture-insert scratch assay, a SC aggregate sphere migration assay on the axons of dorsal root ganglions (DRGs), and a SC differentiation model. Chromatin immunoprecipitation (ChIP) united with quantitative real-time PCR (qPCR), known as ChIP-qPCR, and luciferase activity reporter assays were performed to explore the possible mechanisms by which Etv1 controls SC differentiation and myelination.ResultsThe results demonstrated that Etv1 promoted myelination by facilitating SC proliferation, migration, and differentiation. Etv1 expression in SCs was upregulated during re-myelination, and knocking down Etv1 expression dramatically abrogated SC re-myelination in the crushed sciatic nerves. Moreover, silencing of Etv1 by siRNA in SCs in vitro inhibited its migration, proliferation, and differentiation. The results of ChIP-qPCR and luciferase reporter assay showed that Etv1 may regulate SC differentiation and myelination by binding to the promoters of myelination-related genes, such as MAG and Runx2, to initiate their transcription.ConclusionsTaken together, these findings demonstrated a previously unknown role of Etv1 in SC differentiation and myelination, providing a candidate molecular target for clinical interventions in demyelinating diseases.

Development of EST-SSR Markers Related to Polyphyllin Biosynthesis Reveals Genetic Diversity and Population Structure in Paris polyphylla

Paris polyphylla is an important medicinal plant that can biosynthesize polyphyllins with multiple effective therapies, ranging from anti-inflammation to antitumor; however, the genetic diversity of Paris polyphylla is still unclear. To explore the genetic characteristics of cultivation populations in primary planting areas, we developed 10 expressed sequence tag simple sequence repeat (EST-SSR) markers related to polyphyllin backbone biosynthesis and utilized them in 136 individuals from 10 cultivated populations of P. polyphylla var. yunnanensis. The genetic diversity index showed that ten loci had relatively high genetic polymorphism levels. Shannon information of loci suggested that more information occurred within population and less information occurred among population. In addition, the overall populations exhibited a low degree of differentiation among populations, but maintained a high degree of genetic diversity among individuals, resulting in high gene flow and general hybridization. The genetic structure analysis revealed that 10 populations possibly derived from two ancestral groups and all individuals were found with different levels of admixture. The two groups were different from the cultivation groups at population level, suggesting the cross-pollination among cultivars. These findings will provide insights into the genetic diversity of the germplasm resources and facilitate marker-assisted breeding for this medicinal herb.

Initial Description of the Genome of Aeluropus littoralis, a Halophile Grass.

The use of wild plant species or their halophytic relatives has been considered in plant breeding programs to improve salt and drought tolerance in crop plants. Aeluropus littoralis serves as halophyte model for identification and isolation of novel stress adaptation genes. A. littoralis, a perennial monocot grass, grows in damp or arid areas, often salt-impregnated places and wasteland in cultivated areas, can survive periodically high water salinity, and tolerate high salt concentrations in the soil up to 1,100 mM sodium chloride. Therefore, it serves as valuable genetic resource to understand molecular mechanisms of stress-responses in monocots. The knowledge can potentially be used for improving tolerance to abiotic stresses in economically important crops. Several morphological, anatomical, ecological, and physiological traits of A. littoralis have been investigated so far. After watering with salt water the grass is able to excrete salt via its salt glands. Meanwhile, a number of ESTs (expressed sequence tag), genes and promoters induced by the salt and drought stresses were isolated, sequenced and annotated at a molecular level. Transfer of stress related genes to other species resulted in enhanced stress resistance. Here we describe the genome sequence and structure of A. littoralis analyzed by whole genome sequencing and histological analysis. The chromosome number was determined to be 20 (2n = 2x = 20). The genome size was calculated to be 354 Mb. This genomic information provided here, will support the functional investigation and application of novel genes improving salt stress resistance in crop plants. The utility of the sequence information is exemplified by the analysis of the DREB-transcription factor family.

Assessing heat stress tolerance in Castanea sativa

Abstract Increasing temperatures and heat waves decimate the productivity and survival of valuable trees like the European chestnut (Castanea sativa Miller). The main objectives of this study were to assess variation in heat stress tolerance within and between chestnut populations, select molecular markers associated with heat stress tolerance, and to use the selected markers to explore the adaptive potential of C. sativa to tolerate heat stress. Forty-eight trees from three Spanish wild chestnut populations of contrasting climate characteristics were used. Seven out of 20 expressed sequence tag- simple sequence repeat (EST-SSR) markers were selected. To validate the markers, progenies of the 48 trees were subjected to heat stress for 7 days and their heat tolerance was assessed through morphological and physiological changes. Leaf proline content induced by heat was highest in the least thermophilic population. Genetic structure analysis of populations revealed a cluster that included 81 per cent of the seedlings of the most thermophilic population. Signatures of positive selection for heat stress tolerance were detected using VIT099 and POR016 markers, associated with the antioxidant response of plants to heat damage. These markers should be included as candidates for their use in early selection of individuals tolerant to heat stress in C. sativa. Molecular and physiological findings converged in this study to better understand chestnut adaptation to global warming.

A deeper insight into the sialome of male and female Ochlerotatus triseriatus mosquitoes

Over the last 20 years, advancements in sequencing technologies have highlighted the unique composition of the salivary glands of blood-feeding arthropods. Further biochemical and structural data demonstrated that salivary proteins can disrupt host hemostasis, inflammation and immunity, which favors pathogen transmission. Previously, a Sanger-based sialome of adult Ochlerotatus triseriatus female salivary glands was published based on 731 expressed sequence tag (ESTs). Here, we revisited O. triseriatus salivary gland contents using an Illumina-based sequencing approach of both male and female tissues. In the current data set, we report 10,317 DNA coding sequences classified into several functional classes. The translated transcripts also served as a reference database for proteomic analysis of O. triseriatus female saliva, in which unique peptides from 101 proteins were found. Finally, comparison of male and female libraries allowed for the identification of female-enriched transcripts that are potentially related to blood acquisition and virus transmission.

Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae).

Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats derived from expressed sequence tag (EST-SSR), two chloroplast DNA (cpDNA) fragments, and ecological niche modeling (ENM) to investigate the population structure and the phylogeographic history of Lycium ruthenicum, a plant species adapted to the climate in northwestern China. We identified 20 chloroplast haplotypes of which two were dominant and widely distributed in almost all populations. The species has high haplotype diversity and low nucleotide diversity based on the cpDNA data. The EST-SSR results showed a high percentage of total genetic variation within populations. Both the cpDNA and EST-SSR results indicated no significant differentiation among populations. By combining the evidence from ENM and demographic analysis, we confirmed that both the last interglacial (LIG) and late-glacial maximum (LGM) climatic fluctuations, aridification might have substantially narrowed the distribution range of this desert species, the southern parts of the Junggar Basin, the Tarim Basin, and the eastern Pamir Plateau were the potential glacial refugia for L. ruthenicum during the late middle Pleistocene to late Pleistocene Period. During the early Holocene, the warm, and humid climate promoted its demographic expansion in northwestern China. This work may provide new insights into the mechanism of formation of plant diversity in this arid region.

In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses.

Cluster bean popularly known as “guar” is a drought-tolerant, annual legume that has recently emerged as an economically important crop, owing to its high protein and gum content. The guar gum has wide range of applications in food, pharma, and mining industries. India is the leading exporter of various cluster bean-based products all across the globe. Non-coding RNAs (miRNAs) are involved in regulating the expression of the target genes leading to variations in the associated pathways or final protein concentrations. The understanding of miRNAs and their associated targets in cluster bean is yet to be used to its full potential. In the present study, cluster bean EST (Expressed Sequence Tags) database was exploited to identify the miRNA and their predicted targets associated with metabolic and biological processes especially response to diverse biotic and abiotic stimuli using in silico approach. Computational analysis based on cluster bean ESTs led to the identification of 57 miRNAs along with their targets. To the best of our knowledge, this is the first report on identification of miRNAs and their targets using ESTs in cluster bean. The miRNA related to gum metabolism was also identified. Most abundant miRNA families predicted in our study were miR156, miR172, and miR2606. The length of most of the mature miRNAs was found to be 21nt long and the range of minimal folding energy (MFE) was 5.8–177.3 (−kcal/mol) with an average value of 25.4 (−kcal/mol). The identification of cluster bean miRNAs and their targets is predicted to hasten the miRNA discovery, resulting in better knowledge of the role of miRNAs in cluster bean development, physiology, and stress responses.

SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species.

We introduce SilkBase as an integrated database for transcriptomic and genomic resources of the domesticated silkworm Bombyx mori and related species. SilkBase is the oldest B. mori database that was originally established as the expressed sequence tag database since 1999. Here, we upgraded the database by including the datasets of the newly assembled B. mori complete genome sequence, predicted gene models, bacterial artificial chromosome (BAC)-end and fosmid-end sequences, complementary DNA (cDNA) reads from 69 libraries, RNA-seq data from 10 libraries, PIWI-interacting RNAs (piRNAs) from 13 libraries, ChIP-seq data of 9 histone modifications and HP1 proteins and transcriptome and/or genome data of four B. mori-related species, i.e. Bombyx mandarina, Trilocha varians, Ernolatia moorei and Samia ricini. Our new integrated genome browser easily provides a snapshot of tissue- and stage-specific gene expression, alternative splicing, production of piRNAs and histone modifications at the gene locus of interest. Moreover, SilkBase is useful for performing comparative studies among five closely related lepidopteran insects. Database URL: https://silkbase.ab.a.u-tokyo.ac.jp