Expression Patterns In Different Tissues Research Articles

The dual-targeted prolyl aminopeptidase PAP1 is involved in proline accumulation in response to stress and during pollen development.

Plant endosymbiotic organelles such as mitochondria and chloroplasts harbour a wide array of biochemical reactions. As a part of protein homeostasis to maintain organellar activity and stability, unwanted proteins and peptides need to be completely degraded in a stepwise mechanism termed the processing pathway, where at the last stage single amino acids are released by aminopeptidases. Here, we determined the molecular and physiological functions of a prolyl aminopeptidase homologue PAP1 (At2g14260) that is able to release N-terminal proline. Transcript analyses demonstrate that an alternative transcription start site gives rise to two alternative transcripts, generating two in-frame proteins PAP1.1 and PAP1.2. Subcellular localization studies revealed that the longer isoform PAP1.1, which contains a 51 residue N-terminal extension, is exclusively targeted to chloroplasts, while the truncated isoform PAP1.2 is located in the cytosol. Distinct expression patterns in different tissues and developmental stages were observed. Investigations into the physiological role of PAP1 using loss-of-function mutants revealed that PAP1 activity may be involved in proline homeostasis and accumulation, required for pollen development and tolerance to osmotic stress. Enzymatic activity, subcellular location, and expression patterns of PAP1 suggest a role in the chloroplastic peptide processing pathway and proline homeostasis.

Systematic Genome-Wide Study and Expression Analysis of SWEET Gene Family: Sugar Transporter Family Contributes to Biotic and Abiotic Stimuli in Watermelon.

The SWEET (Sugars Will Eventually be Exported Transporter) proteins are a novel family of sugar transporters that play key roles in sugar efflux, signal transduction, plant growth and development, plant–pathogen interactions, and stress tolerance. In this study, 22 ClaSWEET genes were identified in Citrullus lanatus (Thunb.) through homology searches and classified into four groups by phylogenetic analysis. The genes with similar structures, conserved domains, and motifs were clustered into the same groups. Further analysis of the gene promoter regions uncovered various growth, development, and biotic and abiotic stress responsive cis-regulatory elements. Tissue-specific analysis showed most of the genes were highly expressed in male flowers and the roots of cultivated varieties and wild cultivars. In addition, qRT-PCR results further imply that ClaSWEET proteins might be involved in resistance to Fusarium oxysporum infection. Moreover, a significantly higher expression level of these genes under various abiotic stresses suggests its multifaceted role in mediating plant responses to drought, salt, and low-temperature stress. The genome-wide characterization and phylogenetic analysis of ClaSWEET genes, together with the expression patterns in different tissues and stimuli, lays a solid foundation for future research into their molecular function in watermelon developmental processes and responses to biotic and abiotic stresses.

Characterization of two lipid metabolism-associated genes and their expression profiles under different feeding conditions in Acipenser dabryanus

Acipenser dabryanus is an endemic species restricted to the upper reaches of the Yangtze River and is listed as a national first-class protected animal in China. In the present study, two lipid metabolism-associated genes, namely, lipoprotein lipase (LPL) and apolipoprotein E (apoE), were identified from the full-length transcriptome analysis of A. dabryanus. The full-length genes encoded polypeptides with typical conserved motifs and functional sites shared with their homologues in other fish. Gene expression profile analysis showed that the LPL and apoE genes were constitutively expressed in A. dabryanus. The highest expression level of LPL was found in the muscle, while apoE was predominantly expressed in the liver. In the fasting and refeeding experiment, one hundred twenty fish were randomly assigned to four groups (fasting 0, 3, 7 or 14 d and then refed for 14 d). Fasting and refeeding significantly regulated the expression level of LPL with various expression patterns in different tissues, whereas starvation showed little effect on apoE expression. In addition, the expression levels of LPL and apoE were significantly affected by feeding frequency. The fish were bred for eight weeks at six different feeding frequencies groups (once a day, two times a day, three times a day, four times a day, five times a day and six times a day). Both LPL and apoE expression levels were significantly upregulated in the liver in the highest feeding frequency group. Our study suggests potential roles for LPL and apoE in lipid metabolism in A. dabryanus and will be useful for further study of nutrition regulation in fish.

Identification, systematic evolution and expression analyses of the AAAP gene family in Capsicum annuum

BackgroundThe amino acid/auxin permease (AAAP) family represents a class of proteins that transport amino acids across cell membranes. Members of this family are widely distributed in different organisms and participate in processes such as growth and development and the stress response in plants. However, a systematic comprehensive analysis of AAAP genes of the pepper (Capsicum annuum) genome has not been reported.ResultsIn this study, we performed systematic bioinformatics analyses to identify AAAP family genes in the C. annuum ‘Zunla-1’ genome to determine gene number, distribution, structure, duplications and expression patterns in different tissues and stress. A total of 53 CaAAAP genes were identified in the ‘Zunla-1’ pepper genome and could be divided into eight subgroups. Significant differences in gene structure and protein conserved domains were observed among the subgroups. In addition to CaGAT1, CaATL4, and CaVAAT1, the remaining CaAAAP genes were unevenly distributed on 11 of 12 chromosomes. In total, 33.96% (18/53) of the CaAAAP genes were a result of duplication events, including three pairs of genes due to segmental duplication and 12 tandem duplication events. Analyses of evolutionary patterns showed that segmental duplication of AAAPs in pepper occurred before tandem duplication. The expression profiling of the CaAAAP by transcriptomic data analysis showed distinct expression patterns in various tissues and response to different stress treatment, which further suggest that the function of CaAAAP genes has been differentiated.ConclusionsThis study of CaAAAP genes provides a theoretical basis for exploring the roles of AAAP family members in C. annuum.

Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

Identification and expression analysis of NRT1 family genes in Rehmannia glutinosa

NRT1 family proteins play an important roles for absorbing and transporting of nitrate in different plants. In order to identify the NRT1 family genes of Rehmannia glutinosa, this study used 11 NRT1 homologous proteins of Arabidopsis as probe sequences and aligned with the transcriptome data of R. glutinosa by using NCBI BLASTN software. Resulting there were 18 NRT1 proteins were identified in R. glutinosa. On basis of this, a series of the molecular characteristics of R. glutinosa NRT1 proteins including the conserved domains, the transmembrane structure, the subcellular location and phylogenetic features were in detail analyzed. At same time, it were systematically analyzed that the temporal and spatial expression patterns and characteristics of R. glutinosa NRT1 family genes in response to different stress factors. The results indicated that 18 R. glutinosa NRT1 family genes with the length of coding region from 1 260 bp to 1 806 bp, encoded proteins ranging from 419 to 601 amino acids, and all of they owned the domains of typical peptide transporter with 7 to 12 transmembrane domains. These R. glutinosa NRT1 family proteins mostly were found to locate on cellular plasma membrane, and belonged to the hydrophobic proteins. Furthermore, the evolutionary analysis found that the 18 R. glutinosa NRT1 protein family could be divided into two subfamilies, of which 14 NRT1 family genes might occur the positive selection, and 4 genes occur the passivation selection during the evolution process of R. glutinosa. In addition the expression analysis showed that 18 R. glutinosa NRT1 family genes have the distinct expression patterns in different tissues of R. glutinosa, and their expression levels were also obvious difference in response to various stress. These findings infield that 18 R. glutinosa NRT1 family proteins might have obviously different functional roles in nitrate transport of R. glutinosa. In conclusion, this study lays a solid theoretical foundation for clarifying the absorption and transport molecular mechanism of N element during R. glutinosa growth and development, and at same time for deeply studying the molecular function of R. glutinosa NRT1 proteins in absorption and transport of nitrate.

Genome-Wide Analysis of RAV Transcription Factors and Functional Characterization of Anthocyanin-Biosynthesis-Related RAV Genes in Pear.

Related to ABSCISIC ACID INSENSITIVE3/VIVIPAROUS1 (ABI3/VP1, RAV), transcription factors (TFs) belonging to the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) TF family play critical roles in plant growth, development, and responses to abiotic and biotic stress. In this study, 11 novel RAV TFs were identified in pear (Pyrus bretschneideri Rehd). A phylogenetic analysis revealed that the TFs clustered into three groups with 10 conserved motifs, some of which were group- or subgroup-specific, implying that they are important for the functions of the RAVs in these clades. RAVs in Pyrus and Malus were closely related, and the former showed a collinear relationship. Analysis of their expression patterns in different tissues and at various growth stages and their responses to abiotic and biotic stress suggested that PbRAV6 and PbRAV7 play important roles in drought stress and salt stress, respectively. We investigated the function of RAVs in pear peel coloration using two red pear varieties with different color patterns and applying data from transcriptome analyses. We found that PbRAV6 participates in the regulation of pericarp color. These findings provide insight into a new TF family in pear and a basis for further studies on the response to drought stress and fruit coloration in this commercially important crop.

Identification and expression analysis of E2 ubiquitin-conjugating enzymes in cucumber

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

Identification and analysis of non-specific lipid transfer protein family in tobacco

Plant non-specific lipid transfer proteins (nsLTPs) can transfer lipids in vitro , regulate plant growth and development, and respond to environmental abiotic and biotic stresses. In this study, 74 nsLTPs genes were identified from the genome of Nicotiana tabacum variety K326, and we analyzed multiple characteristics of these genes, including phylogeny, gene structures, conserved motifs, protein domains, chromosome locations, cis -elements in the promoter sequences, 3D structure, and the expression patterns under different hormones and abiotic stresses. The results revealed that nsLTPs in tobacco could be divided into eight types, including type I, II, III, IV, V, VII, VIII, and XIII, according to the interval and sequence similarity between the eight cysteines. The same types of NtLTPs had similar intron-exon patterns and conserved motifs, motif 2 and motif 3 were the characteristic motifs of NtLTPs family. In the process of evolution, fragment duplication dominated the expansion of the NtLTPs family. RNA-seq analysis after drought treatment revealed that the functional differentiation patterns of repeat gene pairs were diverse during evolution period. Promoter analysis showed that they contained a variety of cis-acting elements in response to light response, hormones, and abiotic stress. Furthermore, qRT-PCR demonstrated that NtLTPs family genes had different expression patterns in different tissues and organs of tobacco plants, which could respond to abiotic stresses such as drought, salt, and hormone treatments (IAA, GA, and SA etc.). These results provide a theoretical reference for the in-depth analysis of the functions of NtLTPs family genes and molecular breeding.

Genome-wide analysis of gibberellin-dioxygenases gene family and their responses to GA applications in maize.

Gibberellin-dioxygenases genes plays important roles in the regulating plant development. However, Gibberellin-dioxygenases genes are rarely reported in maize, especially response to gibberellin (GA). In present study, 27 Gibberellin-dioxygenases genes were identified in the maize and they were classified into seven subfamilies (I-VII) based on phylogenetic analysis. This result was also further confirmed by their gene structure and conserved motif characteristics. And gibberellin-dioxygenases genes only occurred segmental duplication that occurs most frequently in plants. Furthermore, the gibberellin-dioxygenases genes showed different tissue expression pattern in different tissues and most of the gibberellin-dioxygenases genes showed tissue specific expression. Moreover, almost all the gibberellin-dioxygenases genes were significantly elevated in response to GA except for ZmGA2ox2 and ZmGA20ox10 of 15 gibberellin-dioxygenases genes normally expressed in leaves while 10 and 11 gibberellin-dioxygenases genes showed up and down regulated under GA treatment than that under normal condition in leaf sheath. In addition, we found that ZmGA2ox1, ZmGA2ox4, ZmGA20ox7, ZmGA3ox1 and ZmGA3ox3 might be potential genes for regulating balance of GAs which play essential roles in plant development. These findings will increase our understanding of Gibberellin-dioxygenases gene family in response to GA and will provide a solid base for further functional characterization of Gibberellin-dioxygenases genes in maize.

Genome-wide identification and analysis of class III peroxidases in Betula pendula

BackgroundClass III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula.ResultsWe identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times.ConclusionsThe research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea

Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.

Roles of the 14-3-3 gene family in cotton flowering

BackgroundIn plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown.ResultsIn this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering.ConclusionsHere, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides

The 2′,3′-cycling ribonuclease (RNase) genes are catalysts of RNA cleavage and include the RNase T2 gene family. RNase T2 genes perform important roles in plants and have been conserved in the genome of eukaryotic organisms. In this study we identified 21 EURNS genes in Eucommia ulmoides Oliver (E. ulmoides) and analyzed their structure, chromosomal location, phylogenetic tree, gene duplication, stress-related cis-elements, and expression patterns in different tissues. The length of 21 predicted EURNS proteins ranged from 143 to 374 amino acids (aa), their molecular weight (MW) ranged from 16.21 to 42.38 kDa, and their isoelectric point (PI) value ranged from 5.08 to 9.09. Two classifications (class I and class III) were obtained from the conserved domains analysis and phylogenetic tree. EURNS proteins contained a total of 15 motifs. Motif 1, motif 2, motif 3, and motif 7 were distributed in multiple sequences and were similar to the conserved domain of RNase T2. EURNS genes with similar structure and the predicted EURNS proteins with conserved motif compositions are in the same group in the phylogenetic tree. The results of RT-PCR and transcription data showed that EURNS genes have tissue-specific expression and exhibited obvious trends in different developmental stages. Gene duplication analysis results indicated that segment duplication may be the dominant duplication mode in this gene family. This study provides a theoretical basis for research on the RNase T2 gene family and lays a foundation for the further study of EURNS genes.

Identification and expression profiles of chitin deacetylase family genes in the Chinese mitten crab, Eriocheir sinensis

Chitin deacetylases (CDAs) are essential enzymes during moulting and play vital roles in the formation and modification of chitin. Five chitin deacetylase genes were first identified and characterized in the Chinese mitten crab, Eriocheir sinensis. The spatiotemporal expression profiles of the identified CDAs (EsCDAs) have been investigated to reveal their critical functions in moulting of the Chinese mitten crab. Phylogenetic and structural analysis showed that EsCDAs were divided into four of five groups based on sequence similarity and the multiple groups with diverse domain architectures suggested that there were distinctive biological functions among multi-gene family of EsCDAs. Each group contained one or more EsCDAs, except group V, and showed different expression patterns in different tissues and developmental stages. EsCDAs were widely distributed in exoskeleton, digestive organs as well as genital organs, and expressed from eggs to juvenile, especially highly in juvenile stage. During the moulting cycle, the expressions of EsCDAs were up-regulated periodically in the post-moult stage and enhanced by eyestalk resection, which indicate that EsCDAs play an important role in the formation and modification of chitin. Our present study provides fundamental information about crustaceans in terms of chitin deacetylases involved in the chitin metabolic pathway during moulting.

Expression Analysis of miR393 and Target Gene <i>Ve</i> of <i>Solanum torvum</i> Swartz Infected by <i>Verticillium dahliae</i> Kleb

In this study, Solanum torvum Swartz. was used as material and B-Actin gene and U6 were used as internal references. First, the expression characteristics analysis of miR393 and target gene Ve were performed on the root, stem, leaf, flower and fruit of Solanum torvum Swartz. during flowering and fruiting stage. The strong Verticillium dahliae Kleb. were inoculated into Solanum torvum Swartz. during 5-6 leaf stage, and the control group was treated with ultrapure water. The Solanum torvum Swartz. roots were taken at 0 h, 3 h, 6 h, 12 h, 24 h, 36 h, 48 h and 72 h for expression analysis of infection by Verticillium dahliae Kleb.. The results showed that under normal growth conditions, miR393 and target gene Ve had specific expression patterns in different tissues of Solanum torvum Swartz., and the differential expression was significant. Both miR393 and target gene Ve had the highest expression levels in roots, followed by stems, and had the lowest levels in fruits. After infection by Verticillium dahliae Kleb., both miR393 and target gene Ve had certain expression in different infection periods. The expression of target gene Ve showed an upward tendency with the extension of infection time, and the highest expression level appeared at 48 h, followed by 72 h. While the expression of miR393 showed a downward tendency with the extension of infection time, and the highest expression level appeared at 6 h. The expression of miR393 and target gene Ve showed opposite tendencies in different infection periods. These results provided a foundation for further research on the interaction mechanism between miR393 and target gene Ve and the molecular mechanism of resistance to Verticillium wilt.

Developmental and Tissue Patterns of the Basal Expression of Chicken Avian β-Defensins.

Defensins are a class of antimicrobial peptides in vertebrates that function as the first line of innate immunity with potent antimicrobial and immunomodulatory activities. Fourteen defensins, namely, avian β-defensin 1 to 14 (AvBD1-14), have been identified in chickens. Before characterizing the role of AvBDs in innate immunity during the early development of chickens, we collected tissue segments from the liver, spleen, and gastrointestinal (GI) tract including the esophagus, crop, proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and colon from broilers at days 1, 3, 7, 14, and 28. After RNA isolation and reverse transcription, we determined the expression levels of the 14 AvBD genes in these tissues during the first 28 days after hatching by real-time PCR. The results suggested the AvBDs were widely expressed in the chicken liver, spleen, and gastrointestinal (GI) tract. Interestingly, we did not detect AvBD11 expressed in the GI tract, even in the liver and spleen. Additionally, AvBDs were differentially expressed in the chicken GI tract. AvBD5 and AvBD14 were expressed most abundantly in the proximal GI tract, especially the esophagus and crop. Moreover, AvBD5, AvBD7, AvBD9, and AvBD14 were expressed in an inverted-V pattern with the peak being the observed expression at days 3, 7, or 14 in the chicken spleen, esophagus, duodenum, and cecum. Other AvBDs presented biphasic or inverted-V expression patterns in different tissues. The expression levels of all detected AvBDs were strengthened after hatching rather than decreasing steadily. Therefore, AvBDs were found to be expressed widely in the chicken liver, spleen, and GI tract and their expression levels were primarily up regulated during the early development of chicken, implying the potential essential roles of AvBDs in early innate defense and infection resistance of chickens.

Genome-wide identification and characterization of the bZIP gene family in potato (Solanum tuberosum)

The basic leucine zipper (bZIP) transcription factors, as members of the family of transcription regulators, play a role in multiple developmental and biological processes such as organ and tissue development and responses to diverse stresses. However, knowledge of the bZIP genes in potato, which is one of the most valuable crops, is still limited. In this study, 56 bZIP genes in total were identified from the Solanum tuberosum genome and classified into 10 main groups. The classification of potato bZIP genes into ten groups was endorsed by the sets of conserved motifs present and gene structure of bZIP genes. The locations of the bZIP genes on the chromosomes were unevenly scattered over the potato genome, as in other studied plants. Investigation of promoter sequences revealed that Solanum tuberosum bZIP genes possessed variable sets of cis-regulatory elements, such as MYB, MYC, and ABRE elements, which may play roles in response to various stresses. Expression analyses of the potato bZIP genes based on transcriptome data showed that these genes have broad expression patterns in different tissues. Three distinct gene expression patterns observed for potato bZIP genes were similar to other plant species. Overall, this first and broad investigation of bZIP genes in the potato will provide useful insights into stress-responsive potato genes and pave the way for high-stress tolerance potato breeding.

Correction: Identification of the Porcine G Protein-Coupled Receptor 41 and 43 Genes and Their Expression Pattern in Different Tissues and Development Stages

[This corrects the article DOI: 10.1371/journal.pone.0097342.].

Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea.

RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated their evolution relationships. The RWP-RK proteins were classified into two groups, RWP-RK domain proteins and NODULE-INCEPTION-like proteins. Chromosomal distributions, gene structures, and conserved motifs of RWP-RK genes were compared among wild and cultivated peanuts. In addition, we identified 12 orthologous gene pairs from the two wild peanut species, 13 from A. duranensis and A. hypogaea, and 13 from A. ipaensis and A. hypogaea. One, one, and seventeen duplicated gene pairs were identified within the A. duranensis, A. ipaensis, and A. hypogaea genomes, respectively. Moreover, different numbers of cis-acting elements in the RWP-RK promoters were found in wild and cultivated species (87 in A. duranensis, 89 in A. ipaensis, and 92 in A. hypogaea), and as a result, many RWP-RK genes showed distinct expression patterns in different tissues. Our study will provide useful information for further functional and evolutionary analysis of the RWP-RK genes.