Differential Expression In Different Tissues Research Articles

Genome-Wide Identification of BrCAX Genes and Functional Analysis of BrCAX1 Involved in Ca2+ Transport and Ca2+ Deficiency-Induced Tip-Burn in Chinese Cabbage (Brassica rapa L. ssp. pekinensis).

Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ exchanger antiporters (CAXs) in mediating transmembrane transport of Ca2+ have been extensively characterized in multiple plant species, the potential roles of BrCAX genes remain unclear in Chinese cabbage. In this study, eight genes of the BrCAX family were genome-widely identified in Chinese cabbage. These BrCAX proteins contained conserved Na_Ca_ex domain and belonged to five members of the CAX family. Molecular evolutionary analysis and sequence alignment revealed the evolutionary conservation of BrCAX family genes. Expression profiling demonstrated that eight BrCAX genes exhibited differential expression in different tissues and under heat stress. Furthermore, Ca2+ deficiency treatment induced the typical symptoms of tip-burn in Chinese cabbage seedlings and a significant decrease in total Ca2+ content in both roots and leaves. The expression changes in BrCAX genes were related to the response to Ca2+ deficiency-induced tip-burn of Chinese cabbage. Specially, BrCAX1-1 and BrCAX1-2 genes were highly expressed gene members of the BrCAX family in the leaves and were significantly differentially expressed under Ca2+ deficiency stress. Moreover, overexpression of BrCAX1-1 and BrCAX1-2 genes in yeast and Chinese cabbage cotyledons exhibited a higher Ca2+ tolerance, indicating the Ca2+ transport capacity of BrCAX1-1 and BrCAX1-2. In addition, suppression expression of BrCAX1-1 and BrCAX1-2 genes reduced cytosolic Ca2+ levels in the root tips of Chinese cabbage. These results provide references for functional studies of BrCAX genes and to investigate the regulatory mechanisms underlying Ca2+ deficiency disorder in Brassiceae vegetables.

Genome-Wide Survey and Expression Analysis of B-Box Family Genes in Cucumber Reveal Their Potential Roles in Response to Diverse Abiotic and Biotic Stresses

As a class of zinc finger transcription factors, B-box (BBX) proteins play diverse roles in numerous biological processes, and they have been identified in a series of plant species in recent years. However, the roles of BBX genes in regulating cucumber growth regulation and stress response have not yet been established. Here, a total of 22 BBX family genes were identified via an analysis of the latest cucumber genome data, which were classified into five groups (I–V) on the basis of their phylogenetic features and number of B-box domains and CCT domains. The CsBBX genes were unevenly distributed across the seven cucumber chromosomes, and segmental duplication was found to play a significant role in the expansion of the cucumber BBX gene family. Gene structure and motif composition analysis suggested that the evolutionarily close CsBBXs have similar conserved motif composition and gene structure. Most CsBBX genes possessed 1–3 introns, and intron gain rather than intron loss could contribute to the different structures of CsBBX genes across different groups during their evolution. Promoter analysis revealed the presence of 13 kinds of hormone-related and nine kinds of stress-related cis-regulatory elements in the promoter regions of these CsBBX genes. Expression analysis via RNA-seq and qRT-PCR suggested that the CsBBX genes exhibit differential expression in different tissues and in response to various abiotic and biotic stresses. This work constitutes a starting point for further revealing the function of the CsBBX genes and sheds light on the potential molecular mechanism of stress resistance in cucumber.

Genome wide identification and expression pattern analysis of the GRAS family in quinoa.

GRAS, a key transcription factor in plant growth and development, has not yet been reported in quinoa. Therefore, this study used the latest quinoa genomic data to identify and analyse GRAS genes in quinoa: 52 GRAS genes were identified in quinoa, these being unevenly distributed on 19 chromosomes. Fragment duplication and tandem duplication events were the main reasons for the expansion of the GRAS gene family in quinoa. Protein sequence analysis showed that there were some differences in amino acid numbers and isoelectric points amongst different subfamilies, and the main secondary structures were α-helix and random coil. The CqGRAS gene was divided into 14 subfamilies based on results from phylogenetic analysis. The genes located in the same subfamily had similar gene structures, conserved motifs, and three-level models. Promoter region analysis showed that the GRAS family genes contained multiple homeostasis elements that responded to hormones and adversity. GO enrichment indicated that CqGRAS genes were involved in biological processes, cell components, and molecular functions. By analysing the expression of CqGRAS genes in different tissues and different treatments, it was found that GRAS genes had obvious differential expression in different tissues and stress, which indicates that GRAS genes had tissue or organ expression specificity and thus might play an important role in response to stress. These results laid a foundation for further functional research on the GRAS gene family in quinoa.

Identification of a Plasma Microrna Signature as Biomarker of Subaneurysmal Aortic Dilation in Patients with High Cardiovascular Risk.

Patients with subaneurysmal aortic dilation (SAD; 25–29 mm diameter) are likely to progress to true abdominal aortic aneurysm (AAA). Despite these patients having a higher risk of all-cause mortality than subjects with aortic size <24 mm, early diagnostic biomarkers are lacking. MicroRNAs (miRs) are well-recognized potential biomarkers due to their differential expression in different tissues and their stability in blood. We have investigated whether a plasma miRs profile could identify the presence of SAD in high cardiovascular risk patients. Using qRT-PCR arrays in plasma samples, we determined miRs differentially expressed between SAD patients and patients with normal aortic diameter. We then selected 12 miRs to be investigated as biomarkers by construction of ROC curves. A total of 82 significantly differentially expressed miRs were found by qPCR array, and 12 were validated by qRT-PCR. ROC curve analyses showed that seven selected miRs (miR-28-3p, miR-29a-3p, miR-93-3p, miR-150-5p, miR-338-3p, miR-339-3p, and miR-378a-3p) could be valuable biomarkers for distinguishing SAD patients. MiR-339-3p showed the best sensitivity and specificity, even after combination with other miRs. Decreased miR-339-3p expression was associated with increased aortic abdominal diameter. MiR-339-3p, alone or in combination with other miRs, could be used for SAD screening in high cardiovascular risk patients, helping to the early diagnosis of asymptomatic AAA.

Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae

BackgroundEuphorbiaceae is one of the largest families of flowering plants. Due to its exceptional growth form diversity and near-cosmopolitan distribution, it has attracted much interest since ancient times. SBP-box (SBP) genes encode plant-specific transcription factors that play critical roles in numerous biological processes, especially flower development. We performed genome-wide identification and characterization of SBP genes from four economically important Euphorbiaceae species.ResultsIn total, 77 SBP genes were identified in four Euphorbiaceae genomes. The SBP proteins were divided into three length ranges and 10 groups. Group-6 was absent in Arabidopsis thaliana but conserved in Euphorbiaceae. Segmental duplication played the most important role in the expansion processes of Euphorbiaceae SBP genes, and all the duplicated genes were subjected to purify selection. In addition, about two-thirds of the Euphorbiaceae SBP genes are potential targets of miR156, and some miR-regulated SBP genes exhibited high intensity expression and differential expression in different tissues. The expression profiles related to different stress treatments demonstrated broad involvement of Euphorbiaceae SBP genes in response to various abiotic factors and hormonal treatments.ConclusionsIn this study, 77 SBP genes were identified in four Euphorbiaceae species, and their phylogenetic relationships, protein physicochemical characteristics, duplication, tissue and stress response expression, and potential roles in Euphorbiaceae development were studied. This study lays a foundation for further studies of Euphorbiaceae SBP genes, providing valuable information for future functional exploration of Euphorbiaceae SBP genes.

Genome-wide identification and analysis of the aldehyde dehydrogenase gene superfamily in Chinese cabbage (Brassica rapa subsp. pekinensis)

Aldehyde dehydrogenases (ALDHs) encode a class of enzymes that dehydrooxidize aldehydes into corresponding carboxylic acids, which are involved in the growth and development of plants and in the response to various biological and abiotic stresses. In this study, we identified 27 ALDH genes in the Chinese cabbage genome and grouped them into 10 different families. Chromosomal mapping revealed that, except for one gene distributed on Scaffold, the remaining 26 genes were unevenly distributed on 10 chromosomes of Chinese cabbage. Based on a comparison of the homologous relationship between BrALDHs and ALDH genes in Arabidopsis thaliana, duplicated patterns of the ALDH gene family in Chinese cabbage were analyzed. The exon–intron structures, conserved protein motifs, and phylogenetic relationship with ALDH in six other species were also predicted and analyzed. Finally, we used available RNA-Seq data and real-time quantitative PCR to analyze the expression of ALDH genes in different tissues of Chinese cabbage including the roots, stems, leaves, flowers, and siliques. The results showed the tissue specificity and differential expression in different tissues of BrALDHs. The analysis of ALDH gene transcriptome data of Chinese cabbage under different stress conditions (cold, heat, drought, and salinity) showed that the response levels of different genes varied under different stresses, suggesting the function of some genes in these processes. Details of the ALDH gene family in Chinese cabbage has enriched studies on the ALDH gene family in plants and animals and is crucial for understanding ALDH function during plant growth and development.

Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.)

Metacaspases are distant relatives of animal caspases found in plants, protozoa and fungi. Some recent studies have demonstrated that metacaspases are involved in regulating the developmental and environmentally induced programmed cell death in plants. In this study, we identified metacaspase gene family in potato (Solanum tuberosum L.) and analyzed their expression pattern in various developmental tissues and stress responses of plants. There were eight metacaspase genes identified in the Peptidase (Cysteine protease) C14 family and based upon sequence alignment and phylogenetic analysis, a systematic nomenclature of potato metacaspases (SotubMCs) has been proposed. Three of the eight candidate genes showing homology with Arabidopsis thaliana type I metacaspase, AtMC1 were given name SotubMC1, SotubMC2 and SotubMC3 as per the degree of relatedness. Similarly, the next three being homologous to A. thaliana type I metacaspase, AtMC3 were named SotubMC4, SotubMC5, and SotubMC6. The remaining two were named SotubMC7 and SotubMC8, showing significant similarity with type II metacaspases of A. thaliana, AtMC4 and AtMC9, respectively. Evolutionary divergence analysis of SotubMCs from its orthologs in seven other members of Solanaceae family as well as with A. thaliana, Vitis vinifera and Oryza sativa was also carried out. The dN/dS ratios of the orthologous pairs suggested the SotubMCs were under purifying (negative) selection in course of plant evolution. Splicing patterns of potato metacaspases were also analyzed. Amongst all SotubMCs, SotubMC2, SotubMC4, SotubMC6 and SotubMC7 genes appeared to produce multiple alternative spliced variants of different lengths. Furthermore using protein modeling tools, we have predicted the protein structure of identified metacaspases. The cis-regulatory elements analysis was also performed exhibiting the presence of development, stress and hormones related cis-elements in the promoter regions of the SotubMCs. This indicates that potato metacaspases might be playing important roles in the development, stress and hormone responsive pathways. Moreover, relative expression analysis of identified genes was carried out using qRT-PCR in various developmental tissues that also include stolons and tubers. The eight metacaspases showed differential expression in different tissues. Some of the tissues such as leaf undergoing senescence among different leaf developmental stages (immature, mature and senescent) displayed higher relative expression of some of the metacaspases, implying their involvement in leaf senescence. The expression pattern of SotubMCs under various abiotic, biotic and hormonal stresses was also analysed. The results showed that many members of the potato metacaspase gene family displayed differential expression patterns under various stress conditions. Taken together, the study could provide crucial resources for further investigations to understand the functional roles of the identified metacaspases in potato.

Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development

Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as well as their F1 hybrid. The obtained large-scale datasets provided opportunities to monitor the developmental dynamics of differential expression, additivity for gene expression, and regulatory variation. The transcriptome can be divided into ∼30 000 genes that are expressed in at least one tissue of one inbred and an additional ∼10 000 ″silent" genes that are not expressed in any tissue of any genotype, 90% of which are non-syntenic relative to other grasses. Many (∼74%) of the expressed genes exhibit differential expression in at least one tissue. However, the majority of genes with differential expression do not exhibit consistent differential expression in different tissues. These genes often exhibit tissue-specific differential expression with equivalent expression in other tissues, and in many cases they switch the directionality of differential expression in different tissues. This suggests widespread variation for tissue-specific regulation of gene expression between the two maize inbreds B73 and Mo17. Nearly 5000 genes are expressed in only one parent in at least one tissue (single parent expression) and 97% of these genes are expressed at mid-parent levels or higher in the hybrid, providing extensive opportunities for hybrid complementation in heterosis. In general, additive expression patterns are much more common than non-additive patterns, and this trend is more pronounced for genes with strong differential expression or single parent expression. There is relatively little evidence for non-additive expression patterns that are maintained in multiple tissues. The analysis of allele-specific expression allowed classification of cis- and trans-regulatory variation. Genes with cis-regulatory variation often exhibit additive expression and tend to have more consistent regulatory variation throughout development. In contrast, genes with trans-regulatory variation are enriched for non-additive patterns and often show tissue-specific differential expression. Taken together, this study provides a deeper understanding of regulatory variation and the degree of additive gene expression throughout maize development. The dynamic nature of differential expression, additivity, and regulatory variation imply abundant variability for tissue-specific regulatory mechanisms and suggest that connections between transcriptome and phenome will require expression data from multiple tissues.

Genome-wide analysis of oligopeptide transporters and detailed characterization of yellow stripe transporter genes in hexaploid wheat.

Oligopeptide transporters (OPT) are integral cell membrane proteins that play a critical role in the transport of small peptides, secondary amino acids, glutathione conjugates, and mineral uptake. In the present study, 67 putative wheat yellow stripe-like transporter (YSL) proteins belonging to the subfamily of OPT transporters were identified. Phylogeny analysis resulted in the distribution of wheat YSLs into four discrete clades. The highest number of YSLs was present on the A genome and the chromosome 2 of hexaploid wheat. The identified wheat YSL genes showed differential expression in different tissues and during grain development suggesting the importance of this subfamily. Gene expression pattern of TaYSLs during iron starvation experiments suggested an early high transcript accumulation of TaYS1A, TaYS1B, TaYSL3, TaYSL5, and TaYSL6 in roots. In contrast, delayed expression was observed in shoots for TaYS1A, TaYS1B, TaYSL5, TaYSL12, and TaYSL19 as compared to control. Further, their expression under biotic and abiotic response emphasized their alternative functions during the plant growth and development. In conclusion, this work is the first comprehensive study of wheat YSL transporters and would be an important resource for prioritizing genes towards wheat biofortification.

Cloning and Expression Characterization of Four Annexin Genes During Germination and Abiotic Stress in Brassica rapa subsp. rapa ‘Tsuda’

Annexins are a multigene family in most plant species and are suggested to play a role in a wide variety of essential cellular processes. They are well characterized in Arabidopsis; however, no such characterization of turnip annexin gene family has been reported thus far. So, four cDNAs of turnip, Brassica rapa (BrANNEXIN1, BrANNEXIN2, BrANNEXIN3, BrANNEXIN4), encoding annexin proteins using a RT-PCR/RACE-PCR-based strategy were isolated and characterized. The predicted molecular masses of these annexins are ∼36.0 kDa. At the amino acid level, they share high sequence similarity with each other and with annexins from higher plants. Using quantitative real-time reverse transcription PCR to assess their differential expression in different tissues or after different stimuli, we found that these BrANNEXIN genes are differentially expressed in various tissues. The expression patterns of four annexin genes during germination in normal and dark-grown seedlings were determined. Our results indicate that transcripts for all four annexins are present in dark germinating seedlings, and BrANNEXIN1, BrANNEXIN3, and BrANNEXIN4 are present in normal germinating seedlings. Only BrANNEXIN4 was involved in UV-A-induced anthocyanin synthesis in the root epidermis of Tsuda turnip, which accumulates high levels of anthocyanin. All four annexins differently expressed in the UV-A light-induced anthocyanin synthesis in the hypocotyl. When 4.0-day-old etiolated seedlings were treated with red or far-red light, transcript levels of the four annexins in hypocotyls and cotyledons significantly increased. Finally, we monitored annexin expression in response to various abiotic stresses. Expression of these genes also changed in response to abiotic stresses such as high and low temperatures, dehydration, and osmotic and salt stresses. These results indicate that BrANNEXIN genes may play important roles in adaptation of plants to various environmental stresses.

Cloning and differential expression of Na,K-ATPase in Penaeus vannamei

To better understand the adaptive strategies of osmotic and ionic regulation in Penaeus vannamei, a full-length cDNA sequence encoding the Na,K-ATPase alpha subunit was isolated and characterized by rapid amplification of the cDNA ends (RACE). The nucleotide sequence was 3953 bp in length and included a 300 bp 5′ untranslated region (UTR), 536 bp 3′ UTR with an AATAA canonical polyadenylation signal sequence and poly (A) tail, and a 3117 bp open reading frame (ORF) encoding a 1038 amino acid protein. The calculated molecular weight of the protein was 115.4 kDa with an estimated pI of 5.29. This sequence was submitted to the National Center for Biotechnology Information (NCBI) GenBank under accession number KF765670. A phenetic analysis showed that the Na,K-ATPase α-subunit of P. vannamei shared a high degree of identity with other species. The relevant mRNA was detected in all of the tissues examined by fluorescent quantitative real-time polymerase chain reaction. The expression level was higher in the gills and hepatopancreas, and lower in the guts, muscles and epithelia. Increased expression of Na,K-ATPase mRNA levels was observed in all of the tissues examined in response to salinity exposure, and there was a significant difference in the tissues of the gills and hepatopancreas (P < 0.05); however, no statistical difference was observed in the epithelia, guts and muscles compared with the controls (P > 0.05). The findings demonstrated that the Na,K-ATPase α-subunit is highly conserved in crustaceans, and differential expression in different tissues of P. vannamei was observed, indicating that the gene might have multiple functions in the shrimp.

Identification and characterization of 27 conserved microRNAs in citrus

MicroRNAs (miRNAs) are a class of non-protein-coding small RNAs. Considering the conservation of many miRNA genes in different plant genomes, the identification of miRNAs from non-model organisms is both practicable and instrumental in addressing miRNA-guided gene regulation. Citrus is an important staple fruit tree, and publicly available expressed sequence tag (EST) database for citrus are increasing. However, until now, little has been known about miRNA in citrus. In this study, 27 known miRNAs from Arabidopsis were searched against citrus EST databases for miRNA precursors, of which 13 searched precursor sequences could form fold-back structures similar with those of Arabidopsis. The ubiquitous expression of those 13 citrus microRNAs and other 13 potential citrus miRNAs could be detected in citrus leaf, young shoot, flower, fruit and root by northern blotting, and some of them showed differential expression in different tissues. Based on the fact that miRNAs exhibit perfect or nearly perfect complementarity with their target sequences, a total of 41 potential targets were identified for 15 citrus miRNAs. The majority of the targets are transcription factors that play important roles in citrus development, including leaf, shoot, and root development. Additionally, some other target genes appear to play roles in diverse physiological processes. Four target genes have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in Poncirus trifoliate. Overall, this study in the identification and characterization of miRNAs in citrus can initiate further study on citrus miRNA regulation mechanisms, and it can help us to know more about the important roles of miRNAs in citrus.

Molecular analyses of the rice tubby-like protein gene family and their response to bacterial infection

Tubby-like protein family has been identified in various multicellular organisms, indicating its fundamental functions in the organisms. However, the roles of plant tubby-like proteins are unknown. In this study, we have defined the tubby-like protein gene (OsTLP) family with 14 members in rice. Most of the OsTLPs harbor a tubby domain in their carboxyl terminus and an F-box domain in the amino terminus. The expression of all the OsTLPs was induced on infection of Xanthomonas oryzae pv. oryzae, which causes bacterial blight, one of the most devastating diseases of rice worldwide. The maximal expression levels were observed at 2-8 h after infection for all the genes. Eight of the 14 OsTLPs were also responsive to wounding. All the OsTLPs showed differential expression in different tissues at different developmental stages. However, four pairs of the 14 OsTLPs, with each pair having high sequence similarity and distributing on the similar position of different chromosomes, showed similar expression pattern in different tissues, indicating their direct relationship in evolution. These results suggest that the OsTLP family is involved in host-pathogen interaction and it may be also associated with other physiological and developmental activities.

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are generally assumed to be nonconserved, although the level of structural conservation between these has never been investigated. Owing to the limitations in computational methods, comparative genomics has been lacking the ability to compare such nonconserved sequence regions for conserved structural RNA elements. We have investigated the presence of structural RNA elements by conducting a local structural alignment, using FOLDALIGN, on a subset of these 100,000 corresponding regions and estimate that 1800 contain common RNA structures. Comparing our results with the recent mapping of transcribed fragments (transfrags) in human, we find that high-scoring candidates are twice as likely to be found in regions overlapped by transfrags than regions that are not overlapped by transfrags. To verify the coexpression between predicted candidates in human and mouse, we conducted expression studies by RT-PCR and Northern blotting on mouse candidates, which overlap with transfrags on human chromosome 20. RT-PCR results confirmed expression of 32 out of 36 candidates, whereas Northern blots confirmed four out of 12 candidates. Furthermore, many RT-PCR results indicate differential expression in different tissues. Hence, our findings suggest that there are corresponding regions between human and mouse, which contain expressed non-coding RNA sequences not alignable in primary sequence.

Expression profiling of the Arabidopsis annexin gene family during germination, de-etiolation and abiotic stress

Annexins are a multigene family in most plant species and are suggested to play a role in a wide variety of essential cellular processes. In Arabidopsis thaliana there are eight different annexins ( AnnAt1-8), which range from 29% to 83% in deduced amino acid sequence identity. As a first step toward clarifying the individual functions of these annexins, in this study we have used quantitative real time reverse transcription PCR to assess their differential expression in different tissues or after different stimuli. We determined which annexins are expressed during germination and early seedling growth by assaying annexin expression levels in dry and germinating seeds and in 7-day-old light-grown seedlings. Our results indicate that transcripts for all eight annexins are present in germinating seeds and that transcript levels for all the annexins increase by 7 days of normal growth. We assayed transcript levels in dark grown roots, cotyledons, and hypocotyls and found that the relative abundance of each annexin varied in these dark-grown tissues. We also examined the effects of red and far red light treatments on annexin expression in 5.5-day-old etiolated seedlings. Light treatments significantly altered transcript levels in hypocotyls and cotyledons for only two members of the gene family. Finally, we monitored annexin expression changes in response to a variety of abiotic stresses. We found that the expression of most of the Arabidopsis annexin genes is differentially regulated by exposure to salt, drought, and high- and low-temperature conditions, indicating a likely role for members of this gene family in stress responses.