Expression Patterns In Different Tissues Research Articles

Genome-wide identification and expression analysis of the SR gene family in longan (Dimocarpus longan Lour.)

Longan (Dimocarpus longan Lour.) is an important commercial fruit tree in southern China. The embryogenesis of longan affects the quality and yield of fruit. A large number of alternative splicing events occurs during somatic embryogenesis (SE), which is regulated by serine/arginine-rich (SR) proteins. However, the functions of SR proteins in longan are poorly understood. In this study, 21 Dlo-SR gene family members belonging to six subfamilies were identified, among which Dlo-RSZ20a, Dlo-SR30, Dlo-SR17, Dlo-SR53 and Dlo-SR32 were localized in the nucleus, Dlo-RSZ20b, Dlo-RSZ20c, Dlo-RSZ20d, Dlo-SC18, Dlo-RS2Z29, Dlo-SCL41, and Dlo-SR33 were localized in chloroplasts, and Dlo-RS43, Dlo-SC33, Dlo-SC37, Dlo-RS2Z33, Dlo-RS2Z16, Dlo-RS2Z24, Dlo-SCL43, Dlo-SR112, and Dlo-SR59 were localized in the nucleus and chloroplasts. The Dlo-SR genes exhibited differential expression patterns in different tissues of longan. The transcript levels of Dlo-RSZ20a, Dlo-SC18, Dlo-RS2Z29, DLo-SR59, Dlo-SR53, and Dlo-SR17 were low in all analyzed tissues, whereas Dlo-RS43, Dlo-RS2Z16, Dlo-RS2Z24, and Dlo-SR30 were highly expressed in all tissues. To clarify their function during SE, the transcript levels of Dlo-SR genes were analyzed at different four stages of SE, comprising non-embryonic callus (NEC), friable-embryogenic callus (EC), incomplete compact pro-embryogenic culture (ICpEC) and globular embryo (GE). Interestingly, the transcript levels of Dlo-RS2Z29 and Dlo-SR112 were increased in embryogenic cells compared with the NEC stage, whereas transcript levels of Dlo-RSZ20a, Dlo-RS43, Dlo-SC37, and Dlo-RS2Z16 were especially increased at the GE stage compared with the other stages. Alternative splicing events of Dlo-SR mRNA precursors (pre-mRNAs) was detected during SE, with totals of 41, 29, 35, and 44 events detected during NEC, EC, ICpEC, and GE respectively. Protein–protein interaction analysis showed that SR proteins were capable of interaction with each other. The results indicate that the alternative splicing of Dlo-SR pre-mRNAs occurs during SE and that Dlo-SR proteins may interact to regulate embryogenesis of longan.

Transcriptomic analysis and expression of C-type lectins in response to Vibrio parahaemolyticus challenge in Scapharca subcrenata

Little information is available on innate immune defense mechanisms of Scapharca subcrenata. C-type lectins (CTLs) are not only pattern recognition proteins that can bind pathogen-associated molecular patterns, but also crucial maternally-derived immune factors in mollusc egg. In this study, the comparative transcriptome analysis of Vibrio parahaemolyticus-infected and untreated hepatopancreas were performed to identify the key genes involved in maternal transfer of immunity. A total of 3514 and 9327 differentially expressed genes (DEGs) were identified at 6 and 48 h post challenge compared to control groups. Gene Ontology and Cluster of Orthologous Groups analysis showed that most DEGs were classified under regulation of signal transduction, regulation of the metabolic process of carbohydrates and secondary metabolites, while the processes of posttranscriptional modification and protein translation were inhibited manifestly. The DEGs were most enriched in pathways related to lysosome, phagosome and EMC-receptor interaction. Among the DEGs, 191 maternal immune-related genes that could provide developing embryos a better protection against pathogen infection were identified according to previous studies. Additionally, five CTLs (designated as SsCTL1-5) identified from the DEGs were cloned, and their expression patterns in different tissues and post immune stimulation were analyzed. These findings would be beneficial for understanding the innate immune defense mechanisms of S. subcrenata.

Genome-wide survey of the amino acid transporter gene family in wheat (Triticum aestivum L.): Identification, expression analysis and response to abiotic stress

Amino acid transporters (AATs), which transport amino acids across cell membranes, play important roles in alleviating plant damage under stresses and in plant growth. To data, little is known about the AAT genes in wheat because of its complex genome. In this study, a total of 296 AAT genes were identified from the latest wheat genome sequence (IWGSC v1.1) and classified into 12 distinct subfamilies based upon their sequence composition and phylogenetic relationship. The expansion of the wheat AAT family was mainly the results of whole-genome duplication (WGD) and tandem events. The unequal expansion of different subfamilies brought new features to TaAATs. TaAATs were highly expressed and exhibited distinct expression patterns in different tissues. On the basis of homology and expression pattern analysis, we identified several wheat AAT family members that may affect grain quality. In addition, TaAAP3, TaATLa2 and TaATLb13 exhibited sustained expression in response to drought and high-temperature stress. These genes are involved in the response of wheat to abiotic stress by regulating the transport and distribution of amino acids. Overall, our results help to understand the complexity of TaAATs and provide a theoretical basis for further identification and utilization of AATs in wheat and other crop species.

Molecular cloning, tissue expression, and transcriptional regulation of fabp1 and fabp2 in javelin goby (Synechogobius hasta) in response to starvation stress.

Fatty acid binding proteins (FABPs) are intracellular lipid chaperones with low molecular weight, which are widely distributed in a variety of tissues, participating in fatty acid transport, cell proliferation, and angiogenesis. In this study, full-length sequences of two fabp genes (fabp1 and fabp2) from javelin goby (Synechogobius hasta) were cloned via RACE PCR, followed by bioinformatic analyses and gene expression evaluation. The fabp1 and fabp2 cDNA sequences were 493 and 626bp in length, encoding 126 and 132 amino acids, respectively. Phylogenetic analysis revealed that both genes from S. hasta were clustered with those of other fish species in accordance with their known taxonomic relationships. fabp1 and fabp2 mRNA showed distinct expression patterns in different tissues, with fabp1 being most expressed in the liver and fabp2 in the intestine. Furthermore, the expression of fabp1 in the liver was significantly up-regulated during starvation, whereas fabp2 mRNA level in the intestine initially increased and then decreased, indicating that the transcriptional responses of the two genes could be influenced by malnourishment/starvation. Changes in the transcriptional levels of fabp1 and fabp2 also suggested that glycogen was catabolized in the liver of S. hasta at the beginning of starvation prior to lipid depletion, whereas lipids served as fuel reserves in the intestine during short-term starvation. In conclusion, this study provides fundamental insights into the role of Fabps in S. hasta lipid metabolism.

Spatial Divergence of PHR-PHT1 Modules Maintains Phosphorus Homeostasis in Soybean Nodules.

Maintaining phosphorus (Pi) homeostasis in nodules is the key to nodule development and nitrogen fixation, an important source of nitrogen for agriculture and ecosystems. PHOSPHATE-TRANSPORTER1 (PHT1) and its regulator PHOSPHATE-STARVATION-RESPONSE1 (PHR1), which constitute the PHR1-PHT1 module, play important roles in maintaining Pi homeostasis in different organs. However, the PHR1-PHT1 module and its functions in nodules remain unknown. We identified one PHT1 (GmPHT1;11) and four PHR1 (GmPHR1) homologs in soybean (Glycine max) plants, which displayed specific expression patterns in different tissues in nodules, similar to previously reported GmPHT1;1 and GmPHT1;4 Through the integration of different approaches, GmPHR-GmPHT1 modules were confirmed. Combining our results and previous reports, we established multiple GmPHR-GmPHT1 modules acting in the infected or noninfected tissues in nodules. A single GmPHR had more than one GmPHT1 target, and vice versa. Therefore, overlapping and cross-talking modules monitored the wave of available Pi to maintain Pi homeostasis in nodules, which sequentially regulated nodule initiation and development. High levels of GmPHT1;11 enhanced Pi accumulation in nodules, increased nodule size, but decreased nodule number. Nitrogenase activity was also enhanced by GmPHT1;11 Our findings uncover GmPHR-GmPHT1 modules in nodules, which expands our understanding of the mechanism of maintaining Pi homeostasis in soybean plants.

Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity

The endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plant BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified three BiP homologs in the Solanum tuberosum (potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling, and gene structure analysis. These analyses revealed that StBiP1 and StBiP2 grouped with AtBiP2, whereas StBiP3 grouped with AtBiP3. While the protein sequences and folding structures are highly similar, these StBiPs are distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and Arabidopsis BiP1 and BiP2 promoters were highly enriched with cis-regulatory elements (CREs) linked to developmental processes, whereas BiP3 promoters were enriched with stress related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture of BiP promoters potentially define their spatio-temporal expression patterns under developmental and stress related cues.

Gene-wide identification and expression analysis of the PMEI family genes in soybean (Glycine max).

Pectin Methylesterase Inhibitors (PMEI) gene family is widely spread in plants and plays crucial roles in plant development as well as biotic and abiotic stress response. However, little information was known about the function of PMEI genes in soybean. Herein, we identified 170 PMEI genes in soybean. These PMEI genes were divided into four groups (I-IV) based on phylogenetic analysis, and they were unevenly distributed in 18 soybean chromosomes. Gene structures and motif pattern analyses revealed that the PMEI genes in the same group showed the same characteristics. For the GmPMEI genes, gene duplication events occurred broadly, 52 pairs tandem duplication events and 55 pairs segmental duplication events suggested that the GmPMEI genes had high homology. Besides, the PMEI genes presented different expression patterns in different tissues, while several of these genes were expressed only in flowers. Under the biotic and abiotic stresses, PMEI genes had significant positive impact on the tolerance ability of soybean, and the ABA-responsive elements and SA-responsive elements played vital roles in responding to a variety of stresses. This study provides insights into the evolution and potential functions of GmPMEIs.

Genome-wide analysis of the Saccharina japonica sulfotransferase genes and their transcriptional profiles during whole developmental periods and under abiotic stresses

BackgroundAs a unique sulfated polysaccharide, fucoidan is an important component of cell wall in brown seaweeds. Its biochemical properties are determined by the positions and quantity of sulfate groups. Sulfotransferases (STs) catalyze the sulfation process, which transfer the sulfuryl groups to carbohydrate backbones and are crucial for fucoidan biosynthesis. Nevertheless, the structures and functions of STs in brown seaweeds are rarely investigated.ResultsThere are a total of 44 ST genes identified from our genome and transcriptome analysis of Saccharina japonica, which were located in the 17 scaffolds and 11 contigs. The S. japonica ST genes have abundant introns and alternative splicing sites, and five tandem duplicated gene clusters were identified. Generally, the ST genes could be classified into five groups (Group I ~ V) based on phylogenetic analysis. Accordingly, the ST proteins, which were encoded by genes within the same group, contained similar conserved motifs. Members of the S. japonica ST gene family show various expression patterns in different tissues and developmental stages. Transcriptional profiles indicate that the transcriptional levels of more than half of the ST genes are higher in kelp basal blades than in distal blades. Except for ST5 and ST28, most ST genes are down-regulated with the kelp development stages. The expression levels of nine ST genes were detected by real-time quantitative PCR, which demonstrates that they responded to low salinity and drought stresses.ConclusionsVarious characteristics of the STs allow the feasibilities of S. japonica to synthesize fucoidans with different sulfate groups. This enables the kelp the potential to adapt to the costal environments and meet the needs of S. japonica growth.

High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development.

Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.

Abstract C100: Identification and functional characterization of a novel GLI1 splice variant in breast cancer

Abstract The purpose of this study is to investigate the biologic significance of novel GLI1 splice variants in breast cancer. African American (AA) women suffer a disproportionately high burden of basal-like breast cancer, an aggressive subtype that has no targeted therapy (1). About 15-20% of breast cancers are triple-negative/basal-like, are associated with poor clinical outcomes and show disproportionately higher prevalence in younger women of African descent (2-4). The Hedgehog (Hh)/GLI1 developmental pathway has emerged as a therapeutic target in many cancers, including breast cancer studies from our lab (5, 6). Overexpression of the main Hh transcriptional mediator GLI1, correlates with poor patient prognosis and relapse. The human GLI1 transcript undergoes alternative splicing producing two shorter isoforms, an N-terminal deletion variant (GLI1ΔN) (7) and a truncated GLI1 (tGLI1) (8), which have been reported to have different patterns of tissue expression and function. tGLI1 has been identified as being highly expressed in several cancers, including in breast cancer (9). We performed in silico analysis of the NCBI database for evidence of additional human GLI1 transcripts and identified a novel GLI1 splice variant, GLI1-X2, that has an in-frame deletion of the entire exon 10-zinc finger 5 domain of the GLI1 gene. Our preliminary data show that GLI1-X2 is expressed in basal-like breast cancers at substantially higher levels than GLI1, tGLI1, or GLI1ΔN. To our knowledge, we are the first to demonstrate expression of GLI1-X2 in any model and our findings expand the GLI1 family of zinc finger transcription factors. Our objectives are to examine the expression differences of the GLI1 splice variants in basal-like and luminal breast cancer cell models, AA and White patient samples and to investigate the biologic function of GLI1-X2 in breast cancer. Previous studies report that GLI1ΔN and tGLI1 proteins retain intact functional zinc finger domains. Thus, we hypothesize that the loss of zinc-finger 5 is critical for GLI1-X2's functional role and regulation of downstream target genes in breast cancer. As the biologic significance of GLI1-X2 in normal and cancer biology is unknown, this proposed work is the first to characterize its function and potential role in cancer. Citation Format: Maria S. Dixon, Lhoucine Chdid, David R. Lamson, Michael T. Tarpley, Helen O. Oladapo, Jodie M. Fleming, Jennifer A. Freedman, Gayathri R. Devi, Kevin P. Williams. Identification and functional characterization of a novel GLI1 splice variant in breast cancer [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C100.

Studies on the clinical symptoms, virus distribution, and mRNA expression of several antiviral immunity-related genes in grass carp after infection with genotype II grass carp reovirus.

The viral hemorrhage disease caused by grass carp reovirus (GCRV) is a serious contagious disease of grass carp that mainly infects fingerlings and yearlings. Epidemiological studies have shown that GCRV genotype II is currently the prominent genotype. However, little is known about the histopathological characteristics, virus distribution, and expression of immunity-related genes in grass carp infected by GCRV genotype II. In this study, we found that grass carp infected by GCRV genotype II lost appetite, swam alone, and rolled, and their fins, eyes, operculum, oral cavity, abdomen, intestine, and muscles showed pronounced punctate hemorrhage. Congestion, swelling, deformation, thinning of membranes, dilatation and darkened color of nucleoli, cathepsis, erythrocyte infiltration, and vacuole formation were observed in some infected tissues. A qRT-PCR test showed that the 11 genome segments of GCRV had similar expression patterns in different tissues. The S8 segment, with unknown function and no homologous sequences, had the highest expression level, while the most conserved segment, L2, had the lowest expression level. GCRV particles were distributed in different tissues, especially in the intestine. In the infected intestine, the expression of various receptors and adaptor molecules was modulated at different levels. Pro-inflammatory cytokine interleukin-1β (IL-1β) expression was 2160.9 times higher than that in the control group. The upregulation of immunity-related genes activated the antiviral immunity pathways. Therefore, the intestine might play a dual role in mediating GCRV infection and the antiviral immune response. This study provides detailed information about the pathogenicity of GCRV and expression of immunity-related genes, laying the foundation for further research on virus control and treatment.

Cloning and characterization of chst11 from Procambarus clarkii involved in the host immune response of white spot syndrome virus and Aeromonas hydrophila

Carbohydrate sulfotransferases 11 (chst11) is one of the enzymes that synthesize chondroitin sulfate (CS), which has extensive immune functions in vitro and plays a critical role in mediating the infection of host by pathogenic microorganisms. However, whether it has immune functions in crayfish is still poorly understood. In our previous study of transcriptome, chst11 was differentially expressed in susceptible individuals and resistant individuals of Procambarus clarkii after white spot syndrome virus (WSSV) injection. Thus, in this study, the sequence of chst11 was obtained from P. clarkii for the first time and analyzed, and the expression pattern of chst11 was investigated. Besides, the purified recombinant protein of chst11 effect in protection in WSSV infection was explored. The full length of chst11 was 1536 bp with an 831-bp open reading frame (ORF), which encoding 276 amino acids residues with a calculated molecular mass of 33.1 kDa. The chst11 contains a Sulfotransfer_2 domain, one N-glycosylation site and three O-glycosylation sites. Phylogenetic analysis results showed that chst11 had the highest similarity to Penaeus vannamei (79.93%). The expression pattern of chst11 in different tissues indicated that chst11 was expressed highest in gut, gill and hypodermis, lowest in testicular duct, periesophageal nerve and hemocytes. The chst11 had different expression patterns in different tissues when the crayfish was challenged by WSSV, Aeromonas hydrophila and CpG ODN. Recombinant chst11 protein significantly reduced the amount of WSSV copy number in hepatopancreas at 6 h and 12 h post injection compared to the control group injected with bovine serum albumin (BSA). It was found that chst11 protein enhanced the expression of peroxinectin, proPO in hepatopancreas and midgut and the C-type lectin (ctl) in hemocytes and hepatopancreas. Intramuscularly injection of juvenile crayfish with chst11 protein decreased 60% mortality compared to the control group with BSA. This study is the first report on the antiviral function of chst11 in the immune system of crustacean.

Characterization of AOX family members from Aquilaria sinensis and their responses to wounding

Aquilaria sinensis is a typical inducible medicinal plant, that can produce agarwood only after it is wounded by external stimuli. Alternative oxidase(AOX) is one of the terminal oxidases of the plant mitochondrial electron transport, which plays an important role in plants' response to environmental stress. In order to reveal the physiological function of AOX gene in the process of agarwood formation from A.sinensis induced by wounding, AOX gene was cloned based on the transcriptome database and then identified by the bioinformatics analysis, and their expression pattern in different tissues and under wounding stress were detected by qRT-PCR. The results as follows. Three AOX genes were cloned from A.sinensis for the first time. They were named AsAOX1a, AsAOX1d and AsAOX2, respectively. The tissue expression shown that AsAOX1a is mainly expressed in the stem and the seed, and the AsAOX1d and AsAOX2 genes are mainly expressed in the pulp and the stem. AsAOX1a and AsAOX1d genes are highly responsive to wounding stress, and their response time was different. In addition, the expression of AsAOX1a and AsAOX2 induced by wounding are reduced by H_2O_2 treatment, but promoted by AsA treatment. The cloning, bioinformatics analysis and expression characteristics of AOX genes from A.sinensis provided basic information for further study the function of AOX genes in the development of A.sinensis, especially in the process of agarwood formation of A. sinensis induced by wounding.

Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response

Annexins (ANN) are a multigene, evolutionarily conserved family of calcium-dependent and phospholipid-binding proteins that play important roles in plant development and stress resistance. However, a systematic comprehensive analysis of ANN genes of Brassicaceae species (Brassica rapa, Brassica oleracea, and Brassica napus) has not yet been reported. In this study, we identified 13, 12, and 26 ANN genes in B. rapa, B. oleracea, and B. napus, respectively. About half of these genes were clustered on various chromosomes. Molecular evolutionary analysis showed that the ANN genes were highly conserved in Brassicaceae species. Transcriptome analysis showed that different group ANN members exhibited varied expression patterns in different tissues and under different (abiotic stress and hormones) treatments. Meanwhile, same group members from Arabidopsis thaliana, B. rapa, B. oleracea, and B. napus demonstrated conserved expression patterns in different tissues. The weighted gene coexpression network analysis (WGCNA) showed that BnaANN genes were induced by methyl jasmonate (MeJA) treatment and played important roles in jasmonate (JA) signaling and multiple stress response in B. napus.

Quantitative real-time PCR based evaluation and validation of reference genes in Gossypium arboreum

Estimation of gene expression levels plays a crucial role in understanding the function of the target gene(s). Intersample variance in gene expression can be more precisely measured if transcripts levels are accurately normalized. Normalization is pre-requisite step prior to the determination of candidate gene expression by qPCR. In this study conducted at ICAR-Central Institute for Cotton Research, Nagpur during 2015–16, six candidate reference genes, viz. actin4 (ACT4), actin7(ACT7), RNA Helicase (RNAH), Serine/threonine-protein phosphatase PP2A-1(PP2A1), ubiquitin7 (UBQ7) and α tubulin (αTUB) were systematically analysed for their expression patterns in different tissues pertaining to three development stages of cotton namely seedling, early reproductive and fiber development. The study has identified actin-4/actin-7/ubiquitin-7 as the most ideal reference genes for fiber development stages whereas actin-4/ ubiquitin-7 and actin-7/RNA helicases for seedling and early reproductive development stages, respectively. Validation of identified reference genes for relative expression analysis of Gacobl9, a COBRA-like protein, demonstrated their usefulness in qPCR analysis in Gossypium arboreum.

In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses.

Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses.

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates.

Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species. Our study reveals that adaptive selection plays a key role in the evolution of PD1 and its ligands in the majority of vertebrate species, which is in agreement with the contribution of these residues to the mechanisms of pathogen identification and coevolution in the complexity and novelties of vertebrate immune systems.

Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress

BackgroundBroomcorn millet is a drought-tolerant cereal that is widely cultivated in the semiarid regions of Asia, Europe, and other continents; however, the mechanisms underlying its drought-tolerance are poorly understood. The NAM, ATAF1/2, and CUC2 (NAC) transcription factors form a large plant-specific gene family that is involved in the regulation of tissue development and abiotic stress. To date, NAC transcription factors have not been systematically researched in broomcorn millet.ResultsIn the present study, a total of 180 NAC (PmNAC) genes were identified from the broomcorn millet genome and named uniformly according to their chromosomal distribution. Phylogenetic analysis demonstrated that the PmNACs clustered into 12 subgroups, including the broomcorn millet-specific subgroup Pm_NAC. Gene structure and protein motif analyses indicated that closely clustered PmNAC genes were relatively conserved within each subgroup, while genome mapping analysis revealed that the PmNAC genes were unevenly distributed on broomcorn millet chromosomes. Transcriptome analysis revealed that the PmNAC genes differed greatly in expression in various tissues and under different drought stress durations. The expression of 10 selected genes under drought stress was analyzed using quantitative real-time PCR.ConclusionIn this study, 180 NAC genes were identified in broomcorn millet, and their phylogenetic relationships, gene structures, protein motifs, chromosomal distribution, duplication, expression patterns in different tissues, and responses to drought stress were studied. These results will be useful for the further study of the functional characteristics of PmNAC genes, particularly with regards to drought resistance.

Genome-Wide Identification of Aluminum-Activated Malate Transporter (ALMT) Gene Family in Rubber Trees (Hevea brasiliensis) Highlights Their Involvement in Aluminum Detoxification

The rubber tree (Hevea brasiliensis) is a widely cultivated crop in tropical acidic soil that is tolerant to high concentration of aluminum and the aluminum-activated malate transporter (ALMT) plays an important role in plant aluminum detoxification. However, the effects of ALMT on rubber tree aluminum tolerance, growth performance, and latex production are unclear. In this study, 17 HbALMT genes were identified from the genome of rubber trees. The physiological and biochemical characteristics, phylogenetic relationships, gene structures, conserved motifs, cis-elements of promoter, and expression patterns of the identified HbALMT genes were studied. Phylogenetic relationships indicated that these genes were divided into four clusters and genes in the same cluster have similar gene structures and conserved motifs. The promoters of HbALMT genes contain many cis-elements associated with biotic stress and abiotic stress. Quantitative real-time PCR analysis revealed HbALMTs showed various expression patterns in different tissues, indicating the functional diversity of HbALMT genes in different tissues of rubber trees. Transcriptome analysis and qRT-PCR assay showed that most of the HbALMT genes responded to aluminum stress, and among the 17 HbALMTs, HbALMT1, HbALMT2, HbALMT13, and HbALMT15 displayed higher expression levels in roots after two or five days of Al treatments, indicating their potential involvement in aluminum detoxification. Taken together, this study laid a foundation for further understanding the molecular evolution of the ALMT genes and their involvement in rubber tree aluminum adaption.

Sugar transporter proteins in Capsicum: identification, characterization, evolution and expression patterns

Sugar transporter proteins (STPs) play an important role in plant growth and development and stress resistance. Pepper (Capsicum annuum L.) is a significant economic crop and is widely cultivated worldwide. However, the evolution and the roles of STP genes in the growth and development and in coping with abiotic stresses in pepper are poorly known. Here, we characterized STP gene family in pepper through integration of chromosomal location, gene structure, conserved motif, phylogeny, expression patterns in different tissues and abiotic stresses. Using bioinformatics-based methods, we identified 17 putative STP genes in pepper. Chromosome mapping indicated that they are unevenly distributed on 9 chromosomes and there are tandem duplication events. Gene structure analysis revealed that intron numbers among these CaSTP genes ranged from 2 to 5, except that CaSTP12 and CaSTP13 genes contained no introns. The phylogenetic tree of STP genes from pepper and other plant species revealed that STP genes were grouped into 4 subfamilies, suggesting that these gene subfamilies may have diverged from a single common ancestor prior to the mono-dicot split. Gene expression analysis based on RNA-seq data showed that three genes were expressed constitutively in all the tissues analyzed, implying that these genes might have specific function in pepper. Stress data analysis showed that the expression profiles of some members of the CaSTP gene family were altered under cold, heat, salt and hormone stress conditions. The present results will provide valuable information into the evolutionary relationships and functional divergence of the STP family in the future.