TIP aquaporins in Cyperus esculentus: genome-wide identification, expression profiles, subcellular localizations, and interaction patterns.

BACKGROUND: Tonoplast intrinsic proteins (TIPs), which typically mediate water transport across vacuolar membranes, play an essential role in plant growth, development, and stress responses. However, their characterization in tigernut (Cyperus esculentus L.), an oil-bearing tuber plant of the Cyperaceae family, is still in the infancy. RESULTS: In this study, a first genome-wide characterization of the TIP subfamily was conducted in tigernut, resulting in ten members representing five previously defined phylogenetic groups, i.e., TIP1-5. Although the gene amounts are equal to that present in two model plants Arabidopsis and rice, the group composition and/or evolution pattern were shown to be different. Except for CeTIP1;3 that has no counterpart in both Arabidopsis and rice, complex orthologous relationships of 1:1, 1:2, 1:3, 2:1, and 2:2 were observed. Expansion of the CeTIP subfamily was contributed by whole-genome duplication (WGD), transposed, and dispersed duplications. In contrast to the recent WGD-derivation of CeTIP3;1/-3;2, synteny analyses indicated that TIP4 and - 5 are old WGD repeats of TIP2, appearing sometime before monocot-eudicot divergence. Expression analysis revealed that CeTIP genes exhibit diverse expression profiles and are subjected to developmental and diurnal fluctuation regulation. Moreover, when transiently overexpressed in tobacco leaves, CeTIP1;1 was shown to locate in the vacuolar membrane and function in homo/heteromultimer, whereas CeTIP2;1 is located in the cell membrane and only function in heteromultimer. Interestingly, CeTIP1;1 could mediate the tonoplast-localization of CeTIP2;1 via protein interaction, implying complex regulatory patterns. CONCLUSIONS: Our findings provide a global view of CeTIP genes, which provide valuable information for further functional analysis and genetic improvement through manipulating key members in tigernut.

Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales.

Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization of lipid droplets (LDs) in seeds of oil crops. Despite the proposal of five oleosin clades (i.e., U, SL, SH, T, and M) in angiosperms, their evolution in eudicots has not been well-established. In this study, we employed Brassicales, an economically important order of flowering plants possessing the lineage-specific T clade, as an example to address this issue. Three to 10 members were identified from 10 species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, and Cleomaceae. Evolutionary and reciprocal best hit-based homologous analyses assigned 98 oleosin genes into six clades (i.e., U, SL, SH, M, N, and T) and nine orthogroups (i.e., U1, U2, SL, SH1, SH2, SH3, M, N, and T). The newly identified N clade represents an ancient group that has already appeared in the basal angiosperm Amborella trichopoda, which are constitutively expressed in the tree fruit crop Carica papaya, including pulp and seeds of the fruit. Moreover, similar to Clade N, the previously defined M clade is actually not Lauraceae-specific but an ancient and widely distributed group that diverged before the radiation of angiosperm. Compared with A. trichopoda, lineage-specific expansion of the family in Brassicales was largely contributed by recent whole-genome duplications (WGDs) as well as the ancient γ event shared by all core eudicots. In contrast to the flower-preferential expression of Clade T, transcript profiling revealed an apparent seed/embryo/endosperm-predominant expression pattern of most oleosin genes in Arabidopsis thaliana and C. papaya. Moreover, the structure and expression divergence of paralogous pairs was frequently observed, and a good example is the lineage-specific gain of an intron. These findings provide insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in nonmodel plants such as C. papaya.

Thaumatin-like protein family genes VfTLP4-3 and VfTLP5 are critical for faba bean's response to drought stress at the seedling stage.

Thaumatin-like proteins (TLPs) are a diverse family of pathogenesis-related proteins (PR-5) found in various plant species. Faba bean is an economically important crop known for its nutritional value and resilience to harsh environmental conditions, including drought. In this study, we conducted a comprehensive analysis of the gene structure, phylogenetics, and expression patterns of TLP genes in faba bean, with a specific focus on their response to drought stress. A total of 10 TLP genes were identified and characterized from the faba bean transcriptome, which could be classified into four distinct groups based on their evolutionary relationships. Conserved cysteine residues and REDDD motifs, which are characteristic features of TLPs, were found in most of the identified VfTLP members, and these proteins were likely to reside in the cytoplasm. Two genes, VfTLP4-3 and VfTLP5, exhibited significant upregulation under drought conditions. Additionally, ectopically expressing VfTLP4-3 and VfTLP5 in tobacco leaves resulted in enhanced drought tolerance and increased peroxidase (POD) activity. Moreover, the protein VfTLP4-3 was hypothesized to interact with glycoside hydrolase family 18 (GH18), endochitinase, dehydrin, Barwin, and aldolase, all of which are implicated in chitin metabolism. Conversely, VfTLP5 was anticipated to associate with peptidyl-prolyl cis-trans isomerase-like 3, a molecule linked to the synthesis of proline. These findings suggest that these genes may play crucial roles in mediating the drought response in faba bean through the regulation of these metabolic pathways, and serve as a foundation for future genetic improvement strategies targeting enhanced drought resilience in this economically important crop.

Molecular characterization of oleosin genes in Cyperus esculentus, a Cyperaceae plant producing oil in underground tubers.

KEY MESSAGE: CeOLE genes exhibit a tuber-predominant expression pattern and their mRNA/protein abundances are positively correlated with oil accumulation during tuber development. Overexpression could significantly increase the oil content of tobacco leaves. Oleosins (OLEs) are abundant structural proteins of lipid droplets (LDs) that function in LD formation and stabilization in seeds of oil crops. However, little information is available on their roles in vegetative tissues. In this study, we present the first genome-wide characterization of the oleosin family in tigernut (Cyperus esculentus L., Cyperaceae), a rare example accumulating high amounts of oil in underground tubers. Six members identified represent three previously defined clades (i.e. U, SL and SH) or six out of seven orthogroups (i.e. U, SL1, SL2, and SH1-3) proposed in this study. Comparative genomics analysis reveals that lineage-specific expansion of Clades SL and SH was contributed by whole-genome duplication and dispersed duplication, respectively. Moreover, presence of SL2 and SH3 in Juncus effuses implies their appearance sometime before Cyperaceae-Juncaceae divergence, whereas SH2 appears to be Cyperaceae specific. Expression analysis showed that CeOLE genes exhibit a tuber-predominant expression pattern and transcript levels are considerably more abundant than homologs in the close relative Cyperus rotundus. Moreover, CeOLE mRNA and protein abundances were shown to positively correlate with oil accumulation during tuber development. Additionally, two dominant isoforms (i.e. CeOLE2 and -5) were shown to locate in LDs as well as the endoplasmic reticulum of tobacco (Nicotiana benthamiana) leaves, and are more likely to function in homo and heteromultimers. Furthermore, overexpression of CeOLE2 and -5 in tobacco leaves could significantly increase the oil content, supporting their roles in oil accumulation. These findings provide insights into lineage-specific family evolution and putative roles of CeOLE genes in oil accumulation of vegetative tissues, which facilitate further genetic improvement for tigernut.

Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways.

Indian mustard (Brassica juncea L. Czern and Coss) is an important oil and vegetable crop frequently affected by seasonal drought stress during seed germination, which retards plant growth and causes yield loss considerably. However, the gene networks regulating responses to drought stress in leafy Indian mustard remain elusive. Here, we elucidated the underlying gene networks and pathways of drought response in leafy Indian mustard using next-generation transcriptomic techniques. Phenotypic analysis showed that the drought-tolerant leafy Indian mustard cv. 'WeiLiang' (WL) had a higher germination rate, antioxidant capacity, and better growth performance than the drought-sensitive cv. 'ShuiDong' (SD). Transcriptome analysis identified differentially expressed genes (DEGs) in both cultivars under drought stress during four germination time points (i.e., 0, 12, 24, and 36 h); most of which were classified as drought-responsive, seed germination, and dormancy-related genes. In the Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three main pathways (i.e., starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction) were unveiled involved in response to drought stress during seed germination. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified several hub genes (novel.12726, novel.1856, BjuB027900, BjuA003402, BjuA021578, BjuA005565, BjuB006596, novel.12977, and BjuA033308) associated with seed germination and drought stress in leafy Indian mustard. Taken together, these findings deepen our understanding of the gene networks for drought responses during seed germination in leafy Indian mustard and provide potential target genes for the genetic improvement of drought tolerance in this crop.

Analysis of Lhc family genes reveals development regulation and diurnal fluctuation expression patterns in Cyperus esculentus, a Cyperaceae plant.

MAIN CONCLUSION: Sixteen Lhc genes representing 13 phylogenetic groups were identified from the full-length transcriptome of tigernut, exhibiting development regulation and diurnal fluctuation expression patterns in leaves. Nuclear encoded light-harvesting chlorophyll a/b-binding (Lhc) proteins play indispensable roles in oxygenic photosynthesis. In this study, we present the first transcriptome-based characterization of Lhc family genes in tigernut (Cyperus esculentus L.), a Cyperaceae C4 plant producing oil in underground tubers. A number of 16 Lhc genes representing 13 phylogenetic groups identified from the full-length tigernut transcriptome are equal to that found in both Carex littledalei (another Cyperaceae plant) and papaya, slightly more than 15 members present in both rice and jatropha, but relatively less than 18, 20, and 21 members present in sorghum, cassava, and Arabidopsis, respectively. Nevertheless, nearly one-vs-one orthologous relationship was observed in most groups, though some of them are no longer located in syntenic blocks and species-specific expansion was frequently found in Lhcb1. Comparative genomics analysis revealed that the loss of two groups (i.e., Lhca2 and Lhca5) in C. littledalei is species-specific, sometime after the split with tigernut, and the expansion of Lhcb1 was mainly contributed by tandem duplication as observed in most species. Interestingly, a transposed duplication, which appears to be shared by monocots, was also identified in Lhcb1. Further transcriptome profiling revealed a predominant expression pattern of most CeLhc family genes in photosynthetic tissues and enhanced transcription during leaf maturation, reflecting their key roles in light absorption. Moreover, qRT-PCR analysis revealed an apparent diurnal fluctuation expression pattern of 11 dominant CeLhc genes. These findings not only highlight species-specific evolution of Lhc genes in the Cyperaceae family as well as the monocot lineage, but also provide valuable information for further functional analysis and genetic improvement in tigernut.

Overexpression of soybean microRNA156b enhanced tolerance to phosphorus deficiency and seed yield in Arabidopsis.

microRNAs (miRNAs) are endogenous small RNAs that are key regulatory factors participating in various biological activities such as the signaling of phosphorus deficiency in the plant. Previous studies have shown that miR156 expression was modulated by phosphorus starvation in Arabidopsis and soybean. However, it is not clear whether the over-expression of soybean miR156b (GmmiR156b) can improve a plant's tolerance to phosphorus deficiency and affect yield component traits. In this study, we generated Arabidopsis transgenic lines overexpressing GmmiR156b and investigated the plant's response to phosphorus deficiency. Compared with the wild type, the transgenic Arabidopsis seedlings had longer primary roots and higher phosphorus contents in roots under phosphorus-deficit conditions, but lower fresh weight root/shoot ratios under either phosphorus-deficient or sufficient conditions. Moreover, the GmmiR156b overexpression transgenic lines had higher phosphorus content in shoots of adult plants and grew better than the wide type under phosphorus-deficient conditions, and exhibited increased seed yields as well as strong pleiotropic developmental morphology such as dwarfness, prolonged growth period, bushy shoot/branching, and shorter silique length, suggesting that the transgenic lines were more tolerant to phosphorus deficiency. In addition, the expression level of four SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes (i.e., AtSPL4/5/6/15) were markedly suppressed in transgenic plants, indicating that they were the main targets negatively regulated by GmmiR156b (especially AtSPL15) and that the enhanced tolerance to phosphorus deficiency and seed yield is conferred mainly by the miR156-mediated downregulation of AtSPL15.

Recovery of Acid and Alkaline from Industrial Saline Wastewater by Bipolar Membrane Electrodialysis under High-Chemical Oxygen Demand Concentration.

Actual high saline wastewater containing concentrated organics and sodium chloride is a bioenergy and renewable resource. This study compared two different bipolar membrane electrodialysis membranes from two companies' stacks to recover HCl and NaOH from sodium chloride solution and actual chemical wastewater. The results demonstrated that the electrolysis rates were around 1.5 kg/m2h, the HCl and NaOH production rates were about 0.9 kg/m2h, energy consumption was in the range of 1.05-1.27 kWh/kg, and the economic benefits were above 1 yuan/h in BMED systems. From analyzing the performance of seven different BMED membrane stacks, the B2 stack was chosen for electrolyzing actual high salt wastewater to observe the effect of chemical oxygen demand on BMED systems, where electrolytic salt performance, HCl-NaOH alkali production rates, and energy consumption show linear dependence on time for 5000 mg/L chemical oxygen demand wastewater. It illustrated chemical oxygen demand can enhance energy consumption and reduce electrolytic salt performance and the acid and alkali production rates, due to improving the membrane area resistance. In this study, the effect of high COD saline wastewater on the performance of a BMED membrane stack was clarified and the mechanism was analyzed for its practical application in treating chemical high salt wastewater.

Complete mitochondrial genome sequence and comparative analysis of the cultivated yellow nutsedge.

As a monocotyledonous plant in family Cyperaceae, yellow nutsedge (Cyperus esculentus L.) is unique in accumulating a substantial amount of oil in underground tubers and provides a model system for studying oil accumulation in nonseed tissues. However, no data on the mitochondrial and nuclear genome sequences of this species are available, which greatly limits our understanding of its evolutionary characteristics and some essential biological mechanisms. In the present study, we report the first complete mitochondrial genome sequence of the cultivated yellow nutsedge. The analysis of the genome showed that the yellow nutsedge mitochondrial genome is 1,002,696 bp in size and encodes 62 genes consisting of 36 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and six ribosomal RNA (rRNA) genes. Compared with other angiosperms, yellow nutsedge mitochondrial genome contains much higher percentage of noncoding sequences (95.36%). Sixteen plastid-derived fragments were identified to be strongly associated with mitochondrial genes including one intact plastid-related gene (ndhH). Comparative analysis with seven other sequenced plant mitochondrial genomes revealed that two syntenic gene clusters, rps3-rpl16 and rps12-nad3, are highly conserved in all plant mitochondrial genomes, and the mitochondrial genome of yellow nutsedge is more similar to those of monocotyledons in the gene order. Phylogenetic analysis based on 13 shared protein-encoding genes in eight plant species showed that yellow nutsedge is evolutionarily more closely related to monocotyledonary species. Overall, the species-specific features of the cultivated yellow nutsedge mitochondrial genome provide additional information for the evolutionary and comparative genomic studies in the yellow nutsedge and other Cyperus species of the Cyperaceae family.

Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae.

BACKGROUND: Lipid droplets (LDs) present in land plants serve as an essential energy and carbon reserve for seed germination and seedling development. Oleosins, the most abundant structural proteins of LDs, comprise a small family involved in LD formation, stabilization and degradation. Despite their importance, our knowledge on oleosins is still poor in Euphorbiaceae, a large plant family that contains several important oil-bearing species. RESULTS: To uncover lineage-specific evolution of oleosin genes in Euphorbiaceae, in this study, we performed a genome-wide identification and comprehensive comparison of the oleosin family in Euphorbiaceae species with available genome sequences, i.e. castor bean (Ricinus communis), physic nut (Jatropha curcas), tung tree (Vernicia fordii), Mercurialis annua, cassava (Manihot esculenta) and rubber tree (Hevea brasiliensis), and a number of five, five, five, five, eight and eight members were found, respectively. Synteny analysis revealed one-to-one collinear relationship of oleosin genes between the former four (i.e. castor bean, physic nut, tung tree and M. annua) as well as latter two species (i.e. cassava and rubber tree), whereas one-to-one and one-to-two collinear relationships were observed between physic nut and cassava, reflecting the occurrence of one recent whole-genome duplication (WGD) in the last common ancestor of cassava and rubber tree. The presence of five ortholog groups representing three previously defined clades (i.e. U, SL and SH) dates back at least to the Malpighiales ancestor, because they are also conserved in poplar (Populus trichocarpa), a tree having experienced one Salicaceae-specific recent WGD. As observed in poplar, WGD was shown to be the main driver for the family expansion in both cassava and rubber tree. Nevertheless, same retention patterns of WGD-derived duplicates observed in cassava and rubber tree are somewhat different from that of poplar, though certain homologous fragments are still present in rubber tree. Further transcriptional profiling revealed an apparent seed-predominant expression pattern of oleosin genes in physic nut, castor bean and rubber tree. Moreover, structure and expression divergence of paralogous pairs were also observed in both cassava and rubber tree. CONCLUSION: Comparative genomics analysis of oleosin genes reported in this study improved our knowledge on lineage-specific family evolution in Euphorbiaceae, which also provides valuable information for further functional analysis and utilization of key members and their promoters.

iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean.

Adzuki bean is an important legume crop due to its high-quality protein, fiber, vitamins, minerals as well as rich bioactive substances. However, it is vulnerable to drought at the germination stage. However, little information is available about the genetic control of drought tolerance during seed germination in adzuki bean. In this study, some differential expression proteins (DEPs) were identified during seed germination between the drought-tolerant variety 17235 and drought-sensitive variety 17033 in adzuki bean using iTRAQ method. A total of 2834 proteins were identified in the germinating seeds of these two adzuki beans. Compared with the variety 17033, 87 and 80 DEPs were increased and decreased accumulation in variety 17235 under drought, respectively. Meanwhile, in the control group, a few DEPs, including 9 up-regulated and 21 down-regulated proteins, were detected in variety 17235, respectively. GO, KEGG, and PPI analysis revealed that the DEPs related to carbohydrate metabolism and energy production were significantly increased in response to drought stresses. To validate the proteomic function, the ectopic overexpression of V-ATPase in tobacco was performed and the result showed that V-ATPase upregulation could enhance the drought tolerance of tobacco. The results provide valuable insights into genetic response to drought stress in adzuki bean, and the DEPs could be applied to develop biomarkers related to drought tolerant in adzuki bean breeding projects.

Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis.

The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.

Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean.

Respiratory burst oxidase homologs (RBOHs), which catalyze the production of superoxide from oxygen and NADPH, play key roles in plant growth and development, hormone signaling, and stress responses. Compared with extensive studies in model plants arabidopsis and rice, little is known about RBOHs in other species. This study presents a genome-wide analysis of Rboh family genes in jatropha (Jatropha curcas) as well as the comparison with castor bean (Ricinus communis), another economically important non-food oilseed crop of the Euphorbiaceae family. The family number of seven members identified from the jatropha genome is equal to that present in castor bean, and further phylogenetic analysis assigned these genes into seven groups named RBOHD, -C, -B, -E, -F, -N, and -H. In contrast to a high number of paralogs present in arabidopsis and rice that experienced several rounds of recent whole-genome duplications, no duplicate was identified in both jatropha and castor bean. Conserved synteny and one-to-one orthologous relationship were observed between jatropha and castor bean Rboh genes. Although exon-intron structures are usually highly conserved between orthologs, loss of certain introns was observed for JcRbohB, JcRbohD, and RcRbohN, supporting their divergence. Global gene expression profiling revealed diverse patterns of JcRbohs over various tissues. Moreover, expression patterns of JcRbohs during flower development as well as various stresses were also investigated. These findings will not only improve our knowledge on species-specific evolution of the Rboh gene family, but also provide valuable information for further functional analysis of Rboh genes in jatropha.

IP telephony--new horizon for telemedicine and e-health.

Internet Protocol (IP) based networks are increasingly being used as alternatives to the traditional circuit-switched networks for carrying voice traffic. IP telephony is taking a firm hold in the world telecommunication market for a wide range of applications including telemedicine. The merits of IP telephony for telemedicine lie in cost-savings and new applications and functionalities it may render. In this paper, we try to discuss and analyze the implications of IP telephony on the evolution and deployment of telemedicine and e-health.

On-site investigation of the early phase of Bhutan Health Telematics Project.

Telemedicine is valuable to many developing countries. International use of telemedicine is widespread. Telemedicine can improve health care in the developing countries by removing time and distance barrier, and optimize the use of limited health services in developing countries. The purpose of this paper is to investigate the current situation of healthcare services and telecommunications infrastructure in Bhutan. It summarizes the experience gained from a previous telemedicine pilot project initiated and implemented by the Telecommunication Development Bureau, International Telecommunication Union (BDT/ITU). It also introduces the priorities of telemedicine development set out by the local health authorities as well as the international organizations. By analyzing the common and most urgent problems in the country, which could be alleviated by using telemedicine, it formulates several recommendations concerning the future development strategy of telemedicine in Bhutan.