cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21824892
title: Arabidopsis clathrin adaptor EPSIN1 but not MODIFIED TRANSPORT TO THE VACOULE1 contributes to effective plant immunity against pathogenic <i>Pseudomonas</i> bacteria

description: In eukaryotes, EPSINs are Epsin <i>N</i>-terminal Homology (ENTH) domain-containing proteins that serve as monomeric clathrin adaptors at the plasma membrane (PM) or the <i>trans-</i>Golgi Network (TGN)/early endosomes (EE). The model plant <i>Arabidopsis thaliana</i> encodes for seven ENTH proteins, of which so far, only <i>At</i>EPSIN1 (<i>At</i>EPS1) and MODIFIED TRANSPORT TO THE VACUOLE1 (<i>At</i>MTV1) localize to the TGN/EE and contribute to cargo trafficking to both the cell surface and the vacuole. However, relatively little is known about role(s) of any plant EPSIN in governing physiological responses. We have recently shown that <i>At</i>EPS1 is a positive modulator of plant immune signaling and pattern-triggered immunity against flagellated <i>Pseudomonas syringae</i> pv. <i>tomato</i> (<i>Pto</i>) DC3000 bacteria. In <i>eps1</i> mutants, impaired immune responses correlate with reduced accumulation of the receptor FLAGELLIN SENSING2 (<i>At</i>FLS2) and the convergent immune co-receptor BRASSINOSTEROID INSENTIVE1-ASSOCIATED RECEPTOR KINASE1 (<i>At</i>BAK1) in the PM. Here, we report that in contrast to <i>At</i>EPS1, the TGN/EE-localized <i>At</i>MTV1 did not contribute significantly to immunity against pathogenic <i>Pto</i> DC3000 bacteria. We also compared the amino acid sequences, peptide motif structures and <i>in silico</i> tertiary structures of the ENTH domains of <i>At</i>EPS1 and <i>At</i>MTV1 in more detail. We conclude that despite sharing the classical tertiary alpha helical ENTH-domain structure and clathrin-binding motifs, the overall low amino acid identity and differences in peptide motifs may explain their role(s) in trafficking of some of the same as well as distinct cargo components to their site of function, with the latter potentially contributing to differences in physiological responses.
DOI: 10.6084/m9.figshare.21824892.v1
title: Arabidopsis clathrin adaptor EPSIN1 but not MODIFIED TRANSPORT TO THE VACOULE1 contributes to effective plant immunity against pathogenic <i>Pseudomonas</i> bacteria

description: In eukaryotes, EPSINs are Epsin <i>N</i>-terminal Homology (ENTH) domain-containing proteins that serve as monomeric clathrin adaptors at the plasma membrane (PM) or the <i>trans-</i>Golgi Network (TGN)/early endosomes (EE). The model plant <i>Arabidopsis thaliana</i> encodes for seven ENTH proteins, of which so far, only <i>At</i>EPSIN1 (<i>At</i>EPS1) and MODIFIED TRANSPORT TO THE VACUOLE1 (<i>At</i>MTV1) localize to the TGN/EE and contribute to cargo trafficking to both the cell surface and the vacuole. However, relatively little is known about role(s) of any plant EPSIN in governing physiological responses. We have recently shown that <i>At</i>EPS1 is a positive modulator of plant immune signaling and pattern-triggered immunity against flagellated <i>Pseudomonas syringae</i> pv. <i>tomato</i> (<i>Pto</i>) DC3000 bacteria. In <i>eps1</i> mutants, impaired immune responses correlate with reduced accumulation of the receptor FLAGELLIN SENSING2 (<i>At</i>FLS2) and the convergent immune co-receptor BRASSINOSTEROID INSENTIVE1-ASSOCIATED RECEPTOR KINASE1 (<i>At</i>BAK1) in the PM. Here, we report that in contrast to <i>At</i>EPS1, the TGN/EE-localized <i>At</i>MTV1 did not contribute significantly to immunity against pathogenic <i>Pto</i> DC3000 bacteria. We also compared the amino acid sequences, peptide motif structures and <i>in silico</i> tertiary structures of the ENTH domains of <i>At</i>EPS1 and <i>At</i>MTV1 in more detail. We conclude that despite sharing the classical tertiary alpha helical ENTH-domain structure and clathrin-binding motifs, the overall low amino acid identity and differences in peptide motifs may explain their role(s) in trafficking of some of the same as well as distinct cargo components to their site of function, with the latter potentially contributing to differences in physiological responses.
DOI: 10.6084/m9.figshare.24763379
title: Trees in trees a report from remote Australia

description: Anemochory or Ornithochory does not adequately explain the amount, size or distribution of woody epiphytes here in outback NSW Australia. In a semi-arid ecosystem, epiphytes should be short-lived and randomly dispersed not clustered around old Aboriginal campsites or along their ancient paths aka songlines. These enduring trees in trees we call TinTs, have been here much longer than European Australians. We are hoping to attract archaeobotanical or ethnobotanical research to help us recover the knowledge of the ancestors or at least assist us in protecting these arboreal oddities from future resource extraction activities.
DOI: 10.6084/m9.figshare.23211069
title: Comparative metabolomic profiling reveals molecular mechanisms underlying growth promotion and disease resistance in wheat conferred by <i>Piriformospora indica</i> in the field

description: <i>Piriformospora indica</i>, a plant root-colonizing basidiomycete fungus, exhibits strong growth-promoting activity in symbiosis with a broad range of plants. Here, we report the potential of <i>P.</i><i>indica</i> to improve growth, yield, and disease resistance in wheat in the field. In the present study, <i>P.</i> <i>indica</i> successfully colonized wheat through chlamydospores and formed dense mycelial networks that covered roots. Plants subjected to the seed soaking (SS) treatment with <i>P.</i> <i>indica</i> chlamydospore suspensions enhanced tillering 2.28-fold compared to the non-inoculated wheat in the tillering stage. In addition, <i>P.</i> <i>indica</i> colonization promoted vegetative growth significantly during the three-leaf, tillering, and jointing stages. Moreover, the <i>P.</i> <i>indica</i>-SS-treatment enhanced wheat yield by 16.37 ± 1.63%, by increasing grains per ear and panicle weight and decreased damage to wheat shoot and root architecture markedly, with high field control effects against <i>Fusarium pseudograminearum</i> (81.59 ± 1.32%), <i>Bipolaris sorokiniana</i> (82.19 ± 1.59%), and <i>Rhizoctonia cerealis</i> (75.98 ± 1.36%). Most of the primary metabolites, such as amino acids, nucleotides, and lipids, involved in vegetative reproduction were increased in <i>P.</i> <i>indica</i>-SS-treatment plants, whereas secondary metabolites, such as terpenoids, polyketides, and alkaloids, decreased following <i>P.</i> <i>indica</i> inoculation. The up-regulated processes of protein, carbohydrate, and lipid metabolism indicated that <i>P.</i> <i>indica</i> colonization increased growth, yield, and disease resistance via the acceleration of plant primary metabolism. In conclusion, <i>P.</i> <i>indica</i> improved morphological, physiological, and metabolic substance levels, and further promoted its growth, yield, and disease resistance in wheat.
DOI: 10.6084/m9.figshare.23211069.v1
title: Comparative metabolomic profiling reveals molecular mechanisms underlying growth promotion and disease resistance in wheat conferred by <i>Piriformospora indica</i> in the field

description: <i>Piriformospora indica</i>, a plant root-colonizing basidiomycete fungus, exhibits strong growth-promoting activity in symbiosis with a broad range of plants. Here, we report the potential of <i>P.</i><i>indica</i> to improve growth, yield, and disease resistance in wheat in the field. In the present study, <i>P.</i> <i>indica</i> successfully colonized wheat through chlamydospores and formed dense mycelial networks that covered roots. Plants subjected to the seed soaking (SS) treatment with <i>P.</i> <i>indica</i> chlamydospore suspensions enhanced tillering 2.28-fold compared to the non-inoculated wheat in the tillering stage. In addition, <i>P.</i> <i>indica</i> colonization promoted vegetative growth significantly during the three-leaf, tillering, and jointing stages. Moreover, the <i>P.</i> <i>indica</i>-SS-treatment enhanced wheat yield by 16.37 ± 1.63%, by increasing grains per ear and panicle weight and decreased damage to wheat shoot and root architecture markedly, with high field control effects against <i>Fusarium pseudograminearum</i> (81.59 ± 1.32%), <i>Bipolaris sorokiniana</i> (82.19 ± 1.59%), and <i>Rhizoctonia cerealis</i> (75.98 ± 1.36%). Most of the primary metabolites, such as amino acids, nucleotides, and lipids, involved in vegetative reproduction were increased in <i>P.</i> <i>indica</i>-SS-treatment plants, whereas secondary metabolites, such as terpenoids, polyketides, and alkaloids, decreased following <i>P.</i> <i>indica</i> inoculation. The up-regulated processes of protein, carbohydrate, and lipid metabolism indicated that <i>P.</i> <i>indica</i> colonization increased growth, yield, and disease resistance via the acceleration of plant primary metabolism. In conclusion, <i>P.</i> <i>indica</i> improved morphological, physiological, and metabolic substance levels, and further promoted its growth, yield, and disease resistance in wheat.
DOI: 10.6084/m9.figshare.23938032.v1
title: Both incompatible and compatible rhizobia inhabit the intercellular spaces of leguminous root nodules

description: In addition to rhizobia, many types of co-existent bacteria are found in leguminous root nodules, but their habitats are unclear. To investigate this phenomenon, we labeled <i>Bradyrhizobium diazoefficiens</i> USDA122 and <i>Bradyrhizobium</i> sp. SSBR45 with <i>Discosoma</i> sp. red fluorescent protein (DsRed) or enhanced green fluorescent protein (eGFP). USDA122 enhances soybean growth by forming effective root nodules, but SSBR45 does not form any nodules. Using low-magnification laser scanning confocal microscopy, we found that infected cells in the central zone of soybean nodules appeared to be occupied by USDA122. Notably, high-magnification microscopy after co-inoculation of non-fluorescent USDA122 and fluorescence-labeled SSBR45 also revealed that SSBR45 inhabits the intercellular spaces of healthy nodules. More unexpectedly, co-inoculation of eGFP-labeled USDA122 and DsRed-labeled SSBR45 (and vice versa) revealed the presence of USDA122 bacteria in both the symbiosomes of infected cells and in the apoplasts of healthy nodules. We then next inspected nodules formed after a mixed inoculation of differently-labeled USDA122, without SSBR45, and confirmed the inhabitation of the both populations of USDA122 in the intercellular spaces. In contrast, infected cells were occupied by single-labeled USDA122. We also observed <i>Mesorhizobium loti</i> in the intercellular spaces of active wild-type nodules of <i>Lotus japonicus</i> using transmission electron microscopy. Compatible intercellular rhizobia have been described during nodule formation of several legume species and in some mutants, but our evidence suggests that this type of colonization may occur much more commonly in leguminous root nodules.
DOI: 10.6084/m9.figshare.22239441
title: Aberrant light sensing and motility in the green alga <i>Chlamydomonas priscuii</i> from the ice-covered Antarctic Lake Bonney

description: The Antarctic green alga <i>Chlamydomonas priscuii</i> is an obligate psychrophile and an emerging model for photosynthetic adaptation to extreme conditions. Endemic to the ice-covered Lake Bonney, this alga thrives at highly unusual light conditions characterized by very low light irradiance (&lt;15 μmol m<sup>−2</sup> s<sup>−1</sup>), a narrow wavelength spectrum enriched in blue light, and an extreme photoperiod. Genome sequencing of <i>C. priscuii</i> exposed an unusually large genome, with hundreds of highly similar gene duplicates and expanded gene families, some of which could be aiding its survival in extreme conditions. In contrast to the described expansion in the genetic repertoire in <i>C. priscuii</i>, here we suggest that the gene family encoding for photoreceptors is reduced when compared to related green algae. This alga also possesses a very small eyespot and exhibits an aberrant phototactic response, compared to the model <i>Chlamydomonas reinhardtii</i>. We also investigated the genome and behavior of the closely related psychrophilic alga <i>Chlamydomonas</i> sp. ICE-MDV, that is found throughout the photic zone of Lake Bonney and is naturally exposed to higher light levels. Our analyses revealed a photoreceptor gene family and a robust phototactic response similar to those in the model <i>Chlamydomonas reinhardtii</i>. These results suggest that the aberrant phototactic response in <i>C. priscuii</i> is a result of life under extreme shading rather than a common feature of all psychrophilic algae. We discuss the implications of these results on the evolution and survival of shade adapted polar algae.
DOI: 10.6084/m9.figshare.22239441.v1
title: Aberrant light sensing and motility in the green alga <i>Chlamydomonas priscuii</i> from the ice-covered Antarctic Lake Bonney

description: The Antarctic green alga <i>Chlamydomonas priscuii</i> is an obligate psychrophile and an emerging model for photosynthetic adaptation to extreme conditions. Endemic to the ice-covered Lake Bonney, this alga thrives at highly unusual light conditions characterized by very low light irradiance (&lt;15 μmol m<sup>−2</sup> s<sup>−1</sup>), a narrow wavelength spectrum enriched in blue light, and an extreme photoperiod. Genome sequencing of <i>C. priscuii</i> exposed an unusually large genome, with hundreds of highly similar gene duplicates and expanded gene families, some of which could be aiding its survival in extreme conditions. In contrast to the described expansion in the genetic repertoire in <i>C. priscuii</i>, here we suggest that the gene family encoding for photoreceptors is reduced when compared to related green algae. This alga also possesses a very small eyespot and exhibits an aberrant phototactic response, compared to the model <i>Chlamydomonas reinhardtii</i>. We also investigated the genome and behavior of the closely related psychrophilic alga <i>Chlamydomonas</i> sp. ICE-MDV, that is found throughout the photic zone of Lake Bonney and is naturally exposed to higher light levels. Our analyses revealed a photoreceptor gene family and a robust phototactic response similar to those in the model <i>Chlamydomonas reinhardtii</i>. These results suggest that the aberrant phototactic response in <i>C. priscuii</i> is a result of life under extreme shading rather than a common feature of all psychrophilic algae. We discuss the implications of these results on the evolution and survival of shade adapted polar algae.
DOI: 10.6084/m9.figshare.22225280
title: Characterization of photosynthetic <i>Bradyrhizobium</i> sp. strain SSBR45 isolated from the root nodules of <i>Aeschynomene indica</i>

description: We isolated a novel strain of <i>Bradyrhizobium</i> sp., SSBR45, from the nodulated roots of <i>Aeschynomene indica</i> and labeled it with <i>Discosoma</i> sp. red fluorescent protein (dsRED) or enhanced green fluorescent protein (eGFP) and determined its draft genomic sequence. The labeled SSBR45 stimulated the growth of <i>A. indica</i> markedly on a nitrogen-free medium, as observed by visualizing the fluorescent root nodules. The nodulated roots also exhibited high acetylene reduction activities. The SSBR45 genome included genes involved in nitrogen fixation, photosynthesis, and type IV secretion system; however, it did not consist of canonical <i>nodABC</i> genes and type III secretion system genes. SSBR45, a novel species of the genus <i>Bradyrhizobium</i>, consisted of an average nucleotide identity and average amino acid identity of 87% and 90%, respectively, with the closest strain <i>B. oligotrophicum</i> S58.
DOI: 10.6084/m9.figshare.22225280.v1
title: Characterization of photosynthetic <i>Bradyrhizobium</i> sp. strain SSBR45 isolated from the root nodules of <i>Aeschynomene indica</i>

description: We isolated a novel strain of <i>Bradyrhizobium</i> sp., SSBR45, from the nodulated roots of <i>Aeschynomene indica</i> and labeled it with <i>Discosoma</i> sp. red fluorescent protein (dsRED) or enhanced green fluorescent protein (eGFP) and determined its draft genomic sequence. The labeled SSBR45 stimulated the growth of <i>A. indica</i> markedly on a nitrogen-free medium, as observed by visualizing the fluorescent root nodules. The nodulated roots also exhibited high acetylene reduction activities. The SSBR45 genome included genes involved in nitrogen fixation, photosynthesis, and type IV secretion system; however, it did not consist of canonical <i>nodABC</i> genes and type III secretion system genes. SSBR45, a novel species of the genus <i>Bradyrhizobium</i>, consisted of an average nucleotide identity and average amino acid identity of 87% and 90%, respectively, with the closest strain <i>B. oligotrophicum</i> S58.
DOI: 10.6084/m9.figshare.22949793
title: Genome-wide analysis of the CDPK gene family and their important roles response to cold stress in white clover

description: Calcium-dependent protein kinases (CDPKs) are an important class of calcium-sensitive response proteins that play an important regulatory role in response to abiotic stresses. To date, little is known about the CDPK genes in white clover. White clover is a high-quality forage grass with high protein content, but it is susceptible to cold stress. Therefore, we performed a genome-wide analysis of the CDPK gene family in white clover and identified 50 members of the CDPK genes. Phylogenetic analysis using CDPKs from the model plant Arabidopsis divided the TrCDPK genes into four groups based on their sequence similarities. Motif analysis showed that TrCDPKs within the same group had similar motif compositions. Gene duplication analysis revealed the evolution and expansion of TrCDPK genes in white clover. Meanwhile, a genetic regulatory network (GRN) containing TrCDPK genes was reconstructed, and gene ontology (GO) annotation analysis of these functional genes showed that they contribute to signal transduction, cellular response to stimuli, and biological regulation, all of which are important processes in response to abiotic stresses. To determine the function of TrCDPK genes, we analyzed the RNA-seq dataset and found that most TrCDPK genes were highly up-regulated under cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiments, implying that TrCDPK genes are involved in various gene regulatory pathways in response to cold stress. Our study may help to further investigate the function of TrCDPK genes and their role in response to cold stress, which is important for understanding the molecular mechanisms of cold tolerance in white clover and improving its cold tolerance.
DOI: 10.6084/m9.figshare.22949793.v1
title: Genome-wide analysis of the CDPK gene family and their important roles response to cold stress in white clover

description: Calcium-dependent protein kinases (CDPKs) are an important class of calcium-sensitive response proteins that play an important regulatory role in response to abiotic stresses. To date, little is known about the CDPK genes in white clover. White clover is a high-quality forage grass with high protein content, but it is susceptible to cold stress. Therefore, we performed a genome-wide analysis of the CDPK gene family in white clover and identified 50 members of the CDPK genes. Phylogenetic analysis using CDPKs from the model plant Arabidopsis divided the TrCDPK genes into four groups based on their sequence similarities. Motif analysis showed that TrCDPKs within the same group had similar motif compositions. Gene duplication analysis revealed the evolution and expansion of TrCDPK genes in white clover. Meanwhile, a genetic regulatory network (GRN) containing TrCDPK genes was reconstructed, and gene ontology (GO) annotation analysis of these functional genes showed that they contribute to signal transduction, cellular response to stimuli, and biological regulation, all of which are important processes in response to abiotic stresses. To determine the function of TrCDPK genes, we analyzed the RNA-seq dataset and found that most TrCDPK genes were highly up-regulated under cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiments, implying that TrCDPK genes are involved in various gene regulatory pathways in response to cold stress. Our study may help to further investigate the function of TrCDPK genes and their role in response to cold stress, which is important for understanding the molecular mechanisms of cold tolerance in white clover and improving its cold tolerance.
DOI: 10.6084/m9.figshare.21804157
title: Comprehensive analysis of complete chloroplast genome sequence of <i>Plantago asiatica</i> L. (Plantaginaceae)

description: <i>Plantago asiatica</i> L. is a representative individual species of Plantaginaceae, whose high reputation is owed to its edible and medicinal values. However, the phylogeny and genes of the <i>P. asiatica</i> chloroplast have not yet been well described. Here we report the findings of a comprehensive analysis of the <i>P. asiatica</i> chloroplast genome. The <i>P. asiatica</i> chloroplast genome is 164,992 bp, circular, and has a GC content of 37.98%. The circular genome contains 141 genes, including 8 rRNAs, 38 tRNAs, and 95 protein-coding genes. Seventy-two simple sequence repeats are detected. Comparative chloroplast genome analysis of six related species suggests that a higher similarity exists in the coding region than the non-coding region, and differences in the degree of preservation is smaller between <i>P. asiatica</i> and <i>Plantago depressa</i> than among others. Our phylogenetic analysis illustrates <i>P. asiatica</i> has a relatively close relationship with <i>P. depressa</i>, which was also divided into different clades with <i>Plantago ovata</i> and <i>Plantago lagopus</i> in the genus <i>Plantago</i>. This analysis of the <i>P. asiatica</i> chloroplast genome contributes to an improved deeply understanding of the evolutionary relationships among Plantaginaceae.
DOI: 10.6084/m9.figshare.21804157.v1
title: Comprehensive analysis of complete chloroplast genome sequence of <i>Plantago asiatica</i> L. (Plantaginaceae)

description: <i>Plantago asiatica</i> L. is a representative individual species of Plantaginaceae, whose high reputation is owed to its edible and medicinal values. However, the phylogeny and genes of the <i>P. asiatica</i> chloroplast have not yet been well described. Here we report the findings of a comprehensive analysis of the <i>P. asiatica</i> chloroplast genome. The <i>P. asiatica</i> chloroplast genome is 164,992 bp, circular, and has a GC content of 37.98%. The circular genome contains 141 genes, including 8 rRNAs, 38 tRNAs, and 95 protein-coding genes. Seventy-two simple sequence repeats are detected. Comparative chloroplast genome analysis of six related species suggests that a higher similarity exists in the coding region than the non-coding region, and differences in the degree of preservation is smaller between <i>P. asiatica</i> and <i>Plantago depressa</i> than among others. Our phylogenetic analysis illustrates <i>P. asiatica</i> has a relatively close relationship with <i>P. depressa</i>, which was also divided into different clades with <i>Plantago ovata</i> and <i>Plantago lagopus</i> in the genus <i>Plantago</i>. This analysis of the <i>P. asiatica</i> chloroplast genome contributes to an improved deeply understanding of the evolutionary relationships among Plantaginaceae.