Project description:This is a kinetic model of the monomeric photosystem II (PSII). The model is partially based on the earlier model used for simulation of the flash-induced period-four damped oscillation of oxygen evolution and chlorophyll fluorescence (Jablonsky J and Lazar D (2008) Biophys J, 94: 2725-2736 pubmedID: 18178650 ). For short description of reactions and initial concentrations, see the notes in the model file. For explanation of the value of the rate constants, see: Lazar D (2003) J. theor. Biol. 220:469-503 pubmedID: 12623282 ; Jablonsky J and Lazar D, 2008 Biophys J, 94: 2725-2736 pubmedID: 18178650 and Jablonsky, Susila and Lazar, 2008, DOI: 10.1093/bioinformatics/btn530 pubmedID: 18845578 ). The oxygen signal in the model is defined as a maximum of the sum of concentrations of the model forms in the iS3Yp-state (handled in MATLAB). This version of model cannot be used for simulation of the chlorophyll fluorescence because for simplicity the reactions behind the loss of excited state are not considered. The meaning of the particular letters in the model is as follows: P – P680 (special chlorophyll pair), H – pheophytin, A – QA (the first quinone electron acceptor), B – QB (the second quinone electron acceptor), PQ – oxidized plastoquinone molecules in the PQ pool, PQH – reduced and protonated PQ molecules in the PQ pool, Y/Yp – reduced/oxidized state of tyrosine 161-D1, YD/YDox – reduced/oxidized state of tyrosine 160-D2, Sn (n = 0, 1, 2, 3) – the S-states of oxygen evolving complex (OEC), iSn (n = 0, 1, 2, 3) – the intermediate S-states of OEC. All reactions describing electron transport through PSII entered into the model are assumed to be first order reactions with respect to one reactant and are defined as mass action reactions. This approach enables to consider D1-Y161 (YZ) and oxygen evolving complex (OEC) as the integral parts of the PSII, in contrary of the multi-units PSII model (Jablonsky and Lazar, 2008, Biophys J, 94: 2725-2736 pubmedID: 18178650 ) or model of dimeric PSII (Jablonsky, Susila and Lazar, 2008, DOI: 10.1093/bioinformatics/btn530). initial conditions: S1=100%, YDox=89% PHABm = 0.25 PHAB = 0.75 list of reactions: R1-R144 ... excitation R145- R180... charge separation_open R181- R216... charge separation_closed R217-R324 ... charge stabilisation R325-R360 ... recombination PpHm (P680+pheophytin-) R361-R396... recombination PpAm (P680+QA-) R397-R399 ... recombination S2Am (S2-state of OEC and QA-) R400-R471 ... electron transfer from QA to QB R472-R543 ... electron transfer from QA to QB- R544-R687 ... exchange of double reduced QB by free plastoquinone molecule from the PQ pool R688 ... Ox/red PQ and PQH R689-R700 ... reduction of Pp by Yz in S0 R701-R712 ... reduction of Pp by Yz in S1 R713-R724 ... reduction of Pp by Yz in S2 R725-R736 ... reduction of Pp by Yz in S3 R737-R784 ... formation of the intermediated S-states iS0,1,2, 3 R785-R832 ... electron donation from OEC to YZox during the S0->S1, S1->S2, S2->S3, S3->S0 transitions (Kok cycle) R833-R850 ... YD oxidation by S3/S2 state of OEC; YDox reduction by S0 state of OEC This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 99, 391, 74, and 543 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_C vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a bicolor leaf kale. DEGs related to anthocyanin biosynthesis, chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by anthocyanin biosynthesis, chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for bicolor leaf in ornamental kale and other plants.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of leaf color at different development stages. The goals of this study are to compare chlorophyll metabolism and chloroplast organization transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: leaf mRNA profiles of 12 RNA sequencing libraries (S1, S2, S3_S, and S3_C) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000 system. After removing reads of low quality, those that remained were mapped to the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) using the HISAT package, allowing for a maximum of two mismatches and multiple alignments per read (up to 20 by default). qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 571.74 million sequence reads per sample to the the reference genome (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/) and identified 1028, 4323, 428, and 1033 DEGs were detected in pairwise comparison (S2 vs. S1, S3_S vs. S2, S3_S vs. S2, and S3_S vs. S3_C, respectively). The DEGs were associated with ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘porphyrin and chlorophyll metabolism’ and other pathways in the Kyoto Encyclopedia of Genes and Genomes database; DEGs related to chloroplast organization were identified in the Gene Ontology analysis. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular basis for leaf variegation in ornamental kale and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of a variegated leaf kale. DEGs related to chlorophyll metabolism and chloroplast organization were detected. These results demonstrate that leaf color at different stages of development is influenced by chloroplast and pigment metabolism, providing a foundation for investigating the molecular basis for leaf variegation in ornamental kale and other plants.

Project description:This is a kinetic model of the dimeric photosystem II (PSII). The model has partially based on the earlier model used for simulation of the flash-induced period-four damped oscillation of oxygen evolution and chlorophyll fluorescence (Jablonsky J and Lazar D (2008) Biophys J, 94: 2725-2736 pubmedID: 18178650 ). For short description of reactions and initial concentrations, see the notes in the model file. For explanation of the value of the rate constants, see: Lazar D (2003) J. theor. Biol. 220:469-503 pubmedID: 12623282 ; Jablonsky J and Lazar D, 2008 Biophys J, 94: 2725-2736 pubmedID: 18178650 and Jablonsky, Susila and Lazar, 2008, DOI: 10.1093/bioinformatics/btn530 pubmedID: 18845578 ). In this model the hypothetic cooperation in the water splitting is considered as the cross-backward-oxidation of the P680 (in the PSII which is already in the S2-state) by [YZoxS1] (in the PSII in which the S1-S2 transition is not finished). The cooperation (between compartment1 = 1st PSII and compartment2 = 2nd PSII) is the best explanation of the second turnover of PSII induced by short flashes which is available now. We concluded that the double turnover of the PSII induced by short flashes is caused either by the cooperation in the water splitting or our knowledge of the main pathway of the electron transport through the PSII is incomplete and besides D1-Y161, other cofactor which enables oxidation of the special chlorophyll pair (P680), e.g., L-Y34, must be considered. The oxygen signal in the model is defined as a maximum of the sum of concentrations of the model forms in the iS3Yp-state (handled in MATLAB). This version of model cannot be used for simulation of the chlorophyll fluorescence because for simplicity the reactions behind the loss of excited state are not considered. The meaning of the particular letters in the model is as follows: P – P680 (special chlorophyll pair), H – pheophytin, A – QA (the first quinone electron acceptor), B – QB (the second quinone electron acceptor), PQ – oxidized plastoquinone molecules in the PQ pool, PQH – reduced and protonated PQ molecules in the PQ pool, Y/Yp – reduced/oxidized state of tyrosine 161-D1, YD/YDox – reduced/oxidized state of tyrosine 160-D2, Sn (n = 0, 1, 2, 3) – the S-states of oxygen evolving complex (OEC), iSn (n = 0, 1, 2, 3) – the intermediate S-states of OEC. All reactions describing electron transport through PSII entered into the model are assumed to be first order reactions with respect to one reactant and are defined as mass action reactions. Cooperation between photosystem II within dimer in the water splitting is described by the second order kinetics. This approach shows that the second order kinetics used for description of oxidation of the tyrosine D1-Y161 in the multi-units PSII model can be in this case justified. two compartments => two photosystems II connected by cooperation in the water splitting initial conditions: S1=100%, YDox=89% PHABm = 0.25 PHAB = 0.75 list of reactions (compartments 1 and 2): R1-R144 ... excitation R145- R180... charge separation_open R181- R216... charge separation_closed R217-R324 ... charge stabilisation R325-R360 ... recombination PpHm (P680+pheophytin-) R361-R396... recombination PpAm (P680+QA-) R397-R399 ... recombination S2Am (S2-state of OEC and QA-) R400-R471 ... electron transfer from QA to QB R472-R543 ... electron transfer from QA to QB- R544-R687 ... exchange of double reduced QB by free plastoquinone molecule from the PQ pool R688 ... Ox/red PQ and PQH R689-R700 ... reduction of Pp by Yz in S0 R701-R712 ... reduction of Pp by Yz in S1 R713-R724 ... reduction of Pp by Yz in S2 R725-R736 ... reduction of Pp by Yz in S3 R737-R784 ... formation of the intermediated S-states iS0,1,2, 3 R785-R832 ... electron donation from OEC to YZox during the S0->S1, S1->S2, S2->S3, S3->S0 transitions (Kok cycle) R833-R850 ... YD oxidation by S3/S2 state of OEC; YDox reduction by S0 state of OEC R1701-R1750 ... cooperation between 1st and 2nd PSII This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Project description:To facilitate the functional annotation of the pepper genome, we generated 90.84 Gb of RNA-Seq data from 33 libraries representing all major tissue types and developmental stages of Zunla 1, as well as fruits from other accessions with significant phenotypic differences. Pepper ‘Zunla 1’ and other inbred lines were grown in a greenhouse as described in Table S1, with their different developmental stages Plants at full-bloom stage were harvested for roots, stems, and leaves as the same as the samples for phased small RNAs (see text S3.4.2 for details). Mature plants were harvested for unopened flower buds (buds) and fully open flowers (flowers). Additional flowers were allowed to self-pollinate and fruit was harvested at four pre-breaker stages (1-3cm, 3-4cm, 4-5cm fruit length, and mature green), the breaker stage (when the fruit was turning red) and three post-breaker stages (3, 5, and 7 days after breaker). These samples will respectively be referred to as Root, Stem, Leaf, Bud, Flower, F-Dev-1, F-Dev-2, F-Dev-3, F-Dev-4, F-Dev-5, F-Dev-6, F-Dev-7, F-Dev-8, and F-Dev-9. Similar roots, stems, leaves, immature fruit and red fruit were harvested from other inbred lines from domesticated Capsicum species. Meanwhile, chiltepin plants were grown under long days at controlled temperature and RNA was extracted from a mix of leaves from four stages (seedling, early blooming, full bloom, and fruit breaker phases), a mix of flowers from unopened flower buds (buds) and fully open flowers (flowers), and fruit at breaker and breaker plus five days respectively. All tissues were frozen in liquid nitrogen and then stored at -80℃. Total RNA was isolated from different samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions. Strand-specific RNA-Seq library preparations were performed as previously described (39) with 12 independently bar-coded samples sequenced on one lane of an Illumina HiSeq2000 system. The 200 bp paired-end libraries were sequenced using Illumina HiSeq 2000 (90 bp PE).

			Action	DRS
	SRR22222660.fastq.gz	Fastqsanger.gz
	SRR22222661_1.fastq.gz	Fastqsanger.gz
	SRR22222661_2.fastq.gz	Fastqsanger.gz
	SRR22222662_1.fastq.gz	Fastqsanger.gz
	SRR22222662_2.fastq.gz	Fastqsanger.gz

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