Genome-wide discovery of G-quadruplex forming sequences and their functional
|
|
|
- Myron Quinn
- 5 years ago
- Views:
Transcription
1 *Correspondence and requests for materials should be addressed to R.G. Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants Rohini Garg*, Jyoti Aggarwal, Bijal Thakkar National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
2 Figure S1. a) Enrichment of transcription factor (TF) binding sites in G3-GQS (G3L1-7, G3L1-3) identified in 1 kb promoters of all plant species as predicted by Athamap, AGRIS and PLACE databases. (b) TF-binding sites identified in Arabidopsis G3-GQS motifs.
3 Figure S2. a) Enrichment of transcription factor (TF) binding sites in G2-GQS (G2L1-4, G2L1-2 and G2Ll) identified in 1 kb promoters of all plant species as predicted by AGRIS, Athamap and PLACE databases. (b) TF-binding sites identified in Arabidopsis G2-GQS motifs.
4 Table S1. Number of GQSes in various genomic features of different plant species. A. thaliana gene mrna exon CDS 3 UTR 5 UTR Promoter Intergenic Intron G2L G2L G2L G3L G3L L. japonicus G2L ND ND G2L ND ND G2L ND ND G3L ND ND G3L ND ND M. truncatula G2L ND ND G2L ND ND G2L ND ND G3L ND ND G3L ND ND B. rapa G2L G2L G2L G3L G3L G. max G2L G2L G2L G3L G3L B.distachyon G2L G2L G2L G3L G3L P. patens G2L G2L G2L G3L G3L P. vulgaris G2L G2L G2L G3L G3L S. italica G2L G2L G2L G3L G3L S. bicolor
5 G2L G2L G2L G3L G3L P. trichocarpa G2L G2L G2L G3L G3L V.vinifera G2L G2L G2L G3L G3L S. moellendorffii G2L G2L G2L G3L G3L C. arietinum G2L G2L G2L G3L G3L O. sativa G2L G2L G2L G3L G3L
6 Table S2. Number of orthologous genes harboring GQSes. Dicots Genic-G2L1-4 Genic-G3L1-7 1 kb_g2l1-4 1 kb_g3l1-7 A. thaliana M. truncatula B. rapa G. max P. vulgaris C. arietinum GQSes in all dicot species 1331 NP NP NP Monocots O. sativa B. distachyon S. italica S. bicolor GQSes in all monocot species NP, Not Present
7 Table S3. List of orthologous genes harboring GQSes within gene body or promoter region in Arabidopsis and rice. This table has been provided as separate file in MS Excel format.
8 Table S4. List of orthologous genes harboring G3-type GQSes within promoter region. Oryza sativa Gene description Setaria italica Sorghum bicolor Brachypodium distachyon RNA-binding S4 domain LOC_Os01g54390 containing protein Si002389m Sobic.003G Bradi2g49727 LOC_Os02g58500 PhospholipaseA2 (PLA2) Si018638m Sobic.004G Bradi3g60710 LOC_Os08g05540 Conserved protein (DMRT homologue) Si014452m Sobic.007G Bradi3g17147
9 Table S5. List of genes harboring GQSes used for validation for G-quadruplex formation along with predicted TF- binding sites. Motifs predicted by STAMP Oligo-id Gene-ID Agris database Athamap database PLACE database Os3 LOC_Os12g10100 E2F (E val: e-03) ANAERO5CONSENSUS (E val: e-07) Os4 LOC_Os01g16610 E2F (E val: e-04) AtMYB84 (E val: e-07) ACIIPVPAL2 (E val: e-13) Os6 LOC_Os07g03770 (E val: e-07) E2Ff_oneSite (E val: e-03) E2FAT (E val: e-06) Os9 LOC_Os06g04190 IDRSZMFER1 (E val: e-06) Os11 LOC_Os02g04430 ABI5 (E val: e-05) ABRETAEM (E val: e-08) Os5 LOC_Os09g13940 ALFIN1 (E val: e-05) AMMORESIIUDCRNIA1 (E val: e-08) Os7 LOC_Os04g05010 GT (E val: e-03) ALFIN1 (E val: e-05) ACIIPVPAL2 (E val: e-06) Os10 LOC_Os04g45990 AtMYB84 (E val: e-07) ACIPVPAL2 (E val: e-09) Os13 LOC_Os02g29890 CTRMCAMV35S (E val: e-07) Os18 LOC_Os09g20620 (E val: e-04) AtMYB84 (E val: e-07) ACIIPVPAL2 (E val: e-08) At3 AT3G05620 E2F (E val: e-10) E2Ff_oneSite (E val: e-10) E2FAT (E val: e-10) At8 AT1G32350 (E val: e-05) E2Fc (E val: e-08) PALBOXAPC (E val: e-07) At12 AT5G06839 MYB1 (E val: e-08) GAMYB (E val: e-05) BOXICHS (E val: e-14) At15 AT2G47500 AtMYB2 (E val: e-09) AtMYB44_twoSite (E val: e-04) MYBATRD22 (E val: e-09) At17 AT5G26940 TGA1 (E val: e-07) bzip911_1 (E val: e-11) REGION1OSOSEM (E val: e-09) Ca1 Ca_05841 (E val: e-04) (E val: e-04) AGTACSAO (E val: e-08) Ca2 Ca_19695 GT (E val: e-07) AtMYB84 (E val: e-08) ACIIPVPAL2 (E val: e-09) Gm1 Glyma20g25530 (E val: e-04) (E val: e-08) O2F2BE2S1 (E val: e-06) Gm2 Glyma05g24940 (E val: e-04) (E val: e-04) AMMORESIIUDCRNIA1 (E val: e-05) Gm4 Glyma09g29900 AtMYB84 (E val: e-05) ACIPVPAL2 (E val: e-09)
10 Table S6. Databases used for downloading genomes of different plant species. Organism name webpages L. japonicus ftp://ftp.kazusa.or.jp/pub/lotus/lotus_r2.5/ M. truncatula P. vulgaris C. arietinum C.arietinum_ICC4958_Draft1.fasta G. max A. thaliana ftp://ftp.arabidopsis.org/home/tair/sequences/whole_chromosomes/ B. rapa S. bicolor S. italica O. sativa MSUv7.0; B. distachyon P. patens S. moellendorffii V. vinifera P. trichocarpa
Supplementary Figure 3
Supplementary Figure 3 7.0 Col Kas-1 Line FTH1A 8.4 F3PII3 8.9 F26H11 ATQ1 T9I22 PLS8 F26B6-B 9.6 F27L4 9.81 F27D4 9.92 9.96 10.12 10.14 10.2 11.1 0.5 Mb T1D16 Col % RGR 83.3 101 227 93.5 75.9 132 90 375
Lineage specific conserved noncoding sequences in plants
Lineage specific conserved noncoding sequences in plants Nilmini Hettiarachchi Department of Genetics, SOKENDAI National Institute of Genetics, Mishima, Japan 20 th June 2014 Conserved Noncoding Sequences
Bioinformatics tools to analyze complex genomes. Yves Van de Peer Ghent University/VIB
Bioinformatics tools to analyze complex genomes Yves Van de Peer Ghent University/VIB Detecting colinearity and large-scale gene duplications A 1 2 3 4 5 6 7 8 9 10 11 Speciation/Duplicatio n S1 S2 1
Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots
Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots Sunita Kumari 1, Doreen Ware 1,2 * 1 Cold Spring Harbor Laboratory, Cold Spring Harbor, New
Identification and characterization of the bzip transcription factor involved in zinc homeostasis in cereals
Identification and characterization of the bzip transcription factor involved in zinc homeostasis in cereals A.R. Henriques, D. da R. Farias and A. Costa de Oliveira Centro de Genômica e Fitomelhoramento,
Agave Genomics in Support
Agave Genomics in Support of CAM Engineering cambiodesign.org Xiaohan Yang Biosciences Division Oak Ridge National Laboratory C4-CAM Conference August 09, 2013 Acknowledgements Oak Ridge National Laboratory
Supplemental Figure 1. Comparison of Tiller Bud Formation between the Wild Type and d27. (A) and (B) Longitudinal sections of shoot apex in wild-type
A B 2 3 3 2 1 1 Supplemental Figure 1. Comparison of Tiller Bud Formation between the Wild Type and d27. (A) and (B) Longitudinal sections of shoot apex in wild-type (A) and d27 (B) seedlings at the four
Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags
Evaluation of Genome Sequencing Quality in Selected Plant Species Using Expressed Sequence Tags Lingfei Shangguan 1, Jian Han 1, Emrul Kayesh 1, Xin Sun 1, Changqing Zhang 2, Tariq Pervaiz 1, Xicheng Wen
Cao, J, K Schneeberger, S Ossowski, et al Whole genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:
Figure S1. Syntenic map of SAE1B duplication. We have used the nucleotide sequences of Arabidopsis thaliana Col-0 gene tandem duplicates AT5G50580 and AT5G506800 as queries in independent BLASTN searches
Supplemental Data. Yang et al. (2012). Plant Cell /tpc
Supplemental Figure 1. Mature flowers of P. heterotricha. (A) An inflorescence of P. heterotricha showing the front view of a zygomorphic flower characterized by two small dorsal petals and only two fertile
Research Article mir156- and mir171-binding Sites in the Protein-Coding Sequences of Several Plant Genes
BioMed Research International Volume, Article ID, pages http://dx.doi.org/.// Research Article mir- and mir-binding Sites in the Protein-oding Sequences of Several Plant Genes Assyl Bari, Saltanat Orazova,
Supplementary Material
Supplementary Material Supplementary Table S1. Genomes available in build 47 Supplementary Table S2. Counts of putative contiguous gene split models in 39 plant reference genomes in build 47 Supplementary
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature13082 Supplementary Table 1. Examination of nectar production in wild-type and atsweet9 flowers. No. of flowers with detectable nectar out of the total observed
The evolution of WRKY transcription factors
Rinerson et al. BMC Plant Biology (2015) 15:66 DOI 10.1186/s12870-015-0456-y RESEARCH ARTICLE Open Access The evolution of WRKY transcription factors Charles I Rinerson 1, Roel C Rabara 1, Prateek Tripathi
Paleo-evolutionary plasticity of plant disease resistance genes
Zhang et al. BMC Genomics 2014, 15:187 RESEARCH ARTICLE Paleo-evolutionary plasticity of plant disease resistance genes Rongzhi Zhang 1,2, Florent Murat 1, Caroline Pont 1, Thierry Langin 1 and Jerome
Supplementary Figure 1. Number of CC- and TIR- type NBS- LRR genes and presence of mir482/2118 on sequenced plant genomes.
Number of CC- NBS and CC- NBS- LRR R- genes Number of TIR- NBS and TIR- NBS- LRR R- genes 0 50 100 150 200 250 0 50 100 150 200 250 300 350 400 450 mir482 and mir2118 Cajanus cajan Glycine max Hevea brasiliensis
Potato Genome Analysis
Potato Genome Analysis Xin Liu Deputy director BGI research 2016.1.21 WCRTC 2016 @ Nanning Reference genome construction???????????????????????????????????????? Sequencing HELL RIEND WELCOME BGI ZHEN LLOFRI
Supplementary Information for: The genome of the extremophile crucifer Thellungiella parvula
Supplementary Information for: The genome of the extremophile crucifer Thellungiella parvula Maheshi Dassanayake 1,9, Dong-Ha Oh 1,9, Jeffrey S. Haas 1,2, Alvaro Hernandez 3, Hyewon Hong 1,4, Shahjahan
Regulatory Change in YABBY-like Transcription Factor Led to Evolution of Extreme Fruit Size during Tomato Domestication
SUPPORTING ONLINE MATERIALS Regulatory Change in YABBY-like Transcription Factor Led to Evolution of Extreme Fruit Size during Tomato Domestication Bin Cong, Luz Barrero, & Steven Tanksley 1 SUPPORTING
SUPPLEMENTARY INFORMATION
doi:1.138/nature111 cytosol Model: PILS function in cellular auxin homeostasis ER nucleus IAA degradation? sequestration? conjugation? storage? signalling? PILS IAA ER cytosol Supplemental Figure 1 Model
AtTIL-P91V. AtTIL-P92V. AtTIL-P95V. AtTIL-P98V YFP-HPR
Online Resource 1. Primers used to generate constructs AtTIL-P91V, AtTIL-P92V, AtTIL-P95V and AtTIL-P98V and YFP(HPR) using overlapping PCR. pentr/d- TOPO-AtTIL was used as template to generate the constructs
Genome-wide Identification of Lineage Specific Genes in Arabidopsis, Oryza and Populus
Genome-wide Identification of Lineage Specific Genes in Arabidopsis, Oryza and Populus Xiaohan Yang Sara Jawdy Timothy Tschaplinski Gerald Tuskan Environmental Sciences Division Oak Ridge National Laboratory
GENOME DUPLICATION AND GENE ANNOTATION: AN EXAMPLE FOR A REFERENCE PLANT SPECIES.
GENOME DUPLICATION AND GENE ANNOTATION: AN EXAMPLE FOR A REFERENCE PLANT SPECIES. Alessandra Vigilante, Mara Sangiovanni, Chiara Colantuono, Luigi Frusciante and Maria Luisa Chiusano Dept. of Soil, Plant,
Host_microbe_PPI - R package to analyse intra-species and interspecies protein-protein interactions in the model plant Arabidopsis thaliana
Host_microbe_PPI - R package to analyse intra-species and interspecies protein-protein interactions in the model plant Arabidopsis thaliana Thomas Nussbaumer 1,2 1 Institute of Network Biology (INET),
Stage 1: Karyotype Stage 2: Gene content & order Step 3
Supplementary Figure Method used for ancestral genome reconstruction. MRCA (Most Recent Common Ancestor), AMK (Ancestral Monocot Karyotype), AEK (Ancestral Eudicot Karyotype), AGK (Ancestral Grass Karyotype)
Supplemental Table 1. Primers used for cloning and PCR amplification in this study
Supplemental Table 1. Primers used for cloning and PCR amplification in this study Target Gene Primer sequence NATA1 (At2g393) forward GGG GAC AAG TTT GTA CAA AAA AGC AGG CTT CAT GGC GCC TCC AAC CGC AGC
Impact of recurrent gene duplication on adaptation of plant genomes
Fischer et al. BMC Plant Biology 2014, 14:151 RESEARCH ARTICLE Open Access Impact of recurrent gene duplication on adaptation of plant genomes Iris Fischer 1,2*, Jacques Dainat 3,6, Vincent Ranwez 3, Sylvain
Supplemental Figure 1. Comparisons of GC3 distribution computed with raw EST data, bi-beta fits and complete genome sequences for 6 species.
Supplemental Figure 1. Comparisons of GC3 distribution computed with raw EST data, bi-beta fits and complete genome sequences for 6 species. Filled distributions: GC3 computed with raw EST data. Dashed
Motifs and Logos. Six Introduction to Bioinformatics. Importance and Abundance of Motifs. Getting the CDS. From DNA to Protein 6.1.
Motifs and Logos Six Discovering Genomics, Proteomics, and Bioinformatics by A. Malcolm Campbell and Laurie J. Heyer Chapter 2 Genome Sequence Acquisition and Analysis Sami Khuri Department of Computer
SoyBase, the USDA-ARS Soybean Genetics and Genomics Database
SoyBase, the USDA-ARS Soybean Genetics and Genomics Database David Grant Victoria Carollo Blake Steven B. Cannon Kevin Feeley Rex T. Nelson Nathan Weeks SoyBase Site Map and Navigation Video Tutorials:
Research Article Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon
Comparative and Functional Genomics Volume, Article ID, pages doi:.// Research Article Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon Shenglong Tan,
New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics
Hu et al. BMC Plant Biology (2018) 18:270 https://doi.org/10.1186/s12870-018-1495-y RESEARCH ARTICLE Open Access New insights into the evolution and functional divergence of the SWEET family in Saccharum
training workshop 2015
TransPLANT user training workshop 2015 Slides: http://tinyurl.com/transplant2015 Workshop on variation data EMBL-EBI Hinxton-UK 2nd July 2015 Ensembl Genomes Team Notes: This workshop is based on Ensembl
Genome-wide analysis of the MYB transcription factor superfamily in soybean
Du et al. BMC Plant Biology 2012, 12:106 RESEARCH ARTICLE Open Access Genome-wide analysis of the MYB transcription factor superfamily in soybean Hai Du 1,2,3, Si-Si Yang 1,2, Zhe Liang 4, Bo-Run Feng
Intro Gene regulation Synteny The End. Today. Gene regulation Synteny Good bye!
Today Gene regulation Synteny Good bye! Gene regulation What governs gene transcription? Genes active under different circumstances. Gene regulation What governs gene transcription? Genes active under
Nature Genetics: doi: /ng Supplementary Figure 1. ssp mutant phenotypes in a functional SP background.
Supplementary Figure 1 ssp mutant phenotypes in a functional SP background. (a,b) Statistical comparisons of primary and sympodial shoot flowering times as determined by mean values for leaf number on
USDA-DOE Plant Feedstock Genomics for Bioenergy
USDA-DOE Plant Feedstock Genomics for Bioenergy BERAC Thursday, June 7, 2012 Cathy Ronning, DOE-BER Ed Kaleikau, USDA-NIFA Plant Feedstock Genomics for Bioenergy Joint competitive grants program initiated
SUPPLEMENTARY INFORMATION
doi:1.138/nature11394 Supplementary Note Our study is based on two different tracriptome indices. Both combine tracriptional information with an important evolutionary parameter. For the tracriptome age
Quantitative Measurement of Genome-wide Protein Domain Co-occurrence of Transcription Factors
Quantitative Measurement of Genome-wide Protein Domain Co-occurrence of Transcription Factors Arli Parikesit, Peter F. Stadler, Sonja J. Prohaska Bioinformatics Group Institute of Computer Science University
Swati Puranik, Pranav Pankaj Sahu, Sambhu Nath Mandal, Venkata Suresh B., Swarup Kumar Parida, Manoj Prasad*
Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.) Swati Puranik, Pranav Pankaj Sahu, Sambhu Nath
Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum
Zhang et al. BMC Genomics (2016) 17:88 DOI 10.1186/s12864-016-2419-6 RESEARCH ARTICLE Open Access Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum
Research Article Identification of Immune Related LRR-Containing Genes in Maize (Zea mays L.) by Genome-Wide Sequence Analysis
International Journal of Genomics Volume 2015, Article ID 231358, 11 pages http://dx.doi.org/10.1155/2015/231358 Research Article Identification of Immune Related -Containing Genes in Maize (Zea mays L.)
PLNT2530 (2018) Unit 5 Genomes: Organization and Comparisons
PLNT2530 (2018) Unit 5 Genomes: Organization and Comparisons Unless otherwise cited or referenced, all content of this presenataion is licensed under the Creative Commons License Attribution Share-Alike
Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift
Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift Zhihua Hua 1, Cheng Zou 2, Shin-Han Shiu 2, Richard
Supplementary Information
Supplementary Information Rice APC/C TE controls tillering through mediating the degradation of MONOCULM 1 Qibing Lin 1*, Dan Wang 1*, Hui Dong 2*, Suhai Gu 1, Zhijun Cheng 1, Jie Gong 2, Ruizhen Qin 1,
Предсказание и анализ промотерных последовательностей. Татьяна Татаринова
Предсказание и анализ промотерных последовательностей Татьяна Татаринова Eukaryotic Transcription 2 Initiation Promoter: the DNA sequence that initially binds the RNA polymerase The structure of promoter-polymerase
In-silico identification and phylogenetic analysis of auxin efflux carrier gene family in Setaria italica L.
Vol. 13(2), pp. 211-225, 8 January, 2014 DOI: 10.5897/AJB2014.13617 ISSN 1684-5315 2014 Academic Journals http://www.academicjournals.org/ajb African Journal of Biotechnology Full Length Research Paper
Genome-wide analysis of nucleotide-binding site disease resistance genes in Medicago truncatula
Chin. Sci. Bull. (2014) 59(11):1129 1138 DOI 10.1007/s11434-014-0155-3 Article csb.scichina.com www.springer.com/scp Bioinformatics Genome-wide analysis of nucleotide-binding site disease resistance genes
Mathangi Thiagarajan Rice Genome Annotation Workshop May 23rd, 2007
-2 Transcript Alignment Assembly and Automated Gene Structure Improvements Using PASA-2 Mathangi Thiagarajan mathangi@jcvi.org Rice Genome Annotation Workshop May 23rd, 2007 About PASA PASA is an open
Systematic comparison of lncrnas with protein coding mrnas in population expression and their response to environmental change
Xu et al. BMC Plant Biology (2017) 17:42 DOI 10.1186/s12870-017-0984-8 RESEARCH ARTICLE Open Access Systematic comparison of lncrnas with protein coding mrnas in population expression and their response
Supplemental Data. Perea-Resa et al. Plant Cell. (2012) /tpc
Supplemental Data. Perea-Resa et al. Plant Cell. (22)..5/tpc.2.3697 Sm Sm2 Supplemental Figure. Sequence alignment of Arabidopsis LSM proteins. Alignment of the eleven Arabidopsis LSM proteins. Sm and
Biology. Biology. Slide 1 of 26. End Show. Copyright Pearson Prentice Hall
Biology Biology 1 of 26 Fruit fly chromosome 12-5 Gene Regulation Mouse chromosomes Fruit fly embryo Mouse embryo Adult fruit fly Adult mouse 2 of 26 Gene Regulation: An Example Gene Regulation: An Example
Boyce Thompson Institute
Joyce Van Eck (BTI) Plant Biotechnology and Translational Research Boyce Thompson Institute Mission: To advance and communicate scientific knowledge in plant biology to improve agriculture, protect the
microrna Studies Chen-Hanson Ting SVFIG June 23, 2018
microrna Studies Chen-Hanson Ting SVFIG June 23, 2018 Summary MicroRNA (mirna) Species and organisms studied mirna in mitocondria Huge genome files mirna in human Chromosome 1 mirna in bacteria Tools used
Supplemental Data. Hou et al. (2016). Plant Cell /tpc
Supplemental Data. Hou et al. (216). Plant Cell 1.115/tpc.16.295 A Distance to 1 st nt of start codon Distance to 1 st nt of stop codon B Normalized PARE abundance 8 14 nt 17 nt Frame1 Arabidopsis inflorescence
SUPPLEMENTARY INFORMATION
reverse 3175 3175 F L C 318 318 3185 3185 319 319 3195 3195 315 8 1 315 3155 315 317 Supplementary Figure 3. Stability of expression of the GFP sensor constructs return to warm conditions. Semi-quantitative
biology Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana
Biology 2013, 2, 1465-1487; doi:10.3390/biology2041465 Article OPEN ACCESS biology ISSN 2079-7737 www.mdpi.com/journal/biology Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs
Browsing Genomic Information with Ensembl Plants
Browsing Genomic Information with Ensembl Plants Etienne de Villiers, PhD (Adapted from slides by Bert Overduin EMBL-EBI) Outline of workshop Brief introduction to Ensembl Plants History Content Tutorial
Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/ Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice W
The Plant Cell, Vol. 19: 2329 2348, August 2007, www.plantcell.org ª 2007 American Society of Plant Biologists RESEARCH ARTICLES Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/ Tramtrack/Broad
Variation, Evolution, and Correlation Analysis of C+G Content and Genome or Chromosome Size in Different Kingdoms and Phyla
Variation, Evolution, and Correlation Analysis of C+G Content and Genome or Chromosome Size in Different Kingdoms and Phyla Xiu-Qing Li 1 *, Donglei Du 2 1 Molecular Genetics Laboratory, Potato Research
Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants
Liu et al. BMC Evolutionary Biology (2017) 17:47 DOI 10.1186/s12862-017-0891-5 RESEARCH ARTICLE Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants
Annotation of Plant Genomes using RNA-seq. Matteo Pellegrini (UCLA) In collaboration with Sabeeha Merchant (UCLA)
Annotation of Plant Genomes using RNA-seq Matteo Pellegrini (UCLA) In collaboration with Sabeeha Merchant (UCLA) inuscu1-35bp 5 _ 0 _ 5 _ What is Annotation inuscu2-75bp luscu1-75bp 0 _ 5 _ Reconstruction
The Eukaryotic Genome and Its Expression. The Eukaryotic Genome and Its Expression. A. The Eukaryotic Genome. Lecture Series 11
The Eukaryotic Genome and Its Expression Lecture Series 11 The Eukaryotic Genome and Its Expression A. The Eukaryotic Genome B. Repetitive Sequences (rem: teleomeres) C. The Structures of Protein-Coding
Regulation of Transcription in Eukaryotes. Nelson Saibo
Regulation of Transcription in Eukaryotes Nelson Saibo saibo@itqb.unl.pt In eukaryotes gene expression is regulated at different levels 1 - Transcription 2 Post-transcriptional modifications 3 RNA transport
. Supplementary Information
. Supplementary Information Supplementary Figure S1. Mature embryo sac observations. Supplementary Figure S2. STT observations. Supplementary Figure S3. Comparison of the PTB1 cdna with that of the mutant.
Procedure to Create NCBI KOGS
Procedure to Create NCBI KOGS full details in: Tatusov et al (2003) BMC Bioinformatics 4:41. 1. Detect and mask typical repetitive domains Reason: masking prevents spurious lumping of non-orthologs based
How much non-coding DNA do eukaryotes require?
How much non-coding DNA do eukaryotes require? Andrei Zinovyev UMR U900 Computational Systems Biology of Cancer Institute Curie/INSERM/Ecole de Mine Paritech Dr. Sebastian Ahnert Dr. Thomas Fink Bioinformatics
,(CL806925),(CL ),(CL829057),(CL ),(CL862603) BAC45136 putative nucleotide-binding
Additional Data File 13. List of 83 disease resistance-related genes that matched the unmapped BESs of On, Or, and Og. BESs that had internal stop codons within the aligned regions are presented in parentheses.
L3.1: Circuits: Introduction to Transcription Networks. Cellular Design Principles Prof. Jenna Rickus
L3.1: Circuits: Introduction to Transcription Networks Cellular Design Principles Prof. Jenna Rickus In this lecture Cognitive problem of the Cell Introduce transcription networks Key processing network
Comparative Genomic Analysis of Soybean Flowering Genes
Comparative Genomic Analysis of Soybean Flowering Genes Chol-Hee Jung, Chui E. Wong, Mohan B. Singh, Prem L. Bhalla* Plant Molecular Biology and Biotechnology Laboratory, ARC Centre of Excellence for Integrative
Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa
RESEARCH ARTICLE Open Access Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa Ruibo Hu 1, Guang Qi 1, Yingzhen Kong 1,2, Dejing Kong 1, Qian Gao 1, Gongke Zhou
10-810: Advanced Algorithms and Models for Computational Biology. microrna and Whole Genome Comparison
10-810: Advanced Algorithms and Models for Computational Biology microrna and Whole Genome Comparison Central Dogma: 90s Transcription factors DNA transcription mrna translation Proteins Central Dogma:
Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-regulatory Modules
Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-regulatory Modules Filichkin SA, Breton G, Priest HD, Dharmawardhana P, Jaiswal P, et al.
Grundlagen der Bioinformatik Summer semester Lecturer: Prof. Daniel Huson
Grundlagen der Bioinformatik, SS 10, D. Huson, April 12, 2010 1 1 Introduction Grundlagen der Bioinformatik Summer semester 2010 Lecturer: Prof. Daniel Huson Office hours: Thursdays 17-18h (Sand 14, C310a)
Characterization of the rice NLA family reveals a key role for OsNLA1 in phosphate homeostasis
Yang et al. Rice (2017) 10:52 DOI 10.1186/s12284-017-0193-y SHORT COMMUNICATION Open Access Characterization of the rice NLA family reveals a key role for OsNLA1 in phosphate homeostasis Jian Yang 1, Lan
Development 143: doi: /dev : Supplementary information
Supplementary Materials and Methods Plant materials The mutants and transgenic plants used in the present study were as follows: E361 (from Alex Webb s laboratory); tmm-1, ptmm::tmm-gfp and flp-1 (from
Computational Structural Bioinformatics
Computational Structural Bioinformatics ECS129 Instructor: Patrice Koehl http://koehllab.genomecenter.ucdavis.edu/teaching/ecs129 koehl@cs.ucdavis.edu Learning curve Math / CS Biology/ Chemistry Pre-requisite
SUPPLEMENTAL INFORMATION
SUPPLEMENTAL INFORMATION Identification and validation of circrnas Ribo-minus RNA-seq data sets used in identification of circrnas in Oryza sativa and Arabidopsis thaliana were downloaded from NCBI (https://www.ncbi.nlm.nih.gov/).
Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha
Sharma et al. BMC Genomics 2013, 14:915 RESEARCH ARTICLE Open Access Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha Niharika
A Systems Approach to Cellulose Synthesis. Staffan Persson MPI-MP, Potsdam
A Systems Approach to Cellulose Synthesis Staffan Persson MPI-MP, Potsdam The Cell Wall: A Complex Compartment Inference of gene function from other species difficult Economically important ~500-2000 gene
Accepted Article. Received Date : 19-Oct Accepted Date : 25-Jan-2017
Received Date : 19-Oct-2016 Accepted Date : 25-Jan-2017 Article type : Original Article Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules Colin Ruprecht 1,
SUPPLEMENTARY MATERIAL SUPPLEMENTARY TABLES
SUPPLEMENTARY MATERIAL SUPPLEMENTARY TABLES Supplementary Table 1. Genomes available in Gramene build 38 Supplementary Table 2. Ontology associations in Gramene build 38 Supplementary Table 3. Synteny
Prospecting for Green Revolution Genes
Learning Objectives: Prospecting for Green Revolution Genes 1) Discover how changes in individual genes produce phenotypic change 2) Learn to apply bioinformatics tools to identify groups of related genes
Research Article The WRKY Transcription Factor Genes in Lotus japonicus
International Journal of Genomics Volume 14, Article ID 418, 15 pages http://dx.doi.org/1.1155/14/418 Research Article The WRKY Transcription Factor Genes in Lotus japonicus Hui Song, 1 Pengfei Wang, Zhibiao
Comparative Features of Multicellular Eukaryotic Genomes
Comparative Features of Multicellular Eukaryotic Genomes C elegans A thaliana O. Sativa D. melanogaster M. musculus H. sapiens Size (Mb) 97 115 389 120 2500 2900 # Genes 18,425 25,498 37,544 13,601 30,000
GCD3033:Cell Biology. Transcription
Transcription Transcription: DNA to RNA A) production of complementary strand of DNA B) RNA types C) transcription start/stop signals D) Initiation of eukaryotic gene expression E) transcription factors
SUPPLEMENTARY INFORMATION
doi:10.1038/nature23897 Supplementary Notes 1 Evolution of gene families 1.1 Evolution of gene family sizes We determined the expansion and contraction of orthologous gene families using CAFÉ 2.2 1. One
Journal of Integrative Agriculture 2017, 16(5): Available online at ScienceDirect
Journal of Integrative Agriculture 2017, 16(5): 60345-7 Available online at www.sciencedirect.com ScienceDirect RESEARCH ARTICLE Characterization and expression analysis of a novel RING-HC gene, ZmRHCP1,
South Green Bioinformatics activities at CIRAD
South Green Bioinformatics activities at CIRAD Data Integration Team of the research unit DAP Manuel Ruiz, CIP, Lima, 23rd january The Joint Research Unit DAP (Développement et Amélioration des Plantes
Non-host resistance to wheat stem rust in Brachypodium species
Non-host resistance to wheat stem rust in Brachypodium species Dr. Melania Figueroa Assistant Professor Department of Plant Pathology and Stakman-Borlaug Center for Sustainable Plant Health University
Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants
Mohanta et al. BMC Genomics (2015) 16:58 DOI 10.1186/s12864-015-1244-7 RESEARCH ARTICLE Open Access Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel
Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites
Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites Paper by: James P. Balhoff and Gregory A. Wray Presentation by: Stephanie Lucas Reviewed
Transcription Regulation and Gene Expression in Eukaryotes FS08 Pharmacenter/Biocenter Auditorium 1 Wednesdays 16h15-18h00.
Transcription Regulation and Gene Expression in Eukaryotes FS08 Pharmacenter/Biocenter Auditorium 1 Wednesdays 16h15-18h00. Promoters and Enhancers Systematic discovery of transcriptional regulatory motifs
AUXIN CONJUGATE HYDROLYSIS DURING PLANT-MICROBE INTERACTION AND EVOLUTION
AUXIN CONJUGATE HYDROLYSIS DURING PLANT-MICROBE INTERACTION AND EVOLUTION J. Ludwig-Müller 1, A. Schuller 1, A.F. Olajide 2, V. Bakllamaja 2, J.J. Campanella 2 ABSTRACT Plants regulate auxin balance through
Proteomics. 2 nd semester, Department of Biotechnology and Bioinformatics Laboratory of Nano-Biotechnology and Artificial Bioengineering
Proteomics 2 nd semester, 2013 1 Text book Principles of Proteomics by R. M. Twyman, BIOS Scientific Publications Other Reference books 1) Proteomics by C. David O Connor and B. David Hames, Scion Publishing
Protein Coding Regions of Eukaryotes
Analyses of Highly Conserved Nucleotide Sequences within Protein Coding Regions of Eukaryotes Rumiko Suzuki Department of Genetics School of life science The Graduate University for Advanced Studies 2010
Miloš Duchoslav and Lukáš Fischer *
Duchoslav and Fischer BMC Plant Biology (2015) 15:133 DOI 10.1186/s12870-015-0523-4 RESEARCH ARTICLE Open Access Parallel subfunctionalisation of PsbO protein isoforms in angiosperms revealed by phylogenetic
The Plant Cell, November. 2017, American Society of Plant Biologists. All rights reserved
The Genetics of Floral Development Teaching Guide Overview The development of flowers in angiosperm plants provided a critical evolutionary advantage, allowing more options for pollen dispersal and seed
RNA Processing: Eukaryotic mrnas
RNA Processing: Eukaryotic mrnas Eukaryotic mrnas have three main parts (Figure 13.8): 5! untranslated region (5! UTR), varies in length. The coding sequence specifies the amino acid sequence of the protein
Identification and characterization of two wheat Glycogen Synthase Kinase 3/ SHAGGY-like kinases
Bittner et al. BMC Plant Biology 2013, 13:64 RESEARCH ARTICLE Open Access Identification and characterization of two wheat Glycogen Synthase Kinase 3/ SHAGGY-like kinases Thomas Bittner 1, Sarah Campagne