Supplemental Figure 1S. Alignment and phylogeny of CRY proteins. Comparison of the amino acid sequences of the DNA-photolyase domain (a) and FAD binding.

Slides:

Advertisements

Similar presentations

Class I-A Class II-A Class II-B Class II- Basal Class I-B Class I Class II 0.1 Arabidopsis thaliana PHO1;H2 Capsella rubella PHO1;H Thellungiella.

Advertisements

Supplementary figure S3. Diagram showing the effects of removing data from particular organ types on the relative percentage of gene pairs showing reciprocal.

PAG 2015 Justin Preece Jaiswal Lab, Oregon State University 13 January 2015.

Protein Structure Investigating DFR specificity in anthocyanin biosynthesis Fazeeda Hosein Sarasvati BahadurSingh Nigel Jalsa Cecilia Diaz David Gopaulchan.

Practice retrieving data and running stand alone BLAST. Step 1. Identify genes in the ABA biosynthesis pathway from the Arabidopsis Cyc database

Chloroplast DNA in Molecular Systematics. -organelle found in plant cells and eukaryotic algae -Photosynthesis Chloroplast.

Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.

DAY 1c: Accessing Completed Genomes 1. UCSC Genome Bioinformatics 2. Ensembl 3. NCBI Genomic Biology.

Gene Prediction and Phylogenetic Trees

Glycopeptide MS/MS Spectra Supplemental Data 2. gi| Vacuolar invertase 1 [Gossypium hirsutum] R.LFLFNNASGVNVK.A + Deamidated (NQ)

Figure S1. Effects of AVG, DIECA, DPI, NMMA, STA, and OKA on IbRPK expression in sweet potato (Ipomoea batatas cv. Tainung 57). Leaves with petiole cuts.

MVKFLFSVIILFFLLSAVGSSARNIEEDGVIRLPSEVKDFINGKNIDDDSVGGTRWAVLI 60 AGSSGYWNYRHQADVCHAYQVLKRGGVKDENIVVFMYDDIALNEENPRPGVIINHPKGED 120 VYAGVPKDYTGRDVTAHNFYSVLLGNKTAVKGGSGKVIDSGPNDHIFIYYSDHGGPGVLG.

Calculating branch lengths from distances. ABC A B C----- a b c.

PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1 PfDGAT1-2 AtDGAT1 RcDGAT1 PfDGAT1-1.

Cluster I. Cluster II Cluster III (contiued) Cluster IV.

Prospecting for Genes that Fueled the Green Revolution

Figure S1 Evolutionary relationships of RBG subclasses in Arabidopsis (a) and B. rapa (b). Optimal neighbor-joining trees with sum of branch lengths =

Fig. S1. Amino acid sequence alignment of MYBS3 proteins. MYBS3 protein sequences of Arabidopsis thaliana (MYBH; NP_199550); (At3g16350; NP_188256), Glycine.

LATE BLIGHT RESISTANCE PROTEIN RPI-BLB26 6 NBS-LRR RESISTANCE PROTEIN-LIKE PROTEIN6 LATE BLIGHT RESISTANCE PROTEIN RPI-BLB26 6 LATE BLIGHT RESISTANCE PROTEIN.

I Ia II Ib I IaIb IIIII IV V VI Figure S1. Comparison of amino acid sequence of O. sativa (Os) SUV3 (1-579) with SUV3 from A. thaliana (At) (1-571), H.

Biological clock An innate mechanism in living organisms that controls the periodicity or rhythm of various physiological functions or activities. Circadian.

Supplementary Figures SHUGOSHINs and PATRONUS protect meiotic centromere cohesion in Arabidopsis thaliana Linda Zamariola 1, Nico De Storme 1, Katrijn.

A B C D E F G H I J K FigS1. Supplemental Figure S1. Evolutionary relationships of Arabidopsis and tomato Aux/IAA proteins. The evolutionary history was.

Fig. S1. Carotenoid and chlorophyll composition of Arabidopsis Z-ISO mutants compared to wild type. Seedlings were grown for 6d on half strength MS plus.

Journal: Molecular Breeding Molecular characterization of allelic variation in spontaneous brown midrib mutants of sorghum (Sorghum bicolor L Moench) Sunita.

Supplemental material 1.Spraying with ethephon produces an ethylene physiological response. One-month-old seedlings were sprayed with different concentrations.

Supplementary Fig. 1. (A) PCR amplification of wheat TaHSP26 genomic, cDNA and ORF clones. (B) ORF and protein sequence of TaHSP26. An arrowhead indicates.

WSSP Chapter 10 Literature Search Where do you learn about the function of your gene? atttaccgtg ttggattgaa attatcttgc atgagccagc tgatgagtat gatacagttt.

Myb Transcription Factors Dylan Coughtrey Laboratory Methods in Genomics Spring 2011.

Supplementary Fig 1. Multiple sequence alignment of nucleotide sequences from amplified region of different Oryza sativa lines and wild species of rice.

Analyses of the E3 ubiquitin-ligase target adapter-encoding BTB gene families in algal species Katie Plamann & Derek Gingerich Department of Biology, University.

Supplementary Fig. 1 ClustalW (2.1) multiple sequence alignment and comparison of deduced partial protein sequences of SOS1 in root tissues of wheat genotypes.

MdSFBB3-alpha MSHVRESETPEDRVVEILSRLPPKSLMRFKCIHKSWFSLINNLSFVAKHLSNSVDNKLSSSTCILLNRSQAHIFPDQSWKQEVFWSMINFSIDSDENNLHYDVEDLN-IP 109 MdSFBB3-beta MSQVHESETPEDKVVEILCRLPPKSLMRFKCIRKSWCTLINRPSFVAKHLNNSVDNKLSSSTCILLNRSQAHIFPDQSWKQEVFWSTINLSIDSDEHNLHYDVEDLI-IP.

Supplemental Fig. S1 A B AtMYBS aa AtMYBS

UNIVERSIDADE ESTADUAL PAULISTA FACULDADE DE CIÊNCIAS AGRONÔMICAS

S1 Table. The protein sequences Glycine max St8 MER3 and 18 homologous proteins used for phylogenetic analysis. S. No. Gene Name/ ID Protein type 1 Glyma.06G

(A) rRNA (B) OsAGPL3 rRNA (C) Time after transfer （h）

Generating Multiple Sequence Alignments with ClustalW

a. ZEP ZEP Os04g Selmo Phypa Chlre CTF2B

Figure S1. Sequence alignment of Arabidopsis NodGS with other plant and fungal orthologues. Abbreviations are as follows: Populus trichocarpa (Ptr), Ricinus.

Phylogenetic analysis of CADs and oxidoreductases involved in specialized metabolism (ORSMs). Phylogenetic analysis of CADs and oxidoreductases involved.

Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research Jeongsik Kim, Hye Ryun Woo, Hong Gil.

Volume 6, Issue 3, Pages (May 2013)

Kazimierz T. Tycowski, Mei-Di Shu, Joan A. Steitz Cell Reports

Angel Vallverdú, BSc, Juan A. Asturias, PhD, M

Plant Photomorphogenesis: A green light for cryptochrome research

Motif 1 Motif 3 Motif 6 Motif 2 Motif 5 Motif 4 Motif 4 Motif 1

Multiple sequence alignment and analysis of SOFL proteins.

Volume 10, Issue 1, Pages (January 2017)

1. Shen et al (MOL Biol Rep (2006) Ginko biloba) 2. Melon

Volume 10, Issue 6, Pages (June 2017)

Volume 5, Issue 2, Pages (March 2012)

Generating Multiple Sequence Alignments with Clustal Omega

Volume 1, Issue 2, Pages (March 2008)

L. Dubourg Clinical Microbiology and Infection

Epstein–Barr virus BZLF1 gene polymorphisms: malignancy related or geographically distributed variants? M.A. Lorenzetti, M. Gantuz, J. Altcheh, E. De.

Evolution of jasmonate and salicylate signal crosstalk

Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research Jeongsik Kim, Hye Ryun Woo, Hong Gil.

Volume 10, Issue 7, Pages (July 2017)

Multiple sequence alignment & Phylogenetics Analysis

The Presence and Localization of Thioredoxins in Diatoms, Unicellular Algae of Secondary Endosymbiotic Origin Weber Till , Gruber Ansgar , Kroth Peter.

Features of the Protein Encoded by the Ruby Transcript

A B 100 PgHMGR1 98 EsHMGR 82 EuHMGR SmHMGR Plant PgHMGR2 77

How to search NCBI.

Volume 11, Issue 6, Pages (June 2018)

Genetic and Physical Maps of W1/Iw1.

Subcellular Localization of At4g19010

Functional Insights of Plant GSK3-like Kinases: Multi-Taskers in Diverse Cellular Signal Transduction Pathways Ji-Hyun Youn, Tae-Wuk Kim Molecular Plant

Volume 3, Issue 2, Pages (March 2010)

Presentation transcript:

Supplemental Figure 1S. Alignment and phylogeny of CRY proteins. Comparison of the amino acid sequences of the DNA-photolyase domain (a) and FAD binding domain (b) from several CRY proteins. AtCRY, SlCRY, GmCRY, OsCRY and FvCRY were from Arabidopsis thaliana, Solanum lycopersicum, Glycine max, Oryza sativa Japonica Group and Fragaria vesca, respectively. Consensus sequences are identified with gray highlighting. c. Phylogeny reconstruction of CRY proteins. A neighbor-joining tree was calculated using clustal W. Branch lengths indicate the number of substitutions per site. FaCRY1 and FaCRY2 are highlighted with open boxes. GenBank accession numbers of the amino acid sequences used include; GmCRY1, Glycine max cryptochrome 1 (NP_ ); NsCRY1, Nicotiana sylvestris cryptochrome 1 (ABB36796); VrCRY1, Vitis riparia cryptochrome 1 (ABX80391); VvCRY1, Vitis vinifera cryptochrome 1 (ABX79355); PsCRY1, Pisum sativum cryptochrome 1 (AAO23970); SlCRY1, Solanum lycopersicum cryptochrome 1 (NP_ ); CbCRY1, Capsella bursa-pastoris cryptochrome 1 (ACX49994); AtCRY1, Arabidopsis thaliana cryptochrome-1 (NP_567341); OsCRY1, Oryza sativa Japonica Group cryptochrome 1a (BAD17529); OmCRY1, Orobanche minor cryptochrome 1 (AAR08429); FvCRY1, Fragaria vesca CRY1 (ACV89993); FaCRY1, Fragaria ananassa cryptochrome1 (AB743569); GmCRY2, Glycine max cryptochrome2 (BAI47558); NsCRY2, Nicotiana sylvestris cryptochrome 2 (ABB36797); SlCRY2, Solanum lycopersicum cryptochrome 2 (NP_ ); BjCRY2, Brassica juncea cryptochrome 2 (ADM47404); ArCRY2, Armoracia rusticana cryptochrome 2 (BAC67178); AtCRY2, Arabidopsis thaliana cryptochrome 2 (NP_171935); OsCRY2, Oryza sativa Indica Group (CAC82538); TaCRY2, Triticum aestivum cryptochrome 2 (ABX58030); FvCRY2, Fragaria vesca Cry2 (ACZ71184); FaCRY2, Fragaria ananassa cryptochrome 2 (AB743570). 1

CRY1 CRY2 Suppl. Fig 1S. a: DNA-photolyase domain

CRY2 Suppl. Fig 1S. b: FAD binding domain CRY1

Suppl. Fig 1S. c

Supplemental Figure 2S. Alignment and phylogeny of PHY proteins. Comparison of the amino acid sequences of the (a) PAS, (b) GAF, and (c) PHY domains of various PHY proteins. AtPHY, SlPHY, VvPHY, OsPHY, and FvPHY were from Arabidopsis thaliana, Solanum lycopersicum, Vitis vinifera, Oryza sativa Japonica Group and Fragaria vesca, respectively. Consensus sequences are identified with gray highlighting. d. Phylogeny reconstruction of PHY proteins. A neighbor-joining tree was calculated using clustal W. Branch lengths indicate the number of substitutions per site. FaPHYA and FaPHYB are highlighted with open boxes. GenBank accession numbers of the amino acid sequences used include: VvPHYA, Vitis vinifera phytochrome A (ACC60965); VrPHYA, Vitis riparia phytochrome A (ACC60969); ArPHYA, Armoracia rusticana phytochrome A (BAA99410); AtPHYA, Arabidopsis thaliana phytochrome A (NP_172428); StPHYA, Solanum tuberosum phytochrome A (ABA46868); MgPHYA, Monotropastrum globosum phytochrome A (AAR08427); AfPHYA, Aquilegia formosa phytochrome A (ACV87353); BvPHYA, Beta vulgaris phytochrome A (ACY01932); GmPHYA, Glycine max phytochrome A (BAG72094); SbPHYA, Sorghum bicolor phytochrome A (AAR30884); OsPHYA, Oryza sativa Japonica Group phytochrome A (AAM47309); AmPHYA, Amblyopyrum muticum phytochrome A (AEA40447); HvPHYA, Hordeum vulgare subsp. vulgare phytochrome A (ABB13322); SlPHYA, Solanum lycopersicum phyA (CAA05089); FaPHYA, Fragaria ananassa phytochrome A (AB743571); VrPHYB, Vitis riparia phytochrome B (ACC60970); VvPHYB, Vitis vinifera phytochrome B (ACC60966); StPHYB, Solanum tuberosum phytochrome B (ABC72086); NpPHYB, Nicotiana plumbaginifolia phytochrome B (CAA74992); AfPHYB, Aquilegia formosa phytochrome B (ACV87354); AePHYB, Amphicarpaea edgeworthii phytochrome B (AEA41043); AtPHYB, Arabidopsis thaliana phytochrome B (ABY61307); OsPHYB, Oryza sativa Indica Group phytochrome B (CAA40795); SbPHYB, Sorghum bicolor phytochrome B (AAR30903); GmPHYB, Glycine max phytochrome B (AAA34000); SlPHYB, Solanum lycopersicum phytochrome B1 (CAA05293); FaPHYB, Fragaria ananassa phytochrome B (AB743572); CfPHY, Chara foetida phytochrome (CAA ). FvPHYA and FvPHYB were obtained by blastp searches using FaPHYA and FaPHYB sequences from DATABASE: vescagenemodels2.faa ( Sequence numbers of FvPHYA and FvPHYB are from Fragaria vesca Phytochrome A (gene 22948) and Fragaria vesca Phytochrome B (gene 05117), respectively.

PHYA PHYB Suppl. Fig 2S. a: PER-ARNT-SIM (PAS) domain

PHYA PHYB Suppl. Fig 2S. b: cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) domain

PHYA PHYB Suppl. Fig 2S. c: phytochrome (PHY) domain

Suppl. Fig 2S. d