Mobilo ģenētisko elementu izplatība priežu gēnu rajonos
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1 Mobilo ģenētisko elementu izplatība priežu gēnu rajonos Angelika Voronova, Martha Rendon, Par Ingvarsson, Dainis Ruņģis Latvijas Valsts mežzinātnes institūts Silava ; Zviedrijas Lauksaimniecības Zinātņu universitāte
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3 Kukurūzas (Zea mays) 2S hromosomas fragmenta salīdzinošā shēma starp divām kukurūzas inbrīdām līnijām Mo17 un B73 (modificēts no Brunner et al. 2005).
4 Kobayashi S, Goto-Yamamoto N, Hirochika H: Retrotransposon- induced mutations in grape skin color.science, 2004,304:982. Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges (Butelli et.al. 2012), The Plant Cell, 2012 July 2012, 24 (7)
5 Makarevitch et al., 2015
6 Voronova et al. 2017
7 Pētījuma mērķis ir identificēt parastās priedes (Pinus sylvestris L.) gēnus sasitītus ar transponējamo elementu izraisītajām strukturālajām izmaiņām Pirmais pētījuma posms- bioinformātiskā pieejamo priežu genomu analīze
8 Pinus taeda/ P. lambertiana/ P.sylvestris Pinus taeda v.2.01 (6,58 GB; gēnu) Pinus lambertiana v.1.0.(hq-8 779;LQ ) Pinus sylvestris unannotated scaff (474 gēnu- P.taeda homologu, eksonu, no tiem 2021 aizņēma visu kontingu) TE atkārtojamība NGS sekvences kvalitāte Transponējamo elementu datubāzes kvalitāte, automātiskā anotēšana Genomu versiju atsķirības GO anotācija jaunākai genoma versijai vēl nav pieejama
9 Bioinformātisko analīžu gaita PIER db conifer TEs Ref genome P.taeda v.2.0. P.lambertiana v gene db Bedtools, Samtools BLASTn 3 and 5 UTR db LTR isolation Full length TEs CD-hit LTR db full-length TEs db Pita- LTR in genes Pita-fulllength TEs in genes Pila- LTR in genes Pila-fulllength TEs in genes Pita LTR in UTRs Pita fulllength TEs in UTRs Pila LTR in UTRs Pila fulllength TEs in UTRs gene ID & fasta extractions GO-terms-IDs db for P.taeda Blast2GO & PLAZA pita-pila genes homologs db Gene Networks analysis Cytoscape v.3. BINGO, DyNet BP MF CC
10 Pinus taeda NPR1 gēna homologa 2.introna struktūra
11 PIER v.2.0 skujkoku transponējamo elementu datubāze Transponējamo elementu datubāze ( garumā no bp) Total CPU time Garo terminālo atkārtojumu (LTR) datubāze ( ) Total CPU time
12 Mobilo elementu izplatība gēnu rajonos, % TE class/superfamily Pilna izmēra TE gēnos LTR gēnos pilns RE gēna UTR RE 50% from UTR LTR in UTR DNS transpozoni Retrotranspozoni (RE) Bez klasifikācijas LTR Retrotranspozoni Copia Gypsy bez-ltr RE Nezināmi LTR RE Nezināmi RE
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16 Gēnu ontoloģijas (GO) analīze No gēniem varēja piesķirt GO kategoriju ierakstu, no kuriem ir jaunākajā Gene Ontology Consortium anotācijā, 1845 unikālo GO P.lambertiana gēnu, 1368 unikālo GO
17 Gene network example LTR in UTR (BP) Regulation of signal transduction Transport Organonitrogen Carbohydrate protein mp; Ox-red Cellular response to stimulus
18 Gene network example LTR in UTR (BP)
19 Gene network example LTR in UTR (BP)
20 Gene network example LTR in UTR (BP)
21 Gene network example LTR in UTR (MF) Hydrolase activity serine hydrolase ATPase activity, coupled to transmembrane movement of substances Transmembrane transporter activity Ligase Pila-adenylosuccinate synthase Pita-4-coumarate-CoA ligase activity Oxidoreducta se activity hydroxymethylglutaryl-coa reductase (NADPH) activity primary amine oxidase activity oxidoreductase activity, acting on paired donors Glucosyltransferase activity sucrose synthase activity; xyloglucosyl transferase; fucosyltransferase
22 Gēnu tīklu salīdzinājums MF compare RLC760 BP compare RLC760
23 Comparison of gene networks
24 P.Sylvestris pieejamā transkriptoma analīze 118 transkripti sakrita ar iepriekš atrastā Appalachian RE
25 GO-ID p-value Nb. Description E-3 1 proteasome-mediated ubiquitin-dependent protein catabolic process E-6 3 cellular component biogenesis E-5 2 hemicellulose metabolic process E-5 2 xyloglucan metabolic process E-5 2 cell wall polysaccharide metabolic process E-4 2 cell wall biogenesis E-1 1 protein phosphorylation E-1 2 nitrogen compound metabolic process E-1 4 organic substance metabolic process E-1 4 macromolecule metabolic process E-1 1 zinc ion binding P.Sylvestris eksonu homologu analīze 11 sakritības ar 4671 LTR
26 P.Sylvestris eksonu homologu analīze 9 sakritības ar 3935 LTR
27 P.Sylvestris eksonu homologu analīze 17 sakritības ar PtRLC285 GO-ID p-value Nb Description Genes in test set E-3 2 peptide transport PITA_00121 PITA_ E-4 1 COPII-coated vesicle budding PITA_ E-4 1 Golgi vesicle budding PITA_ E-4 1 vesicle budding from membrane PITA_ E-2 2 RNA-dependent DNA biosynthetic process PITA_05238 PITA_ E-1 4 nucleic acid metabolic process PITA_05238 PITA_07231 PITA_20665 PITA_ E-2 2 nucleic acid phosphodiester bond hydrolysis PITA_07231 PITA_ E-1 1 protein kinase activity PITA_ E-1 phosphotransferase activity, alcohol group as 1 acceptor PITA_ E-1 1 protein phosphorylation PITA_01401
28 *Nozīmīgu augu rezistencē iesaistīto gēnu struktūras analīze un citu gēnu analīze, kas satur līdzīgus pārkārtojumus. NPR-1 gēns (NONEXPRESSOR OF PATHOGENESIS-RELATED PROTEINS1) defense response to fungus Source: EnsemblPlants induced systemic resistance Source: EnsemblPlants negative regulation of defense response Source: EnsemblPlants positive regulation of transcription, DNA-templated Source: EnsemblPlants regulation of jasmonic acid mediated signaling pathway Source: EnsemblPlants regulation of salicylic acid mediated signaling pathway Source: EnsemblPlants regulation of systemic acquired resistance Source: EnsemblPlants response to heat Source: EnsemblPlants response to hypoxia Source: EnsemblPlants response to insect Source: EnsemblPlants response to wounding Source: EnsemblPlants systemic acquired resistance, salicylic acid mediated signaling pathway Source: EnsemblPlants
29 Genes significantly overrepresented in the network (p-value 0.05) are indicated
30 Secinājumi P.taeda un P.lambertiana references genoma sekvence nesniedz vienozīmīgu informāciju par pilna izmēra transponējamo elementu esamību gēnu rajonos šo sekvenču atkārtojamības un homoloģijas dēļ. Gēnos biežāk sastopamo TE ģimeņu profils starp abām sugām ir daļēji līdzīgs pēc sastāva, taču izplatības proporcijas variē. Lielāko identificēto gēnu tīklu bioinformātiskā analīze, kura pamatojās uz homologo gēnu salīdzīnāšanu starp P.taeda un P.lambertiana, neatrada konservatīvus gēnus ar vienādu TE sastāvu. Taču tīkla dalībnieki tiek kategorizēti un iespējams ņem dalību līdzīgajos stresa inducētos metabolītiskajos ceļos. Tā kā P.sylvestris genoma labas kvalitātes sekvence nav pieejama, tiks identificēti gēnu tīkli, kas ir biežāk atrodami abām sugam un izvēti kandidātgēni turpmākiem pētījumiem.
31 Paldies!
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GO ID GO term Number of members GO: translation 225 GO: nucleosome 50 GO: calcium ion binding 76 GO: structural
GO ID GO term Number of members GO:0006412 translation 225 GO:0000786 nucleosome 50 GO:0005509 calcium ion binding 76 GO:0003735 structural constituent of ribosome 170 GO:0019861 flagellum 23 GO:0005840
1 GO: regulation of cell size E-04 2 GO: negative regulation of cell growth GO:
Table S2: The biological modulated by mir-5701 Sr. No Term Id 1 Term Name 2 Hit Gene Number 3 P-Value 4 1 GO:0008361 regulation of cell size 9 4.37E-04 2 GO:0030308 negative regulation of cell growth 8
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