Identification of genes involved in morphogenesis in vitro in Centaurium erythraea Rafn. as a model organism
2016
Autori:
Simonović, AnaDragićević, Milan
Giurato, Giorgio
Filipović, Biljana
Todorović, Slađana
Bogdanović, Milica
Ćuković, Katarina
Subotić, Angelina
Ostala autorstva
Mitić, NenadTip dokumenta:
Konferencijski prilog (Objavljena verzija)
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© 2016 University of Belgrade, Faculty of Mathematics
Metapodaci
Prikaz svih podataka o dokumentuApstrakt:
Centaurium erythraea is a n endangered medicinal plant with great regeneration potential and developmental plasticity in vitro [1]. Identification of genes involved in organogenesis and somatic embryogenesis (SE) is the first step towards elucidation of molecular mechanisms underlying centaurys morphogenic plasticity. RNA from leaves (L), roots (R), embryogenic calii (EC), globular somatic embryos (GSE), cotyledonary somatic embryos (CSE) and adventitious buds (AB) was sequenced, resulting in 29-37 million reads/sample. Sequencing, de novo transcriptome assembly using Trinity and annotation were operated by Genomix4Life. The reference transcriptome (142 Mbp) contained 160,839 Trinity transcripts comprising 105,726 "genes". Of 160,839 transcripts, 44,288 had Blast hits, 26,435 had GO Slim annotation, whereas 9,552 were with GO mapping. The top-hit species was Coffea canephora. Relative expression was computed by aligning high quality reads to the Trinity transcripts and presented as TMM-FPKM. In each sample >=30,000 transcripts were expressed. Transcripts involved in different morphogenetic paths were filtered using R. Potential SE markers (FPKM >=1 in EC or GSE and >=8X higher FPKM in EC or GSE than in L, R and AB) included 1989 sequences, such as LRR receptor-like PK, germin-like proteins, TFs WRKY, AINTEGUMENTA and others. There were 1203 transcripts important for later SE development, including seed storage proteins and expansins. Finally, 727 transcripts with at least 8x higher FPKM in AB than in other samples were considered as important for organogenesis.
Ključne reči:
organogenesis; somatic embryogenesis; RNA sequencing; transcriptomeFinansiranje / projekti:
- Razvoj i primena biotehnoloških postupaka u dobijanju zdravog sadnog materijala ukrasnih biljaka (RS-MESTD-Technological Development (TD or TR)-31019)
U:
- Mitić N, editor. Book of Abstracts: Belgrade Bioinformatics Conference: BelBI2016; 2016 Jun 20-24; Belgrade, Serbia. Belgrade: Faculty of Mathematics, University; 2016. p. 97-8.