Gl Global transcriptome analysis of non-se seed vasc scular plant - - PowerPoint PPT Presentation

Gl Global transcriptome analysis of non-se seed vasc scular plant Se Selaginella moe

• ellendor
• rffii

Yan Zhu Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

Se Selaginella mo moellendorffii

• Selaginella moellendorffiiis a lycophyte, that is an important model
• rganism to study the early evolution of vascular plant.
• It is a member of an ancient vascular plant lineage that first appeared in

the fossil record some 400 million years ago.

• As the oldest extant division of the vascular plants, they are essential to

understanding the evolution of plant as a whole.

Aquatic green algae

Phycophyta

Embryophyte

Bryophyte Lycophyte

Euphyllophyte

Pteridophyte Gymnosperm Angiosperm

Tracheophyte Spermatophyte Anthophyte

Th The lycophyte tes occupy a a ke key phylogenetic position in in ev evolut ution n of

• f gr

green n pl plant nts

First and only sequence ced genome of fern： Sel Selaginel ella mo moellendorffii

212.6 Mb (diploid) 22,285 coding genes 58 microRNA loci

Jo Ann Banks, et al. Science, 2011, 332: 960-963.

Qu Questions need to be answered from m the study y of s. mo moellendorffii transcr criptome

• No transcriptome study on gene modeling, gene expression pattern

were reported for S. moellendorffii.

• Alternative splicing of genes in S. moellendorffii remains a mystery?
• How about long non-coding RNA (lncRNA) ?
• Importantly, the expression profiles and regulation for key genes in

vascular development ?

St Study design and s sequencing data

Sequencing Type Length (bp) Reads Num Reads (Gb) Organ Treatment Platform Strand-Specific PE125 47,787,568 12.50 Root Ribo-minus Hiseq2500 Strand-Specific PE125 61,227,393 14.84 Stem Ribo-minus Hiseq2500 Strand-Specific PE125 52,573,643 13.77 Leaf Ribo-minus Hiseq2500

Who Whole geno nome mappi pping ng and nd ana nalysis of RNA-se seq data fr from

• m S.
• S. moellendorffii ti

tissues

• 2,461 existing coding gene models modified
• 7,930 new coding genes identified (35% increase in coding gene number)
• 11,030 alternative splicing forms for 5,957 coding genes
• 4,422 lncRNAs identified

Ne Newly ly dis iscovered codin ing genes in in S.

• S. moe

moellendor

• rffii
• A total of 7,930 coding genes were first

identified in Selaginella;

• All of these genes with an open reading frame

(ORF) longer than 100aa;

• 7,929 (99.99%) novel genes have homologies

in at least two databases;

• 4,220 (53.22%) novel genes have homologies

in all of the five databases.

100 200 300 400 500 600 700

signal transducer activity response to stress lipid metabolic process multicellular organism … carbohydrate binding external encapsulating structure receptor binding lipid binding cell differentiation response to endogenous … extracellular space embryo development growth cell death cell-cell signaling cell wall thylakoid vacuole nuclear envelope translation factor activity, RNA … Golgi apparatus endoplasmic reticulum photosynthesis abscission

Gene Number

MF CC BP

• The Gene Ontology (GO) analysis

showed that the newly discovered coding genes occupied almost all the major functions of plant growth, development, metabolism and stress response.

Funct ctions of newly disco covered co coding genes

11, 11,030 030 Al Alternative Splicing events in S.

• S. moellendorffii
• 5,957 (19.7%) coding genes with AS events;
• 42% AS events were Intron Retention.

Intron retention (4,616) Exon skipping (1,149) Mutually exclusive exons (696) Alternative 3’ splice site (2,763) Alternative 5’ splice site (1,806)

lncR cRNA in S. mo moellendorffii

• A total of 4,422 lncRNAs were identified in Selaginella
• The length of lncRNA was shorter than mRNA, and with fewer exons

Average length Number of Exons

lncR cRNAs havi ving lower exp xpressi ssion leve vels s than mRNA

lncR cRNAs having lower GC co content than mRNA

• The GC content of intergenic

lncRNA was lower than mRNA;

• The GC content of antisense

lncRNA was similar to mRNA.

No Tissue speci cifici city observed for both lncR cRNA and mRNA in S. . moel ellen endorffii

Key ey gen genes es for vascu cular de developm pment nt found und in n S. . mo moellendorffii gen genome e

Expression levels of vascu cular development genes in S. S. mo moellendorffii ti tissues

Ev Evolutionary trend of

tr transcrip ipt t facto tor familie ilies in in va vascular development

l TF

TFs in vascular development existed in uni unicellul ular alg algae ae；

l Gr

Growth wi with the de developm pment nt of va vascular ti tissue;

l In

Increa easing rapidly in Se Selaginella.

Vascular Gene Arabidopsis S. moellendorffii P. Patents C. reinhardtii

ANAC007

• ANAC010
• ANAC012
• ANAC030
• ANAC037
• ANAC043
• ANAC066
• ANAC076
• ANAC083
• ANAC101
• ANAC104
• ANAC105
• AFB1
• AFB2
• AFB3
• AFB4
• AFB5
• IAA12
• IAA20
• IAA28
• IAA30
• IAA31
• IAA8
• IRX1
• IRX12
• IRX14
• IRX3
• IRX9
• MYB20
• MYB42
• MYB43
• MYB46
• MYB61
• MYB85
• PIN1
• PIN3
• PIN4
• PIN7
• KAN1
• KAN2
• KAN3
• Total

41 26 11 2

Su Summary

• The deep RNA-seq study of S. moellendorffii discovered extensive

new gene contents, including novel coding genes, lncRNAs, AS events, and refined gene models.

• Compared to flowering vascular plants, S. moellendorffii displayed

a less complexity in both gene structure, alternative splicing, and regulatory elements of vascular development.

• We gained important insight into the evolution of vascular plants,

and the regulation of vascular development genes in a non-seed plant.

Ackn cknowledgement

Ø We thank Drs. Chengjun zhang, Wenzhang Ma and Wenbin Yu from Kunming Institute of Botany for help with collection of the S. moellendorffii samples. Ø Thank Longxian Chen, we complete this work together. Ø Thank Drs Xuan Li, he directed this work. Ø Thank all the members of my lab.

Thank You！