Gl Global transcriptome analysis of non-se seed vasc scular plant Se Selaginella moe oellendor orffii Yan Zhu Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Se Selaginella mo moellendorffii • Selaginella moellendorffii is a lycophyte, that is an important model organism 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 .
Th The lycophyte tes occupy a a ke key phylogenetic position in ev in evolut ution n of of gr green n pl plant nts Angiosperm Gymnosperm Anthophyte Pteridophyte Spermatophyte Lycophyte Euphyllophyte Bryophyte Phycophyta Tracheophyte Embryophyte Aquatic green algae
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 Length Reads Reads Sequencing Type Organ Treatment Platform (bp) Num (Gb) 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 om 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 orffii • 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.
abscission Funct ctions of newly disco covered photosynthesis endoplasmic reticulum coding genes co Golgi apparatus translation factor activity, RNA … nuclear envelope vacuole thylakoid • The Gene Ontology (GO) analysis cell wall cell-cell signaling showed that the newly discovered cell death growth embryo development coding genes occupied almost all the extracellular space response to endogenous … major functions of plant growth, cell differentiation lipid binding development, metabolism receptor binding external encapsulating structure carbohydrate binding and stress response. multicellular organism … lipid metabolic process response to stress signal transducer activity 0 100 200 300 400 500 600 700 Gene Number MF CC BP
11,030 11, 030 Al Alternative Splicing events in S. S. moellendorffii Mutually exclusive exons Intron retention Exon skipping (696) (4,616) (1,149) Alternative 3’ splice site Alternative 5’ splice site (2,763) (1,806) • 5,957 (19.7%) coding genes with AS events; • 42% AS events were Intron Retention.
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 Number of Exons Average length
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
Vascular Gene Arabidopsis S. moellendorffii P. Patents C. reinhardtii Ev Evolutionary trend of ANAC007 ● ● ● ANAC010 ● ● ANAC012 ● ● tr transcrip ipt t facto tor familie ilies in in ANAC030 ● ANAC037 ● ● ANAC043 ● ● ANAC066 ● ● ● ANAC076 ● ● vascular development va ANAC083 ● ● ANAC101 ● ● ANAC104 ● ANAC105 ● ● AFB1 ● ● AFB2 ● ● AFB3 ● ● ● AFB4 ● AFB5 ● IAA12 ● ● l TF TFs in vascular development existed in IAA20 ● IAA28 ● ● IAA30 ● unicellul uni ular alg algae ae ； IAA31 ● IAA8 ● ● IRX1 ● ● IRX12 ● ● l Gr Growth wi with the de developm pment nt of IRX14 ● ● IRX3 ● ● IRX9 ● MYB20 vascular ti va tissue; ● ● ● MYB42 ● MYB43 ● ● ● ● MYB46 ● ● MYB61 l In Increa easing rapidly in Se Selaginella. ● ● ● MYB85 ● ● PIN1 ● PIN3 ● ● PIN4 ● ● ● PIN7 ● ● ● KAN1 ● ● KAN2 ● ● KAN3 ● 41 26 11 2 Total
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 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. 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.
Thank You ！
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