Since the discovery of Chromera velia, a novel microalga in 2008 during a study of Australian coral symbionts, great interest in this new algal species has developed. C. velia is an important organism being considered to sit phylogenetically between the photosynthetic dinoflagellate algae and the parasitic Apicomplexa. C. velia has been detected and isolated from different scleractinian corals in Australia including corals of the Great Barrier Reef. However little is known about the ecology and genetics of this microorganism. The study aims to use next generation sequencing technology (Illumina RNAseq) to generate a reference transcriptome assembly of C. velia isolated from Montipora digitata at the GBR. Differential gene expression in altered experimental treatments is investigating the diversity and dynamics of C. velia transcripts (mRNAs). Cultures were subjected to heat shock, heat stress, cold shock, cold stress, and darkness with control cultures grown under normal conditions, cultures grown under mixotrophic condition and cultures containing motile/immotile stages. Analysis of the transcriptome of C. velia will provide genomic insight into this novel chromerid alga through identifying genes involved in various physiological and metabolic processes as investigated under different experimental conditions.

1. Amin Mohamed1,2,4,6 , Vivian Cumbo2, Susanne Sprungala2,4, David Bourne3, Bette Willis2,5, David Miller2,4
1AIMS@JCU,*Australian*Ins3tute*of*Marine*Science,*School*of*Marine*and*Tropical*Biology,*James*Cook*University,*Townsville,*QLD*
4810,*Australia;*2ARC*Centre*of*Excellence*for*Coral*Reef*Studies,*James*Cook*University,*Townsville,*QLD*4810,*Australia*
3Australian*Ins3tute*of*Marine*Science*(AIMS),*PMB3,*Townsville,*QLD*4810,*Australia;*4School*of*Pharmacy*and*Molecular*Sciences,*
James*Cook*University,*Townsville,*QLD*4810,*Australia;*5School*of*Marine*and*Tropical*Biology,*James*Cook*University,*Townsville,*
QLD*4810,*Australia;*6Zoology*Department,*Faculty*of*Science,*Benha*University,*Benha*13518,*Egypt*
Transcriptome-Analysis-of-Chromera(velia,-a-Chromerid-
Alga-Associated-with-Corals-of-the-Great-Barrier-Reef--
PROJECT*AIM*
METHODOLOGY* NEXT*STEPS*
Fig.3:*Life*cycle*of*C.#velia:*(a)*predominant*coccoid*cells,*(b_c)*
dividing*cells*(d_e)released*autospores*star3ng*a*new*cycle,*(f)*
autospores*can*form*bi_flagellated*cells*in*favorable*condi3ons.*
Oborník*et*al.,*2011,*Pro3st*
• Chromera(velia(is*a*newly*discovered*algal*species*found*
to*be*associated*with*corals*
*
• C.#velia#was*isolated*from*Magne<c-Island-at*the*GBR*in*
2012*from#Mon.pora(digitata#(Cumbo*et#al.,*2012)#
I. Control-condi<on--
II. Mixotrophic-condi<on--
III. Mo<le/immo<le--
IV. Heat-stress--
V. Heat-shock-
VI. Cold-stress--
VII. Cold-shock--
VIII. Darkness--
*
• To*generate*a*reference*transcriptome*assembly*of*C.#velia#isolated*from*the*coral*Mon.pora#digitata##
####at*the*GBR**
• To*Inves3gate*the*diversity*and*dynamics*of*C.#velia#transcripts*(mRNAs)*
*
→ Genomic*insight*into*a*novel*chromerid*alga*via*iden3fying*genes*involved*in*various**
*****physiological*and*metabolic*processes**
→ Differen3al*gene*expression*profiles*in*different*experimental*treatments*
Fig.*4:*Chromera#velia#cells*
Total(RNA(isola.on((
((((((((((((((((((((((((RNA(Quality(check(using#NanoDrop#
#######################RNA(Integrity(check(using#Agilent#Bioanalyzer#
(mRNA-enrichment-
*
*
-cDNA-library-construc<on-
***
*
Illumina-highHthroughput-sequencing(
Fig.*6.*Next_gen*DNA*sequencing*method:*
PCR*bridge*amplifica3on*and**Illumina*
HiSeq*2500*sequencing*plaform*
Experimental--
Treatments--
Magne3c**
Island*
*
• C.#velia#is*closely*related*to*the*apicomplexan-
parasites,*but*also*related*to*the*photosynthe<c-
dinoflagellates*including*the*coral*symbiont-
Symbiodinium##
Fig.*1:*Loca3on*and*the*coral*species*Mon.pora#digitata#that**
hosts*C.#velia**
Fig.*2:*Nuclear*phylogeny*places*C.#velia#between*the*
*Apicomplexa*and*the*dinoflagellates*Oborník*et*al.,*2012,*Pro3st*
• The*func<onal-role-of*C.#velia#in*the*coral*holobiont*
is*currently*unknown--
**
Fig.5:*C.*velia*cultures*growth*curve*and*experimental*
treatments*
Next*Genera3on*Sequencing*(NGS)*
De#novo#Transcriptome*Assembly*and*Analysis*
Sequencing*
reads*
(per*sample)**
Experimental-treatments-
Combine*reads*
Reads*Normaliza3on**
Abundance--es<ma<on-
Assembled*
transcripts*
(all*samples)*
De(novo(assembly---
Iden<fy-differen<ally-expressed-transcripts-
Expression-paMerns-and-transcript-clusters-
Adapted*from*Haas*et*al.,*2013*Nature*Protocols*
*
_ Cumbo,*V.,*Baird,*A.#et#al.,*(2012):*Chromera#velia*is*Endosymbio3c*in*Larvae*of*the*Reef*Corals*Acropora#digi.fera#and*A.#tenuis.#Pro3st,*164:*237_244*
_ Haas,*B.,*Papanicolaou,*A.,*et#al.,#(2013):*De#novo#transcript*sequence*reconstruc3on*from*RNA_seq*using*the*Trinity*plaform*for*reference*genera3on*and*analysis.*Nature*Protocols,*8:1494–1512*
_ Oborník,*M.*Vancová,*M.,*Lai,*D.,*et#al.,#(2011):*Morphology*and*ultrastructure*of*mul3ple*life*cycle*stages*of*the*photosynthe3c*rela3ve*of*apicomplexa,*Chromera#velia.*Pro3st,*162(1):115_30*
_ Oborník,*M.,*Modry,*D.,*Lukes,*M.,*et#al.,#(2012):*Morphology,*ultrastructure*and*life*cycle*of*Vitrella#brassicaformis#n.*sp.,*n.*gen.,*a*novel*chromerid*from*the*Great*Barrier*Reef.*Pro3st,*163(2):*306_323*
BACKGROUND*
References*
Assembled*
transcripts*
3-replicates/-
treatment-
KEGG-Metabolic-Pathways-