The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.
Trinity_Assemblies_Unmodified.tar
Unmodified Trinity assemblies for H. erythrogramma, H. tuberculata, and L. variegatus
Trinity_Assemblies_Modified.tar
Modified Trinity assemblies for H. erythrogramma, H. tuberculata, and L. variegatus
Fastq Files for L. variegatus, 4-cell stage
These are fastq files for L. variegatus, 4-cell stage. There are three replicates, each is 50 bp PE
L.variegatus_4cell.tar.gz
Fastq Files for L. variegatus, egg stage
These are fastq files for L. variegatus, egg stage. There are three replicates, each is 50 bp PE
L.variegatus_egg.tar.gz
Fastq Files for L. variegatus, 16-cell stage
These are fastq files for L. variegatus, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50bp SE
L.variegatus_16cell.tar.gz
Fastq Files for L. variegatus, 32-cell stage
These are fastq files for L. variegatus, 4-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
L.variegatus_32cell.tar.gz
Fastq Files for L. variegatus, blastula stage
These are fastq files for L. variegatus, blastula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
L.variegatus_blastula.tar.gz
Fastq Files for L. variegatus, gastrula stage
These are fastq files for L. variegatus, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
L.variegatus_Gastrula.tar.gz
Fastq Files for L. variegatus, prism "early larva" stage
These are fastq files for L. variegatus, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
L.variegatus_prism.tar.gz
Fastq Files for H.tuberculata, egg stage
These are fastq files for H.tuberculata, egg stage. There are three replicates, each is 50 bp PE
H.tuberculata_egg.tar.gz
Fastq Files for H.tuberculata, 4-cell stage
These are fastq files for H.tuberculata, 4-cell stage. There are three replicates, each is 50 bp PE
H.tuberculata_4cell.tar.gz
Fastq Files for H.tuberculata, 16-cell stage
These are fastq files for H.tuberculata, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.tuberculata_16cell.tar.gz
Fastq Files for H.tuberculata, 32-cell stage
These are fastq files for H.tuberculata, 32-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.tuberculata_32cell.tar.gz
Fastq Files for H.tuberculata, blastula stage
These are fastq files for H.tuberculata, blastula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.tuberculata_blastula.tar.gz
Fastq Files for H.tuberculata, gastrula stage
These are fastq files for H.tuberculata, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.tuberculata_gastrula.tar.gz
Fastq Files for H.tuberculata, prism "early larva" stage
These are fastq files for H.tuberculata, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.tuberculata_prism.tar.gz
Fastq Files for H.erythrogramma, egg stage
These are fastq files for H.erythrogramma, egg stage. There are three replicates, each is 50 bp PE
H.erythrogramma_egg.tar.gz
Fastq Files for H.erythrogramma, 4-cell stage
These are fastq files for H.erythrogramma, 4-cell stage. There are three replicates, each is 50 bp PE
H.erythrogramma_4cell.tar.gz
Fastq Files for H.erythrogramma, 16-cell stage
These are fastq files for H.erythrogramma, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.erythrogramma_16cell.tar.gz
Fastq Files for H.erythrogramma, 32-cell stage
These are fastq files for H.erythrogramma, 32-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.erythrogramma_32cell.tar.gz
Fastq Files for H.erythrogramma, blastula stage
These are fastq files for H.erythrogramma, blastula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.erythrogramma_blastula.tar.gz
Fastq Files for H.erythrogramma, gastrula stage
These are fastq files for H.erythrogramma, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.erythrogramma_gastrula.tar.gz
Fastq Files for H.erythrogramma, prism "early larva" stage
These are fastq files for H.erythrogramma, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
H.erythrogramma_prism.tar.gz
S1_Data
Log2-transformed, normalized count data
S2_Data
Mfuzz Data for cluster generation in L. variegatus, c=7
S3_Data
Standardized, mean expression profiles of normalized, log2-transformed counts
S5_Data
Mfuzz Data for cluster generation in L. variegatus, c=5
S6_Data
Mfuzz Data for cluster generation in L. variegatus, c=9