DOI: 10.5061/dryad.cr0mb
title: Data from: Comparative developmental transcriptomics reveals rewiring of a highly conserved gene regulatory network during a major life history switch in the sea urchin genus Heliocidaris

description: 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.
description: Trinity_Assemblies_Unmodified.tarUnmodified Trinity assemblies for H. erythrogramma, H. tuberculata, and L. variegatusTrinity_Assemblies_Modified.tarModified Trinity assemblies for H. erythrogramma, H. tuberculata, and L. variegatusFastq Files for L. variegatus, 4-cell stageThese are fastq files for L. variegatus, 4-cell stage. There are three replicates, each is 50 bp PEL.variegatus_4cell.tar.gzFastq Files for L. variegatus, egg stageThese are fastq files for L. variegatus, egg stage. There are three replicates, each is 50 bp PEL.variegatus_egg.tar.gzFastq Files for L. variegatus, 16-cell stageThese are fastq files for L. variegatus, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50bp SEL.variegatus_16cell.tar.gzFastq Files for L. variegatus, 32-cell stageThese are fastq files for L. variegatus, 4-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SEL.variegatus_32cell.tar.gzFastq Files for L. variegatus, blastula stageThese are fastq files for L. variegatus, blastula stage. There are three replicates, two are 50 bp PE and one is 50 bp SEL.variegatus_blastula.tar.gzFastq Files for L. variegatus, gastrula stageThese are fastq files for L. variegatus, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SEL.variegatus_Gastrula.tar.gzFastq Files for L. variegatus, prism "early larva" stageThese are fastq files for L. variegatus, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SEL.variegatus_prism.tar.gzFastq Files for H.tuberculata, egg stageThese are fastq files for H.tuberculata, egg stage. There are three replicates, each is 50 bp PEH.tuberculata_egg.tar.gzFastq Files for H.tuberculata, 4-cell stageThese are fastq files for H.tuberculata, 4-cell stage. There are three replicates, each is 50 bp PEH.tuberculata_4cell.tar.gzFastq Files for H.tuberculata, 16-cell stageThese are fastq files for H.tuberculata, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.tuberculata_16cell.tar.gzFastq Files for H.tuberculata, 32-cell stageThese are fastq files for H.tuberculata, 32-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.tuberculata_32cell.tar.gzFastq Files for H.tuberculata, blastula stageThese are fastq files for H.tuberculata, blastula stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.tuberculata_blastula.tar.gzFastq Files for H.tuberculata, gastrula stageThese are fastq files for H.tuberculata, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.tuberculata_gastrula.tar.gzFastq Files for H.tuberculata, prism "early larva" stageThese are fastq files for H.tuberculata, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.tuberculata_prism.tar.gzFastq Files for H.erythrogramma, egg stageThese are fastq files for H.erythrogramma, egg stage. There are three replicates, each is 50 bp PEH.erythrogramma_egg.tar.gzFastq Files for H.erythrogramma, 4-cell stageThese are fastq files for H.erythrogramma, 4-cell stage. There are three replicates, each is 50 bp PEH.erythrogramma_4cell.tar.gzFastq Files for H.erythrogramma, 16-cell stageThese are fastq files for H.erythrogramma, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.erythrogramma_16cell.tar.gzFastq Files for H.erythrogramma, 32-cell stageThese are fastq files for H.erythrogramma, 32-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.erythrogramma_32cell.tar.gzFastq Files for H.erythrogramma, blastula stageThese are fastq files for H.erythrogramma, blastula stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.erythrogramma_blastula.tar.gzFastq Files for H.erythrogramma, gastrula stageThese are fastq files for H.erythrogramma, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.erythrogramma_gastrula.tar.gzFastq Files for H.erythrogramma, prism "early larva" stageThese are fastq files for H.erythrogramma, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SEH.erythrogramma_prism.tar.gzS1_DataLog2-transformed, normalized count dataS2_DataMfuzz Data for cluster generation in L. variegatus, c=7S3_DataStandardized, mean expression profiles of normalized, log2-transformed countsS4_DataJump scoresS5_DataMfuzz Data for cluster generation in L. variegatus, c=5S6_DataMfuzz Data for cluster generation in L. variegatus, c=9