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Sea urchins have become significant mariculture species globally, and also serve as invertebrate model organisms in developmental biology. Cis-regulatory elements (enhancers) control development and physiology by regulating gene expression. Mutations that affect the function of these sequences may contribute to phenotypic diversity. Cis-regulatory targets offer new breeding potential for the future. Here, we use the CRISPR/Cas9 system to disrupt an enhancer of Endo16 in developing Lytechinus variegatus embryos, in consideration of the thorough research on Endo16’s regulatory region. We designed six gRNAs against Endo16 Module A (the most proximal region of regulatory sequences, which activates transcription in the vegetal plate and archenteron, specifically) and discovered that Endo16 Module A-disrupted embryos failed to undergo gastrulation at 20 h post fertilization. This result partly phenocopies morpholino knockdowns of Endo16. Moreover, we conducted qPCR and clone sequencing experiments to verify these results. Although mutations were not found regularly from sequencing affected individuals, we discuss some potential causes. In conclusion, our study provides a feasible and informative method for studying the function of cis-regulatory elements in sea urchins, and contributes to echinoderm precision breeding technology innovation and aquaculture industry development.

 

Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on interactions with these networks remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyze genomes, epigenomes, and transcriptomes during early development in two sea urchin species in the genus Heliocidaris that exhibit highly divergent life histories and in an outgroup species. Signatures of positive selection and changes in chromatin status within putative gene regulatory elements are both enriched on the branch leading to the derived life history, and particularly so near core dGRN genes; in contrast, positive selection within protein-coding regions have at most a modest enrichment in branch and function. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near dGRN genes with conserved roles in cell fate specification. Experimentally perturbing the function of three key transcription factors reveals profound evolutionary changes in the earliest events that pattern the embryo, disrupting regulatory interactions previously conserved for ~225 million years. Together, these results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change and that even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances. 

Abstract Lytechinus variegatus is a camarodont sea urchin found widely throughout the western Atlantic Ocean in a variety of shallow-water marine habitats. Its distribution, abundance, and amenability to developmental perturbation make it a popular model for ecologists and developmental biologists. Here, we present a chromosomal-level genome assembly of L. variegatus generated from a combination of PacBio long reads, 10× Genomics sequencing, and HiC chromatin interaction sequencing. We show L. variegatus has 19 chromosomes with an assembly size of 870.4 Mb. The contiguity and completeness of this assembly are reflected by a scaffold length N50 of 45.5 Mb and BUSCO completeness score of 95.5%. Ab initio and transcript-informed gene modeling and annotation identified 27,232 genes with an average gene length of 12.6 kb, comprising an estimated 39.5% of the genome. Repetitive regions, on the other hand, make up 45.4% of the genome. Physical mapping of well-studied developmental genes onto each chromosome reveals nonrandom spatial distribution of distinct genes and gene families, which provides insight into how certain gene families may have evolved and are transcriptionally regulated in this species. Lastly, aligning RNA-seq and ATAC-seq data onto this assembly demonstrates the value of highly contiguous, complete genome assemblies for functional genomics analyses that is unattainable with fragmented, incomplete assemblies. This genome will be of great value to the scientific community as a resource for genome evolution, developmental, and ecological studies of this species and the Echinodermata. 

There is significant scientific value to be gained from combining AKARI fluxes with data at other far-infrared (IR) wavelengths from the Infrared Astronomical Satellite (IRAS) and Herschel missions. To be able to do this we must ensure that there are no systematic differences between the data sets that need to be corrected before the fluxes are compatible with each other. One such systematic effect identified in the Bright Source Catalog version 1 (BSCv1) data is the issue of beam corrections. We determine these for the BSC version 2 (BSCv2) data by correlating ratios of appropriate IRAS and AKARI bands with the difference in 2 Micron All Sky Survey (2MASS) J-band extended and point source magnitudes for sources cross-matched between the IRAS Faint Source Catalog (FSC), AKARI BSCv2 and 2MASS catalogs. We find significant correlations (p ≪ 10 −13) indicating that beam corrections are necessary in the 65 and 90 μm bands. We then use these corrected fluxes to supplement existing data in spectral energy distribution (SED) fits for ultraluminous infrared galaxies (ULIRGs) in the Herschel ULIRG Survey (HERUS). The addition of AKARI fluxes makes little difference to the results of simple (T, β) fits to the SEDs of these sources, though there is a general decrease in reduced χ2 values. The utility of the extra AKARI data, however, is in allowing physically more realistic SED models with more parameters to be fitted to the data. We also extend our analysis of beam correction issues in the AKARI data by examining the Herschel Reference Sample (HRS) galaxies, which have Herschel photometry from 100 to 500 μm and which are more spatially extended than the HERUS ULIRGs. 34 of the HRS sources have good Herschel SEDs and matching data from AKARI. This investigation finds that our simple 2MASS-based beam correction scheme is inadequate for these larger and more complex sources. There are also indications that additional beam corrections at 140 and 160 μm are needed for these sources, extended on scales >1′.