Sea Urchin Dna Sequence Variation and Reduced Interspecies Differences of the Less Variable Dna Sequences

Grula, John W.; Hall, Thad E.; Hunt, John M.; Giugni, T. D.; Graham, Geoffrey J.; Davidson, Eric H.; Britten, Roy J.

doi:10.1111/j.1558-5646.1982.tb05434.x

Cited by 26 publications

(5 citation statements)

References 12 publications

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“…Given the apparently swift recombination of the Sp185/333 genes, molecular clock analysis of the evolutionary history of the Sp185/333 family suggests that the last common ancestral Sp185/333 sequence of the extant genes may have been present in the population of purple sea urchins 2.7–10 million years ago (Ghosh et al, 2010 ). This time frame overlaps with the estimated time period when Strongylocentrotus purpuratus diverged from its sister species (Grula et al, 1982 ; Biermann, 1998 ; Lee, 2003 ; Buckley et al, 2008a ). When trace sequences of 185/333 genes from the genomes of two other sea urchins, S. franciscanus and Allocentrotus fragilis are compared to the Sp185/333 sequences from S. purpuratus , molecular clock analysis shows that the divergence times for these three gene families appear older than the three species of sea urchins in which they function.…”

Section: The Sp185/333 Genessupporting

confidence: 55%

Innate immune complexity in the purple sea urchin: diversity of the Sp185/333 system

Smith

2012

Front. Immun.

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The California purple sea urchin, Strongylocentrotus purpuratus, is a long-lived echinoderm with a complex and sophisticated innate immune system. There are several large gene families that function in immunity in this species including the Sp185/333 gene family that has ∼50 (±10) members. The family shows intriguing sequence diversity and encodes a broad array of diverse yet similar proteins. The genes have two exons of which the second encodes the mature protein and has repeats and blocks of sequence called elements. Mosaics of element patterns plus single nucleotide polymorphisms-based variants of the elements result in significant sequence diversity among the genes yet maintains similar structure among the members of the family. Sequence of a bacterial artificial chromosome insert shows a cluster of six, tightly linked Sp185/333 genes that are flanked by GA microsatellites. The sequences between the GA microsatellites in which the Sp185/333 genes and flanking regions are located, are much more similar to each other than are the sequences outside the microsatellites suggesting processes such as gene conversion, recombination, or duplication. However, close linkage does not correspond with greater sequence similarity compared to randomly cloned and sequenced genes that are unlikely to be linked. There are three segmental duplications that are bounded by GAT microsatellites and include three almost identical genes plus flanking regions. RNA editing is detectible throughout the mRNAs based on comparisons to the genes, which, in combination with putative post-translational modifications to the proteins, results in broad arrays of Sp185/333 proteins that differ among individuals. The mature proteins have an N-terminal glycine-rich region, a central RGD motif, and a C-terminal histidine-rich region. The Sp185/333 proteins are localized to the cell surface and are found within vesicles in subsets of polygonal and small phagocytes. The coelomocyte proteome shows full-length and truncated proteins, including some with missense sequence. Current results suggest that both native Sp185/333 proteins and a recombinant protein bind bacteria and are likely important in sea urchin innate immunity.

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Section: The Sp185/333 Genessupporting

confidence: 55%

Innate immune complexity in the purple sea urchin: diversity of the Sp185/333 system

Smith

2012

Front. Immun.

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“…Homologous Tm'S measured for DNAs prepared from multiple individuals will be depressed over homologous T~'s measured for DNAs prepared from a single individual due to intraspecific polymorphism (Britten et al 1978). Reductions in thermal stabilities from intraspecific polymorphism ranged from 2 to 4°C (+0.5°C) for species of Strongylocentrotus (Grula et al 1982). For our data, all homologous Tm'S were based on DNA derived from approximately 20 males, except for Clypeaster where DNA was extracted from just one male (Table 1).…”

Section: Corrections To Raw Datamentioning

confidence: 99%

DNA-DNA hybridization phylogeny of sand dollars and highly reproducible extent of hybridization values

Marshall

Swift

1992

J Mol Evol

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A DNA hybridization phylogeny of four sand dollars using a sea biscuit as an outgroup is presented. The study is unusual in that the normalized percent hybridization (NPH) values were all less than 50%, yet the same topology was obtained regardless of which distance metric was used, i.e., whether reciprocal distances were averaged or not, or whether or not a molecular clock was assumed. The tree also appears robust under jackknifing and bootstrapping. The extent of hybridization between homologous hybrids was measured with a five- to sevenfold higher precision than is typical, and by implication NPH was also measured with a higher than normal precision. The ability to measure highly reproducible NPH values offers the possibility of examining the phylogeny of more widely divergent species than typically studied using DNA hybridization techniques, using 1/NPH as a distance metric. The hypothesis of a molecular clock within the sand dollars was rejected, adding sand dollars to the growing list of groups where significant rate variation is known. A small fraction of the sand dollar genomes hybridized with the distantly related regular sea urchin Lytechinus. These slowly evolving sequences probably represent conserved exonic components of the genome.

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“…Echinoderms are outbred animals that exhibit high levels of heterozygosity (an estimated 4-5% in S. purpuratus [58]). Inbred lines are not currently available for any echinoderm species, which may reflect high numbers of deleterious recessive alleles [59].…”

Section: Bacs Serve As a Stable Invariant Sequence For Confirming Thmentioning

confidence: 99%

Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms

Buckley

Dong

Cameron³

et al. 2017

Briefings in Functional Genomics

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Genome sequences contain all the necessary information-both coding and regulatory sequences-to construct an organism. The developmental process translates this genomic information into a three-dimensional form. One interpretation of this translation process can be described using gene regulatory network (GRN) models, which are maps of interactions among regulatory gene products in time and space. As high throughput investigations reveal increasing complexity within these GRNs, it becomes apparent that efficient methods are required to test the necessity and sufficiency of regulatory interactions. One of the most complete GRNs for early development has been described in the purple sea urchin, Strongylocentrotus purpuratus. This work has been facilitated by two resources: a well-annotated genome sequence and transgenes generated in bacterial artificial chromosome (BAC) constructs. BAC libraries played a central role in assembling the S. purpuratus genome sequence and continue to serve as platforms for generating reporter constructs for use in expression and regulatory analyses. Optically transparent echinoderm larvae are highly amenable to transgenic approaches and are therefore particularly well suited for experiments that rely on BAC-based reporter transgenes. Here, we discuss the experimental utility of BAC constructs in the context of understanding developmental processes in echinoderm embryos and larvae.

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Sea Urchin Dna Sequence Variation and Reduced Interspecies Differences of the Less Variable Dna Sequences

Cited by 26 publications

References 12 publications

Innate immune complexity in the purple sea urchin: diversity of the Sp185/333 system

Innate immune complexity in the purple sea urchin: diversity of the Sp185/333 system

DNA-DNA hybridization phylogeny of sand dollars and highly reproducible extent of hybridization values

Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms

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