Institution
Whitney Laboratory for Marine Bioscience
About: Whitney Laboratory for Marine Bioscience is a based out in . It is known for research contribution in the topics: Population & Genome. The organization has 200 authors who have published 382 publications receiving 11563 citations.
Topics: Population, Genome, Capitella teleta, Aplysia, Gene
Papers published on a yearly basis
Papers
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TL;DR: The genome of the ctenophore the warty comb jelly or sea walnut, Mnemiopsis leidyi, is sequenced and it is concluded that c tenophores alone, not sponges or the clade consisting of both ctenphores and cnidarians, are the most basal extant animals.
Abstract: An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.
621 citations
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Whitney Laboratory for Marine Bioscience1, Auburn University2, Florida State University3, Pompeu Fabra University4, University of Massachusetts Medical School5, University of Illinois at Urbana–Champaign6, University of Groningen7, Sunnybrook Research Institute8, Russian Academy of Sciences9, University of Florida10, Genetic Information Research Institute11, University of Washington12, Royal Holloway, University of London13, Catalan Institution for Research and Advanced Studies14
TL;DR: The draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, are presented, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes.
Abstract: The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.
610 citations
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TL;DR: The genome organization, gene structure and functional content of the owl limpet, a marine polychaete and a freshwater leech are more similar to some invertebrate deuterostome genomes than those of other protostomes that have been sequenced to date.
Abstract: Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.
550 citations
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TL;DR: To study the relationships among all deuterostome groups, an alignment of more than 35,000 homologous amino acids is assembled, including new data from a hemichordate, starfish and Xenoturbella and it is concluded that chordates are monophyletic.
Abstract: Deuterostomes comprise vertebrates, the related invertebrate chordates (tunicates and cephalochordates) and three other invertebrate taxa: hemichordates, echinoderms and Xenoturbella. The relationships between invertebrate and vertebrate deuterostomes are clearly important for understanding our own distant origins. Recent phylogenetic studies of chordate classes and a sea urchin have indicated that urochordates might be the closest invertebrate sister group of vertebrates, rather than cephalochordates, as traditionally believed. More remarkable is the suggestion that cephalochordates are closer to echinoderms than to vertebrates and urochordates, meaning that chordates are paraphyletic. To study the relationships among all deuterostome groups, we have assembled an alignment of more than 35,000 homologous amino acids, including new data from a hemichordate, starfish and Xenoturbella. We have also sequenced the mitochondrial genome of Xenoturbella. We support the clades Olfactores (urochordates and vertebrates) and Ambulacraria (hemichordates and echinoderms). Analyses using our new data, however, do not support a cephalochordate and echinoderm grouping and we conclude that chordates are monophyletic. Finally, nuclear and mitochondrial data place Xenoturbella as the sister group of the two ambulacrarian phyla. As such, Xenoturbella is shown to be an independent phylum, Xenoturbellida, bringing the number of living deuterostome phyla to four.
482 citations
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TL;DR: This work uses transcriptome and genome data from all major lineages (except Monoplacophora) and recovers a well-supported topology for Mollusca to propose the node-based name Pleistomolluscan, which strongly support the Aculifera hypothesis and finds support for advanced cephalization and shells as possibly having multiple origins within Mollsusca.
Abstract: Evolutionary relationships among the eight major lineages of Mollusca have remained unresolved despite their diversity and importance. Previous investigations of molluscan phylogeny, based primarily on nuclear ribosomal gene sequences or morphological data, have been unsuccessful at elucidating these relationships. Recently, phylogenomic studies using dozens to hundreds of genes have greatly improved our understanding of deep animal relationships. However, limited genomic resources spanning molluscan diversity has prevented use of a phylogenomic approach. Here we use transcriptome and genome data from all major lineages (except Monoplacophora) and recover a well-supported topology for Mollusca. Our results strongly support the Aculifera hypothesis placing Polyplacophora (chitons) in a clade with a monophyletic Aplacophora (worm-like molluscs). Additionally, within Conchifera, a sister-taxon relationship between Gastropoda and Bivalvia is supported. This grouping has received little consideration and contains most (>95%) molluscan species. Thus we propose the node-based name Pleistomollusca. In light of these results, we examined the evolution of morphological characters and found support for advanced cephalization and shells as possibly having multiple origins within Mollusca.
424 citations
Authors
Showing all 200 results
Name | H-index | Papers | Citations |
---|---|---|---|
James C. Liao | 93 | 351 | 29976 |
Jeffrey L. Boore | 78 | 158 | 29408 |
David Simmons | 74 | 533 | 25222 |
Mark Q. Martindale | 69 | 233 | 18809 |
Mikhail V. Matz | 55 | 179 | 14226 |
Leonid L. Moroz | 51 | 179 | 8905 |
Li Liu | 43 | 211 | 6952 |
Barry W. Ache | 37 | 123 | 4552 |
William R. Harvey | 37 | 84 | 3621 |
Elaine C. Seaver | 31 | 53 | 4862 |
Joseph F. Ryan | 30 | 82 | 3857 |
Andrea B. Kohn | 27 | 71 | 3377 |
Il Memming Park | 26 | 93 | 2182 |
Peter A. V. Anderson | 26 | 55 | 1731 |
Judit Tóth | 25 | 86 | 2658 |