Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution.
Yue JX
,
Yu JK
,
Putnam NH
,
Holland LZ
.
???displayArticle.abstract???
Cephalochordates, the sister group of tunicates plus vertebrates, have been called "living fossils" due to their resemblance to fossil chordates from Cambrian strata. The genome of the cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both cephalochordates and 10 vertebrates using an echinoderm, a hemichordate, and a mollusk as outgroups showed that cephalochordates are evolving more slowly than the slowest evolving vertebrate known (the elephant shark), with A. lucayanum evolving even more slowly than B. floridae. Against this background of slow evolution, some genes, notably several involved in innate immunity, stand out as evolving relatively quickly. This may be due to the lack of an adaptive immune system and the relatively high levels of bacteria in the inshore waters cephalochordates inhabit. Molecular dating analysis including several time constraints revealed a divergence time of ∼120 Ma for A. lucayanum and B. floridae. The divisions between cephalochordates and vertebrates, and that between chordates and the hemichordate plus echinoderm clade likely occurred before the Cambrian.
Fig. 1.—. Side views of living Asymmetron lucayanum (top) and Branchiostoma floridae (bottom). Asymmetron lucayanum has a single row of gonads on the right side only. Branchiostoma floridae has two rows of gonads—one on each side (anterior to the right).
Fig. 2.—. Fifteen-way maximum-likelihood phylogenetic tree inferred from a concatenated orthologous gene matrix (427 orthologous gene groups). The branch length is proportional to the expected amino acid substitution rate and the scale bar represents 0.08 expected amino acid substitutions per site. The numbers at the internal nodes show the statistical support for the topology of the tree based on the approximate logarithm-likelihood test. The result shown here is based on the analysis for the asymAD library. The Bayesian tree for the asymAD library and parallel analyses for the asym20h library are shown in supplementary figs. S1–S3, Supplementary Material online.
Fig. 3.—. The time frame of cephalochordate evolution inferred by MCMCTree based on the asymAD library. The Bayesian estimations for all internal nodes (nodes a–n) are tabulated in table 5. Each grey bar represents the 95% confidence interval for the corresponding estimate.
Ashkenazy,
Dynamics of a Snowball Earth ocean.
2013, Pubmed
Ashkenazy,
Dynamics of a Snowball Earth ocean.
2013,
Pubmed
Berná,
How fast is the sessile ciona?
2009,
Pubmed
Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014,
Pubmed
Borrell,
Slit/Robo signaling modulates the proliferation of central nervous system progenitors.
2012,
Pubmed
Boto,
Ecological and temporal constraints in the evolution of bacterial genomes.
2011,
Pubmed
Bourlat,
Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.
2006,
Pubmed
,
Echinobase
Bousquet,
Extensive variation in evolutionary rate of rbcL gene sequences among seed plants.
1992,
Pubmed
Castresana,
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
2000,
Pubmed
Conesa,
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
2005,
Pubmed
Dai,
Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution.
2009,
Pubmed
Darriba,
ProtTest 3: fast selection of best-fit models of protein evolution.
2011,
Pubmed
Dehal,
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.
2002,
Pubmed
Delsuc,
Additional molecular support for the new chordate phylogeny.
2008,
Pubmed
Dishaw,
The amphioxus genome provides unique insight into the evolution of immunity.
2012,
Pubmed
Douzery,
The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?
2004,
Pubmed
Downing,
Evidence of the adaptive evolution of immune genes in chicken.
2009,
Pubmed
Dunn,
Broad phylogenomic sampling improves resolution of the animal tree of life.
2008,
Pubmed
Edgar,
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
2004,
Pubmed
Geifman,
The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems.
2010,
Pubmed
Goldman,
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
1994,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Guindon,
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
2010,
Pubmed
Hansen,
Biases in Illumina transcriptome sequencing caused by random hexamer priming.
2010,
Pubmed
Holland,
Chordate roots of the vertebrate nervous system: expanding the molecular toolkit.
2009,
Pubmed
Holland,
The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
2008,
Pubmed
Holland,
Laboratory spawning and development of the Bahama lancelet, Asymmetron lucayanum (cephalochordata): fertilization through feeding larvae.
2010,
Pubmed
Holland,
Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest.
1996,
Pubmed
Holland,
An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution.
1992,
Pubmed
Huang,
Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity.
2008,
Pubmed
,
Echinobase
Huang,
HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.
2012,
Pubmed
Hurst,
Do essential genes evolve slowly?
1999,
Pubmed
Inoue,
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times.
2010,
Pubmed
Jantzen,
GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets.
2011,
Pubmed
Jones,
The rapid generation of mutation data matrices from protein sequences.
1992,
Pubmed
Junier,
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.
2010,
Pubmed
Kidd,
Roundabout controls axon crossing of the CNS midline and defines a novel subfamily of evolutionarily conserved guidance receptors.
1998,
Pubmed
Kocot,
PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.
2013,
Pubmed
Kon,
Phylogenetic position of a whale-fall lancelet (Cephalochordata) inferred from whole mitochondrial genome sequences.
2007,
Pubmed
Langmead,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
2009,
Pubmed
Le,
An improved general amino acid replacement matrix.
2008,
Pubmed
Lechner,
Proteinortho: detection of (co-)orthologs in large-scale analysis.
2011,
Pubmed
Li,
Genetic diversity and population structure of two lancelets along the coast of China.
2013,
Pubmed
Mallatt,
Fossil sister group of craniates: predicted and found.
2003,
Pubmed
Mantovani,
Neutrophils in the activation and regulation of innate and adaptive immunity.
2011,
Pubmed
Martin,
Body size, metabolic rate, generation time, and the molecular clock.
1993,
Pubmed
McTaggart,
Immune genes undergo more adaptive evolution than non-immune system genes in Daphnia pulex.
2012,
Pubmed
Meulemans,
Amphioxus and lamprey AP-2 genes: implications for neural crest evolution and migration patterns.
2002,
Pubmed
Nielsen,
A scan for positively selected genes in the genomes of humans and chimpanzees.
2005,
Pubmed
Nishikawa,
A new deep-water lancelet (Cephalochordata) from off Cape Nomamisaki, SW Japan, with a proposal of the revised system recovering the genus Asymmetron.
2004,
Pubmed
Nohara,
Evolution of the mitochondrial genome in cephalochordata as inferred from complete nucleotide sequences from two epigonichthys species.
2005,
Pubmed
Nohara,
Ancient phylogenetic separation between Pacific and Atlantic cephalochordates as revealed by mitochondrial genome analysis.
2004,
Pubmed
Ohta,
Population size and rate of evolution.
1972,
Pubmed
Peterson,
The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records.
2008,
Pubmed
Putnam,
The amphioxus genome and the evolution of the chordate karyotype.
2008,
Pubmed
Rannala,
Inferring speciation times under an episodic molecular clock.
2007,
Pubmed
Ransohoff,
Innate immunity in the central nervous system.
2012,
Pubmed
Ronquist,
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
2012,
Pubmed
Rothman,
Atmospheric carbon dioxide levels for the last 500 million years.
2002,
Pubmed
Schlenke,
Natural selection drives Drosophila immune system evolution.
2003,
Pubmed
Schmieder,
Fast identification and removal of sequence contamination from genomic and metagenomic datasets.
2011,
Pubmed
Schmieder,
Quality control and preprocessing of metagenomic datasets.
2011,
Pubmed
Seo,
Miniature genome in the marine chordate Oikopleura dioica.
2001,
Pubmed
Shimeld,
The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog.
1999,
Pubmed
Silva,
Wound repair in the Amphioxus (Branchiostoma platae), an animal deprived of inflammatory phagocytes.
1995,
Pubmed
Slater,
Automated generation of heuristics for biological sequence comparison.
2005,
Pubmed
Sperling,
Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous sponge spicules.
2010,
Pubmed
Sternberg,
Neural regulation of innate immunity: a coordinated nonspecific host response to pathogens.
2006,
Pubmed
Tajima,
Simple methods for testing the molecular evolutionary clock hypothesis.
1993,
Pubmed
Venkatesh,
Elephant shark genome provides unique insights into gnathostome evolution.
2014,
Pubmed
Wada,
Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA.
1994,
Pubmed
,
Echinobase
Wang,
Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes.
2011,
Pubmed
Wernersson,
RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences.
2003,
Pubmed
Whitehead,
Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation.
2012,
Pubmed
Wraith,
The adaptive immune system in diseases of the central nervous system.
2012,
Pubmed
Wu,
The neuronal repellent Slit inhibits leukocyte chemotaxis induced by chemotactic factors.
2001,
Pubmed
Yang,
Genome-wide analyses of amphioxus microRNAs reveal an immune regulation via miR-92d targeting C3.
2013,
Pubmed
Yang,
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.
2006,
Pubmed
Yu,
Axial patterning in cephalochordates and the evolution of the organizer.
2007,
Pubmed
Yu,
A novel C1q family member of amphioxus was revealed to have a partial function of vertebrate C1q molecule.
2008,
Pubmed
Zhang,
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging.
2006,
Pubmed
Zhang,
Novel genes dramatically alter regulatory network topology in amphioxus.
2008,
Pubmed
Ziv,
Immune cells contribute to the maintenance of neurogenesis and spatial learning abilities in adulthood.
2006,
Pubmed
dos Reis,
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.
2011,
Pubmed
