A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

Small, Kerrin S.; Brudno, Michael; Hill, M. Manuela; Sidow, Arend

doi:10.1186/gb-2007-8-3-r41

Cited by 94 publications

(87 citation statements)

References 40 publications

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“…S4) of the red flour beetle Tribolium castaneum (58), the fruitfly D. melanogaster (23,59), one crustacean, Daphnia pulex (60), one nematode, C. elegans (61), two lophotrochozoans, the pond snail L.gigantea and C. teleta (62), two ambulacrarians, the sea urchin S. purpuratus (63) and the acorn worm S. kowalevskii, four chordates, the tunicate Ciona intestinalis (64), the amphioxus Branchiostoma floridae (65), the fish Takifugu rubripes (66), and Homo sapiens (67,68). To better support the analysis, we partially included some genomic sequences from another nematode, Pristionchus pacificus (69), a tunicate, Ciona savignyi (70), and an insect, Acyrthosiphon pisum (71). We were also interested in annotating the neuropeptide GPCRs from the Lamprey Petromyzon marinus, whose genome was recently sequenced (72).…”

Section: Methodsmentioning

confidence: 99%

Molecular evolution of peptidergic signaling systems in bilaterians

Mirabeau

Joly

2013

Proc. Natl. Acad. Sci. U.S.A.

377

707

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Peptide hormones and their receptors are widespread in metazoans, but the knowledge we have of their evolutionary relationships remains unclear. Recently, accumulating genome sequences from many different species have offered the opportunity to reassess the relationships between protostomian and deuterostomian peptidergic systems (PSs). Here we used sequences of all human rhodopsin and secretin-type G protein-coupled receptors as bait to retrieve potential homologs in the genomes of 15 bilaterian species, including nonchordate deuterostomian and lophotrochozoan species. Our phylogenetic analysis of these receptors revealed 29 wellsupported subtrees containing mixed sets of protostomian and deuterostomian sequences. This indicated that many vertebrate and arthropod PSs that were previously thought to be phyla specific are in fact of bilaterian origin. By screening sequence databases for potential peptides, we then reconstructed entire bilaterian peptide families and showed that protostomian and deuterostomian peptides that are ligands of orthologous receptors displayed some similarity at the level of their primary sequence, suggesting an ancient coevolution between peptide and receptor genes. In addition to shedding light on the function of human G protein-coupled receptor PSs, this work presents orthology markers to study ancestral neuron types that were probably present in the last common bilaterian ancestor. neuropeptide evolution | GPCR evolution | bilaterian CNS cell types | bilaterian brain evolution

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Section: Methodsmentioning

confidence: 99%

Molecular evolution of peptidergic signaling systems in bilaterians

Mirabeau

Joly

2013

Proc. Natl. Acad. Sci. U.S.A.

377

707

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“…The overall coverage from the C. savignyi data sets was highly variable, due to poor mapping quality ( Figure S1). The C. savignyi reference genome consists of 374 reftigs with an N50 of 1.8 Mb (Vinson et al 2005;Small et al 2007b). Two hundred and twenty-seven of the largest …”

Section: Homozygosity Mapsmentioning

confidence: 99%

“…Reference genome sequences are now available for both C. intestinalis and the closely related species C. savignyi. Both Ciona species have compact genomes (160 Mb) with relatively few protein-encoding genes (16,000 genes) (Shoguchi et al 2006;Small et al 2007b). In addition, both Ciona species display very high levels of natural genomic variation; the two haplotypes in the reference genomes of C. intestinalis and C. savignyi are 1 and 4% different, respectively (Dehal et al 2002;Small et al 2007a;Satou et al 2012).…”

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confidence: 99%

“…For the initial round of mapping we used the two crossfertilized data sets. Mapping with self vs. cross-fertilized data sets will be treated separately, below.To map the homozygosity, the Illumina sequences were first aligned to their respective reference genomes and filtered for mapping and sequence base quality (Dehal et al 2002;Small et al 2007b). Using a cutoff of MapQ $15 (Table 1 and Figure S1), 68% of the C. intestinalis reads mapped to the genome, vs. 40% of the C. savignyi reads (Table 1).…”

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confidence: 99%

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Exploiting the Extraordinary Genetic Polymorphism ofCionafor Developmental Genetics with Whole Genome Sequencing

et al. 2014

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Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, a-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca 2+ channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.A valuable attribute of many model organisms is the ability to conduct forward and reverse genetics. The availability of sequenced genomes and transcriptomes have streamlined reverse genetic approaches, but forward genetic approaches remain time consuming and cumbersome. Even for organisms with well-developed mutation mapping strategies and resources, classical linkage analysis can be slow and subject to chance. Genome-wide association studies now provide an alternative approach, but are severely limited by the need for high-frequency alleles and very large samples (Marchini et al. 2007;Cheng et al. 2010). A need remains for additional phenotype-to-genotype strategies in, for example, the investigation of quantitative traits, natural variation, and disease loci (Hillier et al. 2008;Jelier et al. 2011;Liti and Louis 2012;Lehner 2013). In recent years, new and inexpensive deep sequencing technologies have created opportunities for forward genetic approaches (Hobert 2010). By taking a snapshot of variation across the genome of an outbred population, a researcher can now quickly identify a region of homozygosity unique to mutant individuals. Variations of this method then use a fine-mapping parameter to define a high-confidence mapping interval and to retrieve a list of variable sites in the interval as a list of possible causal mutations. Modeling shows that the mapping power using whole-genome sequencing (WGS) is a function of how many genomes are sampled from mutant individuals, the recombination rate, and genome coverage (Leshchiner et al. 2012;Obholzer et al. 2012). This approach has worked efficiently and accurately for the well-assembled, annotated, and inbred genomes of model organisms such as Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus (Blumenstiel et al. 2009;Andersen et al. 2012;Leshchiner et al. 2012).Tunicates, such as the ascidian Ciona intestinalis, are clas...

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“…1J). The annotated genome sequences of two ascidians (Ciona savignyi and C. intestinalis) and one appendicularian (O. dioica) have been published (Dehal et al, 2002;Small et al, 2007;Denoeud et al, 2010) (Table 1). Genomic sequences in C. intestinalis have been mapped onto its 14 chromosomes, a prerequisite to studying the global organization of the genome (Shoguchi et al, 2006).…”

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confidence: 99%

Evolutionary crossroads in developmental biology: the tunicates

2011

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The tunicates, or urochordates, constitute a large group of marine animals whose recent common ancestry with vertebrates is reflected in the tadpole-like larvae of most tunicates. Their diversity and key phylogenetic position are enhanced, from a research viewpoint, by anatomically simple and transparent embryos, compact rapidly evolving genomes, and the availability of powerful experimental and computational tools with which to study these organisms. Tunicates are thus a powerful system for exploring chordate evolution and how extreme variation in genome sequence and gene regulatory network architecture is compatible with the preservation of an ancestral chordate body plan. Key words: Chordates, Tunicates, Asexual development, Budding, Embryogenesis, EvolutionIntroduction Cephalochordates (including Amphioxus; see Glossary, Box 1), tunicates (or urochordates, see Glossary, Box 1) and vertebrates constitute the chordate phylum, which is characterized by a tadpolelike body plan at the end of embryogenesis. The rigidity of the tail of these tadpoles is ensured by a unique structure, the notochord, which gave its name to the phylum. Fossil evidence, although sometimes controversial, suggests that ancestral chordates roamed Cambrian oceans more than 550 million years ago (Morris, 1999;Shu et al., 1996).It is now thought that cephalochordates are the most basal chordates. Tunicates and vertebrates are sister taxa (see Glossary, Box 1), which diverged more recently (Delsuc et al., 2006;Bourlat et al., 2006;Putnam et al., 2008). This molecular classification is supported at the anatomical level by the presence in tunicate larvae, but not in those of cephalochordates or of any other invertebrate, of cells similar to vertebrate migratory neural crest cells (Jeffery, 2007).The tunicates constitute a diverse group of animals that are united by the cellulose-containing tunic that covers their body (Nakashima et al., 2004). They are traditionally split into three major classes: the ascidians, thaliaceans and appendicularians, whose phylogenetic relationships are depicted in Fig. 1 (Tsagkogeorga et al., 2009;Govindarajan et al., 2010). Ascidians, also called sea squirts, are the most diverse tunicate group and include several developmental models such as Ciona intestinalis, Halocynthia roretzi and Botryllus schlosseri. These vase-like benthic filter feeders (see Glossary, Box 1) ('ascidian' derives from Development 138, 2143Development 138, -2152Development 138, (2011 Filter feeder. Organisms that feed on particulate food suspended in water. In tunicates, water enters the body via the oral siphon, is filtered on the branchial basket and expelled through an atrial siphon (in appendicularians, water is expelled through gill slits).Hybridization. The production of offspring by interbreeding between two individuals of different species. Kernel. A small region of a gene regulatory network that is evolutionarily highly conserved, the retention of which might underlie the conservation of body plans and the development of major ...

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A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

Abstract: The high degree of polymorphism in the genome of the sea squirt Ciona savignyi complicated the assembly of sequence contigs, but a new alignment method results in a much improved sequence.

Cited by 94 publications

References 40 publications

Molecular evolution of peptidergic signaling systems in bilaterians

Molecular evolution of peptidergic signaling systems in bilaterians

Exploiting the Extraordinary Genetic Polymorphism ofCionafor Developmental Genetics with Whole Genome Sequencing

Evolutionary crossroads in developmental biology: the tunicates

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