A phylogenomic framework and timescale for comparative studies of tunicates

Delsuc, Frédéric; Piégay, Hervé; Tsagkogeorga, Georgia; Simion, Paul; Tilak, Marie‐Ka; Turon, Xavier; López‐Legentil, Susanna; Piette, Jacques; Lemaire, Patrick; Douzery, Emmanuel J. P.

doi:10.1101/236448

Cited by 13 publications

(15 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…oculata belong to the order Enterogona while Ciona to the order of Pleurogona. This result was consistent with that of a previous study (Delsuc et al., 2018). In total, 78 gene families were expanded in S .…”

Section: Resultssupporting

confidence: 94%

Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

Wei

Zhang

et al. 2020

Molecular Ecology Resources

View full text Add to dashboard Cite

Tunicates occupy the evolutionary position at the boundary of invertebrates and vertebrates. It exhibits adaptation to broad environmental conditions and is distributed globally. Despite hundreds of years of embryogenesis studies, the genetic basis of the invasive habits of ascidians remains largely unknown. The leathery sea squirt, Styela clava, is an important invasive species. We used the chromosomal‐level genome and transcriptome of S. clava to explore its genomic‐ and molecular‐network‐based mechanisms of adaptation to environments. Compared with Ciona intestinalis type A (C. robusta), the size of the S. clava genome was expanded by 2‐fold, although the gene number was comparable. An increase in transposon number and variation in dominant types were identified as potential expansion mechanisms. In the S. clava genome, the number of genes encoding the heat‐shock protein 70 family and members of the complement system was expanded significantly, and cold‐shock protein genes were transferred horizontally into the S. clava genome from bacteria. The expanded gene families potentially play roles in the adaptation of S. clava to its environments. The loss of key genes in the galactan synthesis pathway might explain the distinct tunic structure and hardness compared with the ascidian Ciona species. We demonstrated further that the integrated thyroid hormone pathway participated in the regulation of larval metamorphosis that provides S. clava with two opportunities for adapting to their environment. Thus, our report of the chromosomal‐level leathery sea squirt genome provides a comprehensive genomic basis for the understanding of environmental adaptation in tunicates.

show abstract

Section: Resultssupporting

confidence: 94%

Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

Wei

Zhang

et al. 2020

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…In our tests, the NG50 of the crocodile assemblies increased to 14.44 Mbp and 12.92 Mbp for saltwater and gharial crocodiles (baseline NG50 0.14 Mbp and 0.07 Mbp), with a corresponding increase in BUSCO (Simão, et al, 2015) gene completeness of 2.6% and 9.5%, respectively. This demonstrates that ntJoin can still leverage synteny between these target and reference assemblies despite the species having diverged around 80 million years ago (Delsuc, et al, 2018).…”

Section: Resultsmentioning

confidence: 96%

“…Existing reference-guided scaffolders such as Ragout (Kolmogorov, et al, 2018) and Ragoo (Alonge, et al, 2019) rely on alignments of the draft assembly to a reference assembly; Ragout utilizes Progressive Cactus (Armstrong, et al, 2019) for large genomes, while Ragoo depends on minimap2 (Li, 2018) for the task. The use of minimizer sketches in tools such as minimap2 is very effective in compactly representing genome sequences.…”

Section: Introductionmentioning

confidence: 99%

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs

Coombe

Nikolić

Chu

et al. 2020

Preprint

View full text Add to dashboard Cite

AbstractSummaryThe ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of different applications, including improving a draft assembly with a reference-grade genome, a short read assembly with a draft long read assembly, and a draft assembly with an assembly from a closely-related species. When scaffolding a human short read assembly using the reference human genome or a long read assembly, ntJoin improves the NGA50 length 23- and 13-fold, respectively, in under 13 m, using less than 11 GB of RAM. Compared to existing reference-guided assemblers, ntJoin generates highly contiguous assemblies faster and using less memory.Availability and implementationntJoin is written in C++ and Python, and is freely available at https://github.com/bcgsc/ntjoin.Contactlcoombe@bcgsc.ca

show abstract

“…Lastly, we included outgroup sequences from Caenorhabditis elegans and Branchiostoma lanceolatum (invertebrate mitochondrial code) and from Mus musculus (vertebrate mitochondrial code) to better highlight conserved amino acid positions. In Figure 1, we illustrate the relation between these species based on the phylogeny of Naville et al (2019) for appendicularians and of Delsuc et al (2018) for the other tunicates. We prepared Cox1 sequences from the selected species using mitochondrial genomes (for ascidians, thaliaceans, and outgroups), from draft genomes in which we found a putative mitochondrial contig after screening with a partial or a related Cox 1 sequence (for O. longicauda, B. stygius, and M. erythrocephalus) and from EST sequences (for O. dioica).…”

Section: Agr Encodes For Gly Across All Tunicatesmentioning

confidence: 99%

“…The relationship between these classes and therefore their mono-or paraphyly has been revised multiple times. For instance the 18S rRNA analysis of Stach and Turbeville (2002) nested Appendicularia within Ascidiacea, but more recently Delsuc et al (2018) placed them as sister groups using a multigene approach. The paraphyly of Ascidiacea is now widely accepted, as the above studies and others demonstrated that they contain the Thaliacea.…”

Section: Introductionmentioning

confidence: 99%

Widespread use of the “ascidian” mitochondrial genetic code in tunicates

Pichon

Luscombe

Plessy

2019

Preprint

View full text Add to dashboard Cite

Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI's GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences.Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes.Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions:We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional speciesspecific differences.

show abstract

A phylogenomic framework and timescale for comparative studies of tunicates

Abstract: Background. Tunicates are the closest relatives of vertebrates and are widely used as

Cited by 13 publications

References 76 publications

Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs

Widespread use of the “ascidian” mitochondrial genetic code in tunicates

Contact Info

Product

Resources

About