On the Extent and Origins of Genic Novelty in the Phylum Nematoda

Wasmuth, James D.; Schmid, Ralf; Hedley, Ann; Blaxter, Mark

doi:10.1371/journal.pntd.0000258

Cited by 71 publications

(65 citation statements)

References 94 publications

(120 reference statements)

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“…Among the families derived from the deeper nodes of the phylogeny were many examples of proteins generally perceived as being involved in conserved housekeeping functions, for example, ribosomal subunits (Supplemental Tables S1-S4). This is in contrast to previous studies of conserved nematode-specific (Wasmuth et al 2008). Whether this is truly reflective of apicomplexan-wide innovations or merely a consequence of Apicomplexa's ancient origins remains to be elucidated (Baldauf 2003).…”

Section: Discussioncontrasting

confidence: 62%

“…For the complete genomes, the global domain model library (''ls'') was used and the curated gathering score (GA) cutoff was applied to each model. For the EST-derived partial genomes, we use a hybrid approach to maximize coverage (Wasmuth et al 2008).…”

Section: Protein Family Alignments and Phylogenymentioning

confidence: 99%

“…2; Carlton et al 2002;Gardner et al 2002Gardner et al , 2005Abrahamsen et al 2004;Xu et al 2004;Pain et al 2005). Furthermore, large expressed sequence tag (EST) collections have been generated for an additional nine species (Ajioka et al 1998;Howe 2001;Li et al 2003a;Cui et al 2005), which can be used to construct so-called ''partial genomes '' (Peregrin-Alvarez and Parkinson 2007;Wasmuth et al 2008). Studies of these data sets have provided insights into adaptations that relate to their parasitic ecology, such as the identification of expanded families of proteases in Plasmodium (Wu et al 2003).…”

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confidence: 99%

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The origins of apicomplexan sequence innovation

Wasmuth¹,

Daub²,

Peregrín-Alvarez³

et al. 2009

Genome Res.

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The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here, we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared with three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles that reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan specialized. These were collated into 9134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription, which have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.

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Section: Discussioncontrasting

confidence: 62%

Section: Protein Family Alignments and Phylogenymentioning

confidence: 99%

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confidence: 99%

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The origins of apicomplexan sequence innovation

Wasmuth¹,

Daub²,

Peregrín-Alvarez³

et al. 2009

Genome Res.

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“…Examples of HGT between unrelated or nonmating species are abundant among prokaryotes (10,11) but less so between prokaryotes and unicellular (12)(13)(14) or multicellular eukaryotes (15)(16)(17)(18)(19)(20). Most of these latter examples are associated with parasitism or phagotrophy, including the elegant studies of HGT from the ␣-proteobacteria Wolbachia to insects and nematodes (16)(17)(18), and the finding of rhizobial-like genes in plant parasitic nematodes (19,20).…”

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confidence: 99%

“…Most of these latter examples are associated with parasitism or phagotrophy, including the elegant studies of HGT from the ␣-proteobacteria Wolbachia to insects and nematodes (16)(17)(18), and the finding of rhizobial-like genes in plant parasitic nematodes (19,20). The exchange of genetic material between two eukaryotes is extremely rare, or at least not well documented to date.…”

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Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

Rumpho

Worful²,

Lee³

et al. 2008

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

239

169

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The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed proteins. Two possible explanations for the persistence of photosynthesis in the sea slug are (i) the ability of V. litorea plastids to retain genetic autonomy and/or (ii) more likely, the mollusc provides the essential plastid proteins. Under the latter scenario, genes supporting photosynthesis have been acquired by the animal via horizontal gene transfer and the encoded proteins are retargeted to the plastid. We sequenced the plastid genome and confirmed that it lacks the full complement of genes required for photosynthesis. In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3 flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty (''green animals'') and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.symbiosis ͉ Vaucheria litorea ͉ evolution ͉ plastid ͉ stramenopile

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Structure, Function and Evolution of The Nematode Genome

Rödelsperger

Streit

Sommer

2013

Encyclopedia of Life Sciences

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In the past few years, an increasing number of draft genome sequences of multiple free‐living and parasitic nematodes have been published. Although nematode genomes vary in size within an order of magnitude, compared with mammalian genomes, they are all very small. Nevertheless, nematodes possess only marginally fewer genes than mammals do. Nematode genomes are very compact and therefore form a highly attractive system for comparative studies of genome structure and evolution. Strikingly, approximately one‐third of the genes in every sequenced nematode genome has no recognisable homologues outside their genus. One observes high rates of gene losses and gains, among them numerous examples of gene acquisition by horizontal gene transfer. Not only does the ‘gene for parasitism’ not exist, but also there appear to be no common genomic characteristics of parasitic nematode genomes which would distinguish them from genomes of free‐living nematodes. Key Concepts: Nematode genomes tend to be compact. Nematode genomes vary in their gene composition due to extensive gene gain and loss. Genes are lost through gene deletion or rapid evolutionary change beyond the point where they can be recognised as homologous to a gene in another species. Genes are acquired through gene duplication, de novo formation and horizontal gene transfer. Horizontal gene transfer allows nematode species to acquire new physiological properties. All nematode genomes sequenced so far contain operons, multigene transcription units giving rise to a single pre‐mRNA, which is broken up into single protein coding mRNAs by trans‐splicing and polyadenylation. Within the nematodes parasitism has arisen multiple times independently and a ‘gene for parasitism’ or unifying parasite genomic features were not identified.

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On the Extent and Origins of Genic Novelty in the Phylum Nematoda

Cited by 71 publications

References 94 publications

The origins of apicomplexan sequence innovation

The origins of apicomplexan sequence innovation

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

Structure, Function and Evolution of The Nematode Genome

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