ABSTRACT
Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
Subject(s)
Biological Evolution , DNA, Algal/genetics , Genome , Phytophthora/genetics , Phytophthora/pathogenicity , Algal Proteins/genetics , Algal Proteins/physiology , Genes , Hydrolases/genetics , Hydrolases/metabolism , Photosynthesis/genetics , Phylogeny , Physical Chromosome Mapping , Phytophthora/classification , Phytophthora/physiology , Plant Diseases/microbiology , Polymorphism, Single Nucleotide , Repetitive Sequences, Nucleic Acid , Sequence Analysis, DNA , Symbiosis , Toxins, Biological/geneticsABSTRACT
The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
Subject(s)
Ciona intestinalis/genetics , Genome , Sequence Analysis, DNA , Alleles , Animals , Apoptosis , Base Sequence , Cellulose/metabolism , Central Nervous System/physiology , Ciona intestinalis/anatomy & histology , Ciona intestinalis/classification , Ciona intestinalis/physiology , Computational Biology , Endocrine System/physiology , Gene Dosage , Gene Duplication , Genes , Genes, Homeobox , Heart/embryology , Heart/physiology , Immunity/genetics , Molecular Sequence Data , Multigene Family , Muscle Proteins/genetics , Organizers, Embryonic/physiology , Phylogeny , Polymorphism, Genetic , Proteins/genetics , Proteins/physiology , Sequence Homology, Nucleic Acid , Species Specificity , Thyroid Gland/physiology , Urochordata/genetics , Vertebrates/anatomy & histology , Vertebrates/classification , Vertebrates/genetics , Vertebrates/physiologyABSTRACT
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.
