Abstract:
:Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene cluster using the bacterial artificial chromosome library of the Lake Victoria cichlid, Haplochromis chilotes. In the cluster region, we found 61 intact OlfC genes, which is the largest number of OlfC genes identified among the seven teleost fish investigated to date. Data mining of the Oreochromis niloticus (Nile tilapia) draft genome sequence, and genomic Southern hybridization analysis revealed that the ancestor of all modern cichlids had already developed almost the same OlfC gene repertoire, which was accomplished by lineage-specific gene expansions. Furthermore, comparison of receptor sequences showed that recently duplicated paralogs are more variable than orthologs of different species at particular sites that were predicted to be involved in amino acid selectivity. Thus, the increase of paralogs through gene expansion may lead to functional diversification in detection of amino acids. This study implies that cichlids have developed a potent capacity to detect a variety of amino acids (and their derivatives) through OlfCs, which may have contributed to the extraordinary diversity of their feeding habitats.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Nikaido M,Suzuki H,Toyoda A,Fujiyama A,Hagino-Yamagishi K,Kocher TD,Carleton K,Okada Ndoi
10.1093/gbe/evt041subject
Has Abstractpub_date
2013-01-01 00:00:00pages
711-22issue
4issn
1759-6653pii
evt041journal_volume
5pub_type
杂志文章abstract::Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trema...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evab010
更新日期:2021-01-23 00:00:00
abstract::Organisms show striking differences in genome structure; however, the functional implications and fundamental forces that govern these differences remain obscure. The intron-exon organization of nuclear genes is involved in a particularly large variety of structures and functional roles. We performed a 22-species stud...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr056
更新日期:2011-01-01 00:00:00
abstract::By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are le...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq067
更新日期:2010-01-01 00:00:00
abstract::Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy177
更新日期:2018-09-01 00:00:00
abstract::OAS (2'-5'-oligoadenylate synthases) proteins and cyclic GMP-AMP synthase (cGAS, gene symbol: MB21D1) patrol the cytoplasm for the presence of foreign nucleic acids. Upon binding to double-stranded RNA or double-stranded DNA, OAS proteins and cGAS produce nucleotide second messengers to activate RNase L and STING (sti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv046
更新日期:2015-03-09 00:00:00
abstract::The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host im...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy124
更新日期:2018-09-01 00:00:00
abstract::To fulfill their physiological functions, bile acids are conjugated with amino acids. In humans, conjugation is catalyzed by bile acid coenzyme A: amino acid N-acyltransferase (BAAT), an enzyme with a highly conserved catalytic triad in its active site. Interestingly, the conjugated amino acids are highly variable amo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz238
更新日期:2019-11-01 00:00:00
abstract::Coliphage phi1, which was isolated for phage therapy in the Republic of Georgia, is closely related to the T-like myovirus RB49. The approximately 275 open reading frames encoded by each phage have an average level of amino acid identity of 95.8%. RB49 lacks 7 phi1 genes while 10 phi1 genes are missing from RB49. Most...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq006
更新日期:2010-02-01 00:00:00
abstract::The mechanistic basis of regulatory variation and the prevailing evolutionary forces shaping that variation are known to differ between sexes and between chromosomes. Regulatory variation of gene expression can be due to functional changes within a gene itself (cis) or in other genes elsewhere in the genome (trans). T...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu060
更新日期:2014-04-01 00:00:00
abstract::Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (blac...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy183
更新日期:2018-10-01 00:00:00
abstract::Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired sh...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu046
更新日期:2014-03-01 00:00:00
abstract::Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male dete...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv128
更新日期:2015-07-02 00:00:00
abstract::The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A. mellifera nest in concealed cavities. Additionally, the worker and reproducti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz277
更新日期:2020-01-01 00:00:00
abstract::The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv244
更新日期:2015-12-08 00:00:00
abstract::The ribonuclease (RNase) A superfamily is a vertebrate-specific gene family. Because of a massive expansion that occurred during the early mammalian evolution, extant mammals in general have much more RNase genes than nonmammalian vertebrates. Mammalian RNases have been associated with diverse physiological functions ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt161
更新日期:2013-01-01 00:00:00
abstract::piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. More...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa064
更新日期:2020-05-01 00:00:00
abstract::African trypanosomiasis is a vector-borne disease of humans and livestock caused by African trypanosomes (Trypanosoma spp.). Survival in the vertebrate bloodstream depends on antigenic variation of Variant Surface Glycoproteins (VSGs) coating the parasite surface. In T. brucei, a model for antigenic variation, monoall...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy186
更新日期:2018-09-01 00:00:00
abstract::A long-standing mystery of genomic/transcriptomic structure involves spliced leader trans-splicing (SLTS), in which short RNA "tags" transcribed from a distinct genomic locus is added near the 5' end of RNA transcripts by the spliceosome. SLTS has been observed in diverse eukaryotes in a phylogenetic pattern implying ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz217
更新日期:2019-10-01 00:00:00
abstract::Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy011
更新日期:2018-02-01 00:00:00
abstract::Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we i...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa065
更新日期:2020-04-01 00:00:00
abstract::Members from Colletotrichum genus adopt a diverse range of lifestyles during infection of plants and represent a group of agriculturally devastating pathogens. In this study, we present the draft genome of Colletotrichum incanum from the spaethianum clade of Colletotrichum and the comparative analyses with five other ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw089
更新日期:2016-05-22 00:00:00
abstract::In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database we...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz208
更新日期:2019-10-01 00:00:00
abstract::Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we d...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx268
更新日期:2018-01-01 00:00:00
abstract::Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa058
更新日期:2020-04-01 00:00:00
abstract::Protein metabolism is one of the most costly processes in the cell and is therefore expected to be under the effective control of natural selection. We stimulated yeast strains to overexpress each single gene product to approximately 1% of the total protein content. Consistent with previous reports, we found that exce...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt154
更新日期:2013-01-01 00:00:00
abstract::Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw047
更新日期:2017-02-01 00:00:00
abstract::The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this perio...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv231
更新日期:2015-11-27 00:00:00
abstract::Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multitissue transcriptome data set from great tit (Parus major), we analyzed patterns of molecular evolution between two pas...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu157
更新日期:2014-08-01 00:00:00
abstract::Gibbons (Hylobatidae) shared a common ancestor with the other hominoids only 15-18 million years ago. Nevertheless, gibbons show very distinctive features that include heavily rearranged chromosomes. Previous observations indicate that this phenomenon may be linked to the attenuated epigenetic repression of transposab...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs048
更新日期:2012-01-01 00:00:00
abstract::Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx085
更新日期:2017-05-01 00:00:00