Abstract:
:Many algal groups acquired complex plastids by the uptake of green and red algae through multiple secondary endosymbioses. As a result of gene loss and transfer during the endosymbiotic processes, algal endosymbiont nuclei disappeared in most cases. However, chlorarachniophytes and cryptophytes still possess a relict nucleus, so-called the nucleomorph, of the green and red algal endosymbiont, respectively. Nucleomorph genomes are an interesting and suitable model to study the reductive evolution of endosymbiotically derived genomes. To date, nucleomorph genomes have been sequenced in four cryptophyte species and two chlorarachniophyte species, including Bigelowiella natans (373 kb) and Lotharella oceanica (610 kb). In this study, we report complete nucleomorph genome sequences of two chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata, to gain insight into the reductive evolution of nucleomorph genomes in the chlorarachniophytes. The nucleomorph genomes consist of three chromosomes totaling 374 and 432 kb in size in A. amoebiformis and L. vacuolata, respectively. Comparative analyses among four chlorarachniophyte nucleomorph genomes revealed that these sequences share 171 function-predicted genes (86% of total 198 function-predicted nucleomorph genes), including the same set of genes encoding 17 plastid-associated proteins, and no evidence of a recent nucleomorph-to-nucleus gene transfer was found. This suggests that chlorarachniophyte nucleomorph genomes underwent most of their reductive evolution prior to the radiation of extent members of the group. However, there are slight variations in genome size, GC content, duplicated gene number, and subtelomeric regions among the four nucleomorph genomes, suggesting that the genomes might be undergoing changes that do not affect the core functions in each species.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Suzuki S,Shirato S,Hirakawa Y,Ishida Kdoi
10.1093/gbe/evv096subject
Has Abstractpub_date
2015-05-22 00:00:00pages
1533-45issue
6issn
1759-6653pii
evv096journal_volume
7pub_type
杂志文章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::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::Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom....
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq032
更新日期:2010-07-19 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::The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metaz...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt052
更新日期:2013-01-01 00:00:00
abstract::Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evy245
更新日期:2019-01-01 00:00:00
abstract::We previously discovered that lagging strand genes evolve faster in Bacillus subtilis (and potentially other bacteria). Lagging strand genes are transcribed in the head-on orientation with respect to DNA replication, leading to collisions between the two machineries that stall replication and can destabilize genomes. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw274
更新日期:2016-12-01 00:00:00
abstract::Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mut...
journal_title:Genome biology and evolution
pub_type: 杂志文章,评审
doi:10.1093/gbe/evy252
更新日期:2019-01-01 00:00:00
abstract::The root-knot nematodes (genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx201
更新日期:2017-10-01 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::RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx046
更新日期:2017-04-01 00:00:00
abstract::The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of N...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu202
更新日期:2014-09-10 00:00:00
abstract::The Arabidopsis DA1 genes appear to have multiple functions in regulating organ size and abiotic stress response, but the biological roles of its closely related genes remain unknown. Evolutionary analyses might provide some clues to aid in an understanding of their functional diversification. In this work, we charact...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu076
更新日期:2014-04-01 00:00:00
abstract::Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of posit...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx199
更新日期:2017-10-01 00:00:00
abstract::We determined the complete mitochondrial (mt) genomes of three evaniomorph species, Ceraphron sp. (Ceraphronoidea), Gasteruption sp. (Evanioidea), and Orthogonalys pulchella (Trigonalyoidea) as well as the nearly complete mt genome from another evaniomorph species, Megalyra sp. (Megalyroidea). Each of them possesses d...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu145
更新日期:2014-07-01 00:00:00
abstract::Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,2...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw138
更新日期:2016-08-25 00:00:00
abstract::Different genes and proteins evolve at very different rates. To identify the factors that explain these differences is an important aspect of research in molecular evolution. One such factor is the role a protein plays in a large molecular network. Here, we analyze the evolutionary rates of enzyme-coding genes in the ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy234
更新日期:2018-11-01 00:00:00
abstract::Intronic DNA is a major component of eukaryotic genes and genomes and can be subject to selective constraint and have functions in gene regulation. Intron size is of particular interest given that it is thought to be the target of a variety of evolutionary forces and has been suggested to be linked ultimately to vario...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs070
更新日期:2012-01-01 00:00:00
abstract::Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz183
更新日期:2019-09-01 00:00:00
abstract::Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz099
更新日期:2019-06-01 00:00:00
abstract::Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu085
更新日期:2014-04-30 00:00:00
abstract::Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abioti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy087
更新日期:2018-04-01 00:00:00
abstract::Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force l...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw097
更新日期:2016-06-03 00:00:00
abstract::The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which, Rab3-interacting molecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channels in vitro via a PDZ domain that binds to the extreme C-termi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa097
更新日期:2020-08-01 00:00:00
abstract::Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene co...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs074
更新日期:2012-01-01 00:00:00
abstract::Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled th...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa108
更新日期:2020-07-01 00:00:00
abstract::Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. Although previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical r...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx035
更新日期:2017-04-01 00:00:00
abstract::Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availabil...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx258
更新日期:2017-12-01 00:00:00
abstract::The adaptive significance of human brain evolution has been frequently studied through comparisons with other primates. However, the evolution of increased brain size is not restricted to the human lineage but is a general characteristic of primate evolution. Whether or not these independent episodes of increased brai...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx028
更新日期:2017-03-01 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