共查询到20条相似文献,搜索用时 31 毫秒
1.
Karen E. Chambers Ryan McDaniell Jeremy D. Raincrow Maya Deshmukh Peter F. Stadler 《Theorie in den Biowissenschaften》2009,128(2):109-120
Large-scale—even genome-wide—duplications have repeatedly been invoked as an explanation for major radiations. Teleosts, the
most species-rich vertebrate clade, underwent a “fish-specific genome duplication” (FSGD) that is shared by most ray-finned
fish lineages. We investigate here the Hox complement of the goldeye (Hiodon alosoides), a representative of Osteoglossomorpha, the most basal teleostean clade. An extensive PCR survey reveals that goldeye has
at least eight Hox clusters, indicating a duplicated genome compared to basal actinopterygians. The possession of duplicated Hox clusters is uncoupled to species richness. The Hox system of the goldeye is substantially different from that of other teleost lineages, having retained several duplicates
of Hox genes for which crown teleosts have lost at least one copy. A detailed analysis of the PCR fragments as well as full length
sequences of two HoxA13 paralogs, and HoxA10 and HoxC4 genes places the duplication event close in time to the divergence of Osteoglossomorpha and crown teleosts. The data are
consistent with—but do not conclusively prove—that Osteoglossomorpha shares the FSGD.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
相似文献
Chi-hua ChiuEmail: |
2.
Previous studies have shown widespread conservation of gene expression levels between species of the Drosophila melanogaster subgroup as well as a positive correlation between coding sequence divergence and expression level divergence between species.
Meanwhile, large-scale misregulation of gene expression level has been described in interspecific sterile hybrids between
D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. Using data from gene expression analysis involving D. simulans, D. melanogaster, and their hybrids, we observed a significant positive correlation between protein sequence divergence and gene expression
differences between hybrids and their parental species. Furthermore, we demonstrate that underexpressed misregulated genes in hybrids are evolving more rapidly at the protein sequence
level than nonmisregulated genes or overexpressed misregulated genes, highlighting the possible effects of sexual and natural
selection as male-biased genes and nonessential genes are the principal gene categories affected by interspecific hybrid misregulation.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Carlo G. Artieri and Wilfried Haerty contributed equally to this publication. 相似文献
3.
4.
M. E. Manetti M. Rossi M. Nakabashi M. A. Grandbastien Marie Anne Van Sluys 《Molecular genetics and genomics : MGG》2009,281(3):261-271
Eukaryotic genome expansion/retraction caused by LTR-retrotransposon activity is dependent on the expression of full length
copies to trigger efficient transposition and recombination-driven events. The Tnt1 family of retrotransposons has served
as a model to evaluate the diversity among closely related elements within Solanaceae species and found that members of the
family vary mainly in their U3 region of the long terminal repeats (LTRs). Recovery of a full length genomic copy of Retrosol
was performed through a PCR-based approach from wild potato, Solanum oplocense. Further characterization focusing on both LTR sequences of the amplified copy allowed estimating an approximate insertion
time at 2 million years ago thus supporting the occurrence of transposition cycles after genus divergence. Copy number of
Tnt1-like elements in Solanum species were determined through genomic quantitative PCR whereby results sustain that Retrosol in Solanum species is a low copy number retrotransposon (1–4 copies) while Retrolyc1 has an intermediate copy number (38 copies) in
S. peruvianum. Comparative analysis of retrotransposon content revealed no correlation between genome size or ploidy level and Retrosol
copy number. The tetraploid cultivated potato with a cellular genome size of 1,715 Mbp harbours similar copy number per monoploid
genome than other diploid Solanum species (613–884 Mbp). Conversely, S. peruvianum genome (1,125 Mbp) has a higher copy number. These results point towards a lineage specific dynamic flux regarding the history
of amplification/activity of Tnt1-like elements in the genome of Solanum species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
5.
Richard P. Meisel 《Journal of molecular evolution》2009,69(1):81-93
Duplicated genes produce genetic variation that can influence the evolution of genomes and phenotypes. In most cases, for
a duplicated gene to contribute to evolutionary novelty it must survive the early stages of divergence from its paralog without
becoming a pseudogene. I examined the evolutionary dynamics of recently duplicated genes in the Drosophila pseudoobscura genome to understand the factors affecting these early stages of evolution. Paralogs located in closer proximity have higher
sequence identity. This suggests that gene conversion occurs more often between duplications in close proximity or that there
is more genetic independence between distant paralogs. Partially duplicated genes have a higher likelihood of pseudogenization
than completely duplicated genes, but no single factor significantly contributes to the selective constraints on a completely
duplicated gene. However, DNA-based duplications and duplications within chromosome arms tend to produce longer duplication
tracts than retroposed and inter-arm duplications, and longer duplication tracts are more likely to contain a completely duplicated
gene. Therefore, the relative position of paralogs and the mechanism of duplication indirectly affect whether a duplicated
gene is retained or pseudogenized.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
6.
The leiognathid genus Nuchequula can be defined by the following combination of characters: mouth protruding downward; a narrow band of small, slender, villiform
teeth in both jaws; teeth on upper jaw strongly recurved; the lateral line almost complete; a dark blotch on the nape. Although
the genus was first established as a subgenus of Eubleekeria, it is here raised to generic level on the basis of the aforementioned morphological characters and recent molecular biological
evidence. The genus comprises six valid species: N. blochii (Valenciennes 1835), distributed in India and Thailand; N. flavaxilla sp. nov., occurring only at Panay I., Philippines; N. gerreoides (Bleeker 1851), widely distributed in the Indo-West Pacific, from the Persian Gulf to Cape York, Australia, and north to
Taiwan; N. glenysae sp. nov., from northern Australia and Ambon, Indonesia; N. longicornis sp. nov., from the Gulf of Thailand and Indonesia; and N. nuchalis (Temminck and Schlegel 1845), occurring in southern China including Taiwan, and southern Japan. Diagnostic characters of
the species belonging to the genus are as follows: N. blochii—breast scaled, cheek naked, and a conspicuous black blotch distally on spinous dorsal fin; N. flavaxilla sp. nov.—breast naked, dorsolateral body surface fully scaled, preorbital spine bicuspid and not expanded distally, and second
dorsal and anal fin spines conspicuously elongated; N. gerreoides—breast naked, anterior part of dorsolateral surface of body almost completely scaled, and second dorsal and anal fin spines
not conspicuously elongated; N. glenysae sp. nov.—breast completely scaled, cheek scaled, and unique complicated sensory canals present on the suborbital area, extending
to the nape; N. longicornis sp. nov.—breast naked, dorsolateral body surface fully scaled, preorbital spine bicuspid or tricuspid and extended distally,
and second dorsal fin spines only conspicuously elongated; N. nuchalis—breast naked, anterior part of dorsolateral surface of body widely naked, and a conspicuous dark blotch distally on spinous
dorsal fin. 相似文献
7.
8.
Raymond Cunin Evelyne Dubois Gerrit Vanthienen Kristof Tinel Annemie Jacobs Marjolaine Crabeel 《Molecular & general genetics : MGG》1986,205(1):170-175
Summary We localized the chromosomal targets of several of the regulatory controls of expression of theCAR1 gene. Fusion tolacZ of several fragments of the 5′ non-coding region showed that induction ofCAR1 by arginine is positively regulated by the products of theARGR genes. The target lies upstream of another site where repression by the CARGRI molecule occurs. The latter control is not
specific to arginine catabolism since it also affectsCYC-1 and indeed does not appear to involve arginine. The primary target of the two other regulatory allelesCARGRII andCARGRIII is not situated in the 5′ non-coding region. Deletion analysis supports the fusion data and confirms the order of the regulatory
regions: 5′—nitrogen catabolite repression—activation by arginine—CARGRI-mediated repression—CAR1. 相似文献
9.
Partial gyrB sequences (>1 kb) were obtained from 34 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships
within the genus. The use of gyrB sequence analysis as an alternative to DNA–DNA hybridization was also assessed for distinguishing closely related species.
The gyrB based phylogeny mostly confirmed the conventional 16S rRNA gene-based phylogeny and thus provides additional support for
certain of these 16S rRNA gene-based phylogenetic groupings. Although pairwise gyrB sequence similarity cannot be used to predict the DNA relatedness between type strains, the gyrB genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the
genus Amycolatopsis. In particular a genetic distance of >0.02 between two Amycolatopsis strains (based on a 315 bp variable region of the gyrB gene) is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization
of the unknown strain is worth undertaking).
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
The GenBank accession numbers for the gyrB gene sequences obtained in this study are shown in Table 1. 相似文献
10.
11.
Martijn F. Schenk Claire-Noëlle Thienpont Wim J. M. Koopman Luud J. W. J. Gilissen Marinus J. M. Smulders 《Tree Genetics & Genomes》2008,4(4):911-924
The genus Betula comprises various species in boreal and temperate climate zones of the Northern Hemisphere. The taxonomy of Betula is controversial and complicated by parallel evolution of morphological traits, polyploidization events, and extensive hybridization
and introgression among species. Multilocus molecular data from AFLPs were used to provide phylogenetic information. A large
number of polymorphic markers (321 variable bands) were produced in 107 Betula accessions from 23 species and 11 hybrids. The AFLP results were largely congruent with the results from previously examined
nuclear DNA markers. Four distinct subgenera were identified within the genus Betula. These subgenera were partly in disagreement with the traditional (but disputed) division of the genus. In addition, the
results indicated several groups of conspecific taxa. The majority of the species fell within subgenus Betula and shared a high degree of similarity with B. pendula. All hybrids were associated with this group, and the AFLP data contained signals on putative parents for some of the interspecific
hybrids. Subgenus Chamaebetula and part of the Neurobetula species should be merged with Betula. The subgenera Betulenta, Betulaster, and the remaining part of Neurobetula are distinct and well supported. Although our results indicate that four major taxonomic groups can be recognized within
the genus Betula, the relationship between them remains unclear. This may be due to the occurrence of hybridization and introgression, which
would have a homogenizing effect on the relationships between species. Naturally occurring Betula species of hybrid origin may explain the low bootstrap values within the Betula clade.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
12.
13.
The indriid genus Propithecus comprises the sifakas, medium-sized lemurs endemic to the forests of Madagascar. Traditionally, scientists divided the genus
into only 2 or 3 species —Propithecus diadema, P. verreauxi, and, since 1988, P. tattersalli— with 4 or 5 subspecies in each of the first 2 taxa, but recent authors have suggested that many more distinct species should
be recognized. We draw from quantitative and qualitative studies of craniodental traits to evaluate further the phenetic distinctiveness
and taxonomic status of each named form of Propithecus. We recognize 9–10 species in the genus. The 4 or 5 species of the Propithecus diadema group —P. diadema, P. candidus, P. perrieri, P. edwardsi, and perhaps P. holomelas, if distinct— share several derived features, including large average body size and a mandible specialized for rotational
chewing, and clearly comprise a closely related complex. The 5 species of the Propithecus verreauxi group —P. verreauxi, P. coquereli, P. deckenii, P. coronatus, P. tattersalli— are each highly distinctive morphologically and likely do not comprise a monophyletic group. In particular, we point out
the highly distinctive cranial features of Propithecus coronatus, which researchers have traditionally largely overlooked. 相似文献
14.
Y. Bao P. Dharmawardhana R. Arias M. B. Allen C. Ma Steven H. Strauss 《Plant cell reports》2009,28(6):947-962
We describe the development of a reporter system for monitoring meristem initiation in poplar using promoters of poplar homologs
to the meristem-active regulatory genes WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM). When ~3 kb of the 5′ flanking regions of close homologs were used to drive expression of the GUSPlus gene, 50–60% of the transgenic events showed expression in apical and axillary meristems. However, expression was also common
in other organs, including in leaf veins (40 and 46% of WUS and STM transgenic events, respectively) and hydathodes (56% of WUS transgenic events). Histochemical GUS staining of explants during callogenesis and shoot regeneration using in vitro stems
as explants showed that expression was detectable prior to visible shoot development, starting 3–15 days after explants were
placed onto callus inducing medium. A minority of WUS and STM events also showed expression in the cambium, phloem, or xylem of regenerated, greenhouse grown plants undergoing secondary
growth. Based on microarray gene expression data, a paralog of poplar WUS was detectably up-regulated during shoot initiation, but the other paralog was not. Both paralogs of poplar STM were down-regulated threefold to sixfold during early callus initiation. We identified 15–35 copies of cytokinin response
regulator binding motifs (ARR1AT) and one copy of the auxin response element (AuxRE) in both promoters. Several of the events
recovered may be useful for studying the process of primary and secondary meristem development, including treatments intended
to stimulate meristem development to promote clonal propagation and genetic transformation.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
15.
Plant acyl-CoA dependent acyltransferases constitute a large specific protein superfamily, named BAHD. Using the conserved
sequence motifs of BAHD members, we searched the genome sequences of Populus and Arabidopsis, and identified, respectively, 94- and 61-putative genes. Subsequently, we analyzed the phylogeny, gene structure, and chromosomal
distribution of BAHD members of both species; then, we profiled expression patterns of BAHD genes by “in silico” northern- and microarray-analyses based on public databases, and by RT-PCR. While our genomic- and bioinformatic- analyses
provided full sets of BAHD superfamily genes, and cleaned up a few existing annotation errors, importantly it led to our recognizing
several unique Arabidopsis BAHD genes that inversely overlapped with their neighboring genes on the genome, and disclosing a potential natural anti-sense
regulation for gene expressions. Systemic gene-expression profiling of BAHD members revealed distinct tissue-specific/preferential
expression patterns, indicating their diverse biological functions. Our study affords a strong knowledge base for understanding
BAHD members’ evolutionary relationships and gene functions implicated in plant growth, development and metabolism.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
16.
Yung-Hun Yang Eunjung Song Eun-Jung Kim Kwangwon Lee Woo-Seong Kim Sung-Soo Park Ji-Sook Hahn Byung-Gee Kim 《Applied microbiology and biotechnology》2009,82(3):501-511
NdgR (regulator for nitrogen source-dependent growth and antibiotic production), an IclR-like regulator, has been initially
identified as a binding protein to the promoters of doxorubicin biosynthetic genes in Streptomcyes peucetius by DNA affinity capture assay method. NdgR is well conserved throughout the Streptomcyes species and many other bacteria such as Mycobacteria and Corynebacteria. In Streptomcyes coelicolor, ndgR deletion mutant showed slow cell growth and defects in differentiation and enhances the production of actinorhodin (ACT)
in minimal media containing certain amino acids where wild-type strain could not produce ACT. Although deletion mutant of
ndgR showed different antibiotic production in minimal media containing Leu or Gln, it only showed reduced mRNA expression levels
of the genes involved in leucine metabolism. Neither NdgR-dependent expression of glnA nor direct binding of NdgR protein to glnA, glnII, and glnR promoters was observed. However, ScbR, which is governed by NdgR shown by gel mobility shift assay, binds to promoter of
glnR, suggesting indirect regulation of glutamine metabolism by NdgR. NdgR protein binds to intergenic region of ndgR–leuC, and scbR–scbA involved in γ-butyrolactone. Two-dimensional gel analysis has shown a global effect of ndgR deletion in protein expression, including up-regulated proteins involved in ACT synthesis and down-regulation of chaperones
such as GroEL, GroES, and DnaK. These results suggest a global regulatory role for NdgR in amino acid metabolisms, quorum
sensing, morphological changes, antibiotic production, and expression of chaperonines in S. coelicolor.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
17.
Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae) 总被引:1,自引:0,他引:1
The evolutionary pattern of the myc-like anthocyanin regulatory gene antR-Cor was examined in the dwarf dogwood species complex (Cornus Subgenus Arctocrania) that contains two diploid species (C. canadensis and C. suecica), their putative hybrids with intermediate phenotypes, and a tetraploid derivative (C. unalaschkensis). Full-length sequences of this gene (∼4 kb) were sequenced and characterized for 47 dwarf dogwood samples representing all
taxa categories from 43 sites in the Pacific Northwest. Analysis of nucleotide diversity indicated departures from neutral
evolution, due most likely to local population structure. Neighbor-joining and haplotype network analyses show that sequences
from the tetraploid and diploid intermediates are much more strongly diverged from C. suecica than from C. canadensis, and that the intermediate phenotypes may represent an ancestral group to C. canadensis rather than interspecific hybrids. Seven amino acid mutations that are potentially linked to myc-like anthocyanin regulatory
gene function correlate with petal colors differences that characterize the divergence between two diploid species and the
tetraploid species in this complex. The evidence provides a working hypothesis for testing the role of the gene in speciation
and its link to the petal coloration. Sequencing and analysis of additional nuclear genes will be necessary to resolve questions
about the evolution of the dwarf dogwood complex. 相似文献
18.
19.