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81.
82.
83.
A. D. Deshpande W. Ramakrishna G. P. Mulay V. S. Gupta P. K. Ranjekar 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(1-2):135-140
Homeobox genes are the master control genes harbouring the homeobox which is crucial for developmental associated functions.
One homeobox gene, knotted1, which has a role in leaf development, is conserved in plants and might have arisen from a single ancestral gene. Using PCR,
we identified multiple kn1 homeoboxes in diverse cereals and showed a cereal/ species-specific organization correlating them to evolutionary changes.
We postulate the insertion of a large intron preceded by duplication of the kn1 homeobox in the lineage leading to rice.
Received: 17 October 1997 / Accepted: 9 December 1997 相似文献
84.
Summary In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern
of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based
on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates
both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin,
C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin
dendrograms computed from DNA and from protein sequences.
In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms
based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that
introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond
to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family.
Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3′-tail sequence, intron
sequences, and intron positions all show significant differences. 相似文献
85.
Edvardsen RB Lerat E Maeland AD Flåt M Tewari R Jensen MF Lehrach H Reinhardt R Seo HC Chourrout D 《Journal of molecular evolution》2004,59(4):448-457
Oikopleura dioica is a pelagic tunicate with a very small genome and a very short life cycle. In order to investigate the intron–exon organizations in Oikopleura, we have isolated and characterized ribosomal protein EF-1, Hox, and -tubulin genes. Their intron positions have been compared with those of the same genes from various invertebrates and vertebrates, including four species with entirely sequenced genomes. Oikopleura genes, like Caenorhabditis genes, have introns at a large number of nonconserved positions, which must originate from late insertions or intron sliding of ancient insertions. Both species exhibit hypervariable intron–exon organization within their -tubulin gene family. This is due to localization of most nonconserved intron positions in single members of this gene family. The hypervariability and divergence of intron positions in Oikopleura and Caenorhabditis may be related to the predominance of short introns, the processing of which is not very dependent upon the exonic environment compared to large introns. Also, both species have an undermethylated genome, and the control of methylation-induced point mutations imposes a control on exon size, at least in vertebrate genes. That introns placed at such variable positions in Oikopleura or C. elegans may serve a specific purpose is not easy to infer from our current knowledge and hypotheses on intron functions. We propose that new introns are retained in species with very short life cycles, because illegitimate exchanges including gene conversion are repressed. We also speculate that introns placed at gene-specific positions may contribute to suppressing these exchanges and thereby favor their own persistence.Supplementary material () is available for this article. 相似文献
86.
Gomulski LM Brogna S Babaratsas A Gasperi G Zacharopoulou A Savakis C Bourtzis K 《Journal of molecular evolution》2004,58(6):732-742
The first intron of the gene encoding one of the alcohol dehydrogenase isoenzymes (ADH-1) in Ceratitis capitata is highly polymorphic in size. Five size variants of this intron were isolated from different strains and populations and characterized. Restriction map and sequence analysis showed that the intron size polymorphism is due to the presence or absence of (a) a copy of a defective mariner-like element, postdoc; (b) an 550-bp 3
indel which exhibits no similarity to any known sequence; and (c) a central duplication of 704 bp consisting of part of the 3 end of the postdoc element, the region between postdoc and the 3
indel, and the first 20 bp of the 3
indel. The homologous Adh-1 intron was amplified from the congeneric species, Ceratitis rosa, in order to obtain an outgroup for comparative and phylogenetic analyses. The C. rosa introns were polymorphic in size, ranging from about 1100 to 2000 bp, the major difference between them being the presence or absence of a mariner-like element Crmar2, unrelated to the postdoc element. Phylogenetic analysis suggests that the shorter intron variants in C. capitata may represent the ancestral form of the intron, the longest variants apparently being the most recent. 相似文献
87.
Phylogenetic Analysis Reveals a Novel Protein Family Closely Related to Adenosine Deaminase 总被引:2,自引:0,他引:2
Adenosine deaminase (ADA) is a well-characterized enzyme involved in the depletion of adenosine levels. A group of proteins
with similarity to ADA, the adenosine deaminase-related growth factors (ADGF; known as CECR1 in vertebrates), has been described
recently in various organisms. We have determined the phylogenetic relationships of various gene products with significant
amino acid similarity to ADA using parsimony and Bayesian methods, and discovered a novel paralogue, termed ADA-like (ADAL).
The ADGF proteins share a novel amino acid motif, “MPKG,” within which the proline and lysine residues are also conserved
in the ADAL and ADA subfamilies. The significance of this new domain is unknown, but it is located just upstream of two ADA
catalytic residues, of which all eight are conserved among the ADGF and ADAL proteins. This conservation suggests that ADGF
and ADAL may share the same catalytic function as ADA, which has been proven for some ADGF members. These analyses also revealed
that some genes previously thought to be classic ADAs are instead ADAL or ADGFs. We here define the ADGF, ADAL, ADA, adenine
deaminase (ADE), and AMP deaminase (AMPD) groups as subfamilies of the adenyl-deaminase family. The availability of genomic
data for the members of this family allowed us to reconstruct the intron evolution within the phylogeny and strengthen the
introns-late hypothesis of the synthetic introns theory. This study shows that ADA activity is clearly more complex than once
thought, perhaps involving a delicately balanced pattern of temporal and spatial expression of a number of paralogous proteins.
Electronic Supplementary Material Electronic Supplementary material is available for this article at
and accessible for authorised users.
[Reviewing Editor: Dr. Martin Kreitman] 相似文献
88.
Wei H Fu Y Arora R 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(7):1347-1356
With a long-term goal of constructing a linkage map of Rhododendron enriched with gene-specific markers, we utilized Rhododendron catawbiense ESTs for the development of high-efficiency (in terms of generating polymorphism frequency) PCR-based markers. Using the
gene-sequence alignment between Rhododendron ESTs and the genomic sequences of Arabidopsis homologs, we developed ‘intron-flanking‘ EST–PCR-based primers that would anneal in conserved exon regions and amplify across
the more highly diverged introns. These primers resulted in increased efficiency (61% vs. 13%; 4.7-fold) of polymorphism-detection
compared with conventional EST–PCR methods, supporting the assumption that intron regions are more diverged than exons. Significantly,
this study demonstrates that Arabidopsis genome database can be useful in developing gene-specific PCR-based markers for other non-model plant species for which the
EST data are available but genomic sequences are not. The comparative analysis of intron sizes between Rhododendron and Arabidopsis (made possible in this study by aligning of Rhododendron ESTs with Arabidopsis genomic sequences and the sequencing of Rhododendron genomic PCR products) provides the first insight into the gene structure of Rhododendron.
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
89.
Background
A commonplace analysis in high-throughput DNA methylation studies is the comparison of methylation extent between different functional regions, computed by averaging methylation states within region types and then comparing averages between regions. For example, it has been reported that methylation is more prevalent in coding regions as compared to their neighboring introns or UTRs, leading to hypotheses about novel forms of epigenetic regulation.Results
We have identified and characterized a bias present in these seemingly straightforward comparisons that results in the false detection of differences in methylation intensities across region types. This bias arises due to differences in conservation rates, rather than methylation rates, and is broadly present in the published literature. When controlling for conservation at coding start sites the differences in DNA methylation rates disappear. Moreover, a re-evaluation of methylation rates at intronexon junctions reveals that the magnitude of previously reported differences is greatly exaggerated. We introduce two correction methods to address this bias, an inferencebased matrix completion algorithm and an averaging approach, tailored to address different underlying biological questions. We evaluate how analysis using these corrections affects the detection of differences in DNA methylation across functional boundaries.Conclusions
We report here on a bias in DNA methylation comparative studies that originates in conservation rate differences and manifests itself in the false discovery of differences in DNA methylation intensities and their extents. We have characterized this bias and its broad implications, and show how to control for it so as to enable the study of a variety of biological questions.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1604-3) contains supplementary material, which is available to authorized users. 相似文献90.
Li Penghui Yao Chen Wang Ting Wu Tong Yi Wenfu Zheng Yue Miao Yuanjiu Sun Jianhong Tan Zhongyuan Liu Yan Zhang Xiaowei Wang Hanzhong Zheng Zhenhua 《中国病毒学》2021,36(6):1375-1386
Virologica Sinica - Tick-borne encephalitis virus (TBEV) is a pathogenic virus known to cause central nervous system (CNS) diseases in humans, and has become an increasing public health threat... 相似文献