Abstract：
:In this paper we present a new method for detecting block duplications in a genome. It is more stringent than previous ones in that it requires a more rigorous definition of paralogous genes and that it requires the paralogous proteins on the two blocks to be contiguous. In addition, it provides three criterion choices: (1) the same composition (i.e., having the same paralogues in the two windows), (2) the same composition and gene order, and (3) the same composition, gene order, and gene orientation. The method is completely automated, requiring no visual inspection as in previous methods. We applied it to analyze the complete genomes of S. cerevisiae and C. elegans. In yeast we detected fewer duplicated blocks than previously reported. In C. elegans, however, we detected more block duplications than previously reported, indicating that although our method has a more stringent definition of block duplication than previous ones, it may be more sensitive in detection because it considers every possible window rather than only fixed nonoverlapping windows. Our results show that block duplication is a common phenomenon in both organisms. The patterns of block duplication in the two species are, however, markedly different. The yeast shows much more extensive block duplication than the nematode, with some chromosomes having more than 40% of the duplications derived from block duplications. Moreover, in the yeast the majority of block duplications occurred between chromosomes, while in the nematode most block duplications occurred within chromosomes.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Cavalcanti AR,Ferreira R,Gu Z,Li WHdoi
10.1007/s00239-002-2377-2keywords:
subject
Has Abstractpub_date
2003-01-01 00:00:00pages
28-37issue
1eissn
0022-2844issn
1432-1432journal_volume
56pub_type
杂志文章abstract：:Fish protamines are highly specialized molecules which are responsible for chromatin condensation during the last stages of spermatogenesis (spermiogenesis). However, not all fish contain protamines in their sperm nuclei; rather, there seems to be a random distribution of protamines within this group. The origin of th...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160152
更新日期：1994-09-01 00:00:00
abstract：:Phylogenetic hypotheses of muscle actin evolution are significantly different when a sea urchin is used as a representative echinoderm than when a sea star is used. While sea urchin muscle actins support an echinoderm-chordate sister relationship, sea star sequences suggest that echinoderm muscle actins are convergent...
journal_title：Journal of molecular evolution
pub_type： 评论,杂志文章
doi：10.1007/s002399910018
更新日期：2000-02-01 00:00:00
abstract：:The attachment site (attlambda) of bacteriophage lambda was examined in wild strains of Escherichia coli. Although the att region is non-coding, the DNA sequence was invariant in the 13 strains examined. Two other non-coding regions showed nine changes, all associated with a single strain. In four of 33 strains, seque...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010247
更新日期：2001-12-01 00:00:00
abstract：:Polymerization of various nucleoside-5'-phosphorimidazolides has been conducted in neutral aqueous solution using divalent metal ions as catalysts. Oligonucleotide formation took place from each of the ribonucleoside-5'-phosphorimidazolides, ImpC, ImpU, ImpA, ImpG, and ImpI. The yields and distributions of the resulti...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02100072
更新日期：1988-01-01 00:00:00
abstract：:At least two polymorphic Alu insertions have been previously identified and characterized within the class I region of the major histocompatibility complex (MHC). We have identified another two new polymorphic Alu insertions, AluyHJ and AluyHF, located near HLA-J and HLA-F, respectively, within the a block of the MHC....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2367-4
更新日期：2002-12-01 00:00:00
abstract：:The relaxin (RLN) and insulin-like (INSL) gene family is a group of genes involved in a variety of physiological roles that includes bone formation, testicular descent, trophoblast development, and cell differentiation. This family appears to have expanded in vertebrates relative to non-vertebrate chordates, but the r...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9403-6
更新日期：2011-01-01 00:00:00
abstract：:Eight new examples of retrotransposons of the Gypsy/Ty3 class have been identified in marine species. A 525-nt pol gene-coding region was amplified using degenerate primers from highly conserved regions and has extended the range of recognition of Gypsy/Ty3 far beyond those previously known. The following matrix shows...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00166592
更新日期：1995-01-01 00:00:00
abstract：:From the cloned mitochondrial DNAs (mtDNAs) isolated from two bisexual species, one Mediterranean, Artemia salina, and one American, Artemia franciscana, and two parthenogenetic (diploid and tetraploid) strains of Artemia parthenogenetica collected in Spain, physical maps have been constructed and compared. They are e...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00166162
更新日期：1994-02-01 00:00:00
abstract：:This study investigated the evolution of a transition metal ion-binding cluster ([H--X--X--X--H](n); Tx) in the alternatively spliced NH(2)-terminal variable region of avian pectoral muscle troponin T (TnT). Encoded by avian fast skeletal muscle TnT-specific P exons, Tx-like structures were expressed in the breast mus...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010139
更新日期：2001-02-01 00:00:00
abstract：:The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (w...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0102-7
更新日期：2005-12-01 00:00:00
abstract：:Introns are generally believed to evolve too rapidly and too erratically to be of much use in phylogenetic reconstructions. Few phylogenetically informative intron sequences are available, however, to ascertain the validity of this supposition. In the present study the supposition was tested on the example of the mamm...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006510
更新日期：1999-06-01 00:00:00
abstract：:Human endogenous retroviruses (HERVs) are the remnants of ancient germ cell infection by exogenous retroviruses and occupy up to 8% of the human genome. It has been suggested that HERV sequences have contributed to primate evolution by regulating the expression of cellular genes and mediating chromosome rearrangements...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-2656-1
更新日期：2004-11-01 00:00:00
abstract：:The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9456-1
更新日期：2011-08-01 00:00:00
abstract：:A long-standing hypothesis posits that morphological changes may be more likely to result from changes in regulation of gene expression than from changes in the protein coding sequences of genes. We have compared the expression pattern of the twisted gastrulation (tsg) gene among five Drosophila species: D. melanogast...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006293
更新日期：1998-02-01 00:00:00
abstract：:Species identification is one of the most important issues in biological studies. Due to recent increases in the amount of genomic information available and the development of DNA sequencing technologies, the applicability of using DNA sequences to identify species (commonly referred to as "DNA barcoding") is being te...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9380-9
更新日期：2010-10-01 00:00:00
abstract：:Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Pr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006160
更新日期：1997-04-01 00:00:00
abstract：:The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny. Although hexamerins and hemocyanins belong to a highly divergen...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006366
更新日期：1998-07-01 00:00:00
abstract：:Evidence from a number of studies indicates that protein folding is dictated not only by factors stabilizing the native state, but also by potentially independent factors that create folding pathways. How natural selection might cope simultaneously with two independent factors was addressed in this study within the fr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9465-0
更新日期：2011-10-01 00:00:00
abstract：:In vitro run-off transcription by T7 RNA polymerase generates heterogeneous 3'-ends because the enzyme tends to add untemplated adenylates. To generate homogeneous 3'-termini, HDV ribozymes have been used widely. Their sequences are added to the 3'-terminus such that co-transcriptional self-cleavage generates homogene...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9861-9
更新日期：2018-08-01 00:00:00
abstract：:We examined the codon usages in well-conserved and less-well-conserved regions of vertebrate protein genes and found them to be similar. Despite this similarity, there is a statistically significant decrease in codon bias in the less-well-conserved regions. Our analysis suggests that although those codon changes initi...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02100090
更新日期：1984-01-01 00:00:00
abstract：:The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9139-8
更新日期：2008-09-01 00:00:00
abstract：:We have further characterized the Asian genotypes (Types 2 and 7) and subtypes of JC virus (JCV). Urine samples from 224 individuals with Han and Mongolian populations were collected in five regions in eastern China: Kunming, Chengdu, Shenyang, Chifeng, and Manzhouli. Also, 99 urine samples were collected from coastal...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2579-2
更新日期：2004-05-01 00:00:00
abstract：:The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9156-7
更新日期：2008-12-01 00:00:00
abstract：:Molluscan shells are composed of calcium carbonates, with small amounts of extracellular matrices secreted from mantle epithelial cells. Many types of shell matrix proteins (SMPs) have been identified from molluscan shells or mantle cells. The pen shell Atrina pectinata (Pinnidae) has two different shell microstructur...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-020-09977-7
更新日期：2020-12-01 00:00:00
abstract：:We constructed a cDNA library for the beetle, Tribolium castaneum. This library was screened using a cloned amylase gene from Drosophila melanogaster as a molecular probe. Beetle amylase cDNA clones were isolated from this bank, and the nucleotide sequence was obtained for a cDNA clone with a coding capacity for 228 a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099856
更新日期：1987-01-01 00:00:00
abstract：:Leucine-rich repeat receptor-like kinases (LRR RLKs) comprise the largest group within the plant receptor-like kinase (RLK) superfamily, and the Arabidopsis genome alone contains over 200 LRR RLK genes. Although there is clear evidence for diverse roles played by individual LRR RLK genes in Arabidopsis growth and deve...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0187-z
更新日期：2006-11-01 00:00:00
abstract：:When an aqueous solution (pH 7.0) of 3H deoxythymidine 5'-triphosphate, deoxythymidine 5'-phosphate, 4-amino-5-imidazolecarboxamide, cyanamide and ammonium chloride was dried and heated at 60 degrees C for 18 h, oligomers were obtained in a yield of approximately 80%. After the chemical degradation of any pyrophosphat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01764595
更新日期：1977-12-29 00:00:00
abstract：:Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed volatility, to estimate selection pressures on proteins on the basis of their synonymous codon usage (Plotkin and Dushoff 2003; Plotkin et al. ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0233-x
更新日期：2006-11-01 00:00:00
abstract：:Cytochrome proteins perform a broad spectrum of biological functions ranging from oxidative metabolism to electron transport and are thus essential to all organisms. The b-type cytochrome proteins bind heme noncovalently, are expressed in many different forms and are localized to various cellular compartments. We repo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160314
更新日期：1995-10-01 00:00:00
abstract：:We examined the nucleotide and amino acid sequence variation of the cytochrome c oxidase subunit II (COII) gene from 25 primates (4 hominoids, 8 Old World monkeys, 2 New World monkeys, 2 tarsiers, 7 lemuriforms, 2 lorisiforms). Marginal support was found for three phylogenetic conclusions: (1) sister-group relationshi...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00176084
更新日期：1994-03-01 00:00:00
