Abstract：
:The mammalian olfactory system utilizes three large receptor families: the olfactory receptors (ORs) of the main nose and the vomeronasal type-1 and type-2 receptor genes (V1Rs and V2Rs) of the vomeronasal organ. We find that these loci are among the most long interspersed nuclear element (LINE)-dense regions of mammalian genomes. We investigate two evolutionary models to account for this cohabitation. First, we investigate an adaptive selection model, in which LINEs have contributed to expansions of mouse V1R repertoires. We find that even evolutionarily stable V1R loci are exceptionally LINE-rich compared to other genome loci, including loci containing other large gene clusters. Also, a more detailed analysis of specific V1R duplications does not reveal LINE patterns predicted by common LINE-mediated duplication mechanisms. Next, we investigate neutral models, in which LINEs were tolerated by, but not advantageous for, surrounding V1R genes. We find that V1R loci are exceptionally LINE-rich compared to other regions of similar AT base composition, and that duplicated V1R gene blocks are generally depleted of LINE elements, suggesting that these loci did not become densely populated with LINEs simply as a consequence of targeted integration or passive multiplication along with the genes. Finally, we show that individual LINE repeats of a given age at V1R, V2R, and OR loci exhibit a significantly longer average length than at other autosomal loci, suggesting a reduced tendency for these LINEs to be disrupted. We speculate that LINEs at V1R, V2R, and OR loci might be selectively retained because they contribute to allelic regulation of these three gene families.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Kambere MB,Lane RPdoi
10.1007/s00239-008-9195-0subject
Has Abstractpub_date
2009-02-01 00:00:00pages
145-59issue
2eissn
0022-2844issn
1432-1432journal_volume
68pub_type
杂志文章abstract：:A 6.0-kb DNA fragment from Gorilla gorilla including the 5' part of the beta-globin gene and about 4.5 kb of its upstream flanking region was cloned and sequenced. The sequence was compared to the human, chimpanzee, and macaque delta-beta intergenic region. This analysis reveals four tandemly repeated sequences (RS), ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00163849
更新日期：1992-01-01 00:00:00
abstract：:We have investigated the evolvability of an insoluble random polypeptide, RP3-34, to a soluble form through iterative mutation and selection with the aid of the green fluorescent protein (GFP) folding reporter. To assess the solubility of the polypeptides in the selected clones of each generation, the polypeptide gene...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2542-2
更新日期：2004-02-01 00:00:00
abstract：:We have previously shown that several multicopy gene families within the major histocompatibility complex (MHC) arose from a process of segmental duplication. It has also been observed that retroelements play a role in generating diversity within these duplicated segments. The objective of this study was to compare th...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002399910042
更新日期：2000-04-01 00:00:00
abstract：:Drosophilidae is a large, widely distributed family of Diptera including 61 genera, of which Drosophila is the most representative. Drosophila feeding is part of the saprophytic trophic chain, because of its dependence upon decomposing organic matter. Many species have adapted to fermenting fruit feeding or to artific...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006378
更新日期：1998-08-01 00:00:00
abstract：:We provide here evidence for a conserved regulatory element for transcription of the β-family globin genes based on a comparative study of 32 genes from 16 mammals. The element is characterized by the appearance of AA or TT dinucleotides in the A + T-rich region located 200-400 bp upstream of the cap sites. G-tracts 3...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9459-y
更新日期：2011-10-01 00:00:00
abstract：:L1 elements are retrotransposons that have been replicating and evolving in mammalian genomes since before the mammalian radiation. Rattus norvegicus shares the young L1mlvi2 clade only with its sister taxon, Rattus cf moluccarius. Here we compared the L1mlvi2 clade in these recently diverged species and found that it...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006246
更新日期：1997-10-01 00:00:00
abstract：:Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-squared-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 sp...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0189-2
更新日期：2005-04-01 00:00:00
abstract：:The efficiency of obtaining the correct tree by the maximum likelihood method (Felsenstein 1981) for inferring trees from DNA sequence data was compared with trees obtained by distance methods. It was shown that the maximum likelihood method is superior to distance methods in the efficiency particularly when the evolu...
journal_title：Journal of molecular evolution
pub_type： 评论,杂志文章
doi：10.1007/BF02101285
更新日期：1991-05-01 00:00:00
abstract：:This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02111283
更新日期：1987-01-01 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
abstract：:The sequences of the adenylate kinase gene (adk) and the RecA gene (recA) were determined from the same isolates of Neisseria gonorrhoeae, N. meningitidis, N. lactamica, N. polysaccharea, N. cinerea, N. mucosa, N. pharyngis var. flava, N. flavescens, and N. animalis. The patterns of sequence divergence observed at adk...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02202111
更新日期：1996-12-01 00:00:00
abstract：:The slow-evolving mitochondrial DNAs of plants have potentially conserved information on the phylogenetic branching of the earliest land plants. We present the nad2 gene structures in hornworts and liverworts and in the presumptive earliest-branching vascular land plant clade, the Lycopodiopsida. Taken together with t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2324-2
更新日期：2002-09-01 00:00:00
abstract：:LINE-1 (L1) elements constitute the major family of retrotransposons in mammalian genomes. Here we report the first investigation of L1 evolution in New World monkeys (NWM). Two regions of the second open-reading frame were analyzed by two methods in three NWM species, the squirrel monkey (Saimiri sciureus), the tamar...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2539-x
更新日期：2004-01-01 00:00:00
abstract：:Several distinct families of endogenous retroviruses exist in the genomes of primates. Most of them are remnants of ancient germ-line infections. The human endogenous retrovirus family HERV-K represents the unique known case of endogenous retrovirus that amplified in the human genome after the divergence of human and ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010213
更新日期：2001-09-01 00:00:00
abstract：:The early evolution of life is a period with many important events with a lot of big and open questions. One of them is the evolution of metabolic pathways, which means the origin and assembly of enzymes that act together. The retrograde hypothesis was the first attempt to explain the origin and evolutionary history o...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-021-09994-0
更新日期：2021-01-28 00:00:00
abstract：:There has been considerable discussion in recent years on the evolution of the tandemly repeated multigene families, since some organisms show a concerted model whereas others show a birth-and-death model. This controversial subject extends to several species of fish. In this study, three species of the Sparidae famil...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-013-9541-8
更新日期：2013-03-01 00:00:00
abstract：:The level reached by the optimization of the polarity distances during the evolution of the genetic code was investigated. The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary min...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02103616
更新日期：1989-10-01 00:00:00
abstract：:Bacterial lipoproteins, characterized by the N-terminal N-acyl S-diacylglyceryl Cysteine, are key membrane proteins in bacterial homeostasis. It is generally thought that during the modification lipoprotein precursors are translocated via the Sec-machinery in an unfolded state. The recent discovery of twin-arginine tr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9334-2
更新日期：2010-04-01 00:00:00
abstract：:Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9836-x
更新日期：2018-04-01 00:00:00
abstract：:We describe the structure of a gene expressed in the salivary gland cells of the dipteran Chironomus tentans and show that it encodes 1 of the approximately 15 secretory proteins exported by the gland cells. This sp115,140 gene consists of approximately 65 copies of a 42-bp sequence in a central uninterrupted core blo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101791
更新日期：1990-07-01 00:00:00
abstract：:As the origin(s) of life on Earth remains an open question, detailed characteristics about the "last universal ancestor" (LUA) continue to be obscured. Here we provide arguments that strengthen the bacterial-like nature of the LUA. Our view attempts to recreate the evolution of archaeal lipids, the major components of...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0141-8
更新日期：2007-03-01 00:00:00
abstract：:Domains are folded structures and evolutionary building blocks of protein molecules. Their three-dimensional atomic conformations, which define biological functions, can be coarse-grained into levels of a hierarchy. Here we build global dynamical models for the evolution of domains at fold and fold superfamily (FSF) l...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-016-9740-1
更新日期：2016-05-01 00:00:00
abstract：:One crucial event during evolution to multicellularity was the development of either direct cell-cell contact or indirect interaction via extracellular matrix (ECM) molecules. The identification of those polypeptides provides conclusive data on the phylogenetic relationship of metazoan phyla and helps us to understand...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010230
更新日期：2001-10-01 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 RpoS sigma factor in proteobacteria regulates genes in stationary phase and in response to stress. Although of conserved function, the RpoS regulon may have different gene composition across species due to high genomic diversity and to known environmental conditions that select for RpoS mutants. In this study, the...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9352-0
更新日期：2010-06-01 00:00:00
abstract：:Universal scale of the sequence conservation has been recently introduced based on omnipresence of the protein sequence motifs across species. A large spectrum of short sequences, up to eight residues has been found to reside in all or almost all prokaryotic organisms. By this discovery a principally novel quantitativ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0190-4
更新日期：2006-11-01 00:00:00
abstract：:Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9348-9
更新日期：2010-05-01 00:00:00
abstract：:The in vitro expression of two distinct proteins from overlapping reading frames in a sequence of rainbow trout genomic DNA has been demonstrated. In vitro transcription of DNA sequences, cloned in a plasmid under the control of Salmonella phage 6 polymerase promoter, led to the synthesis of two distinct and functiona...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099952
更新日期：1986-01-01 00:00:00
abstract：:Single-fly polymerase chain reaction amplification and direct DNA sequencing revealed high levels of length polymorphism in the threonine-glycine encoding repeat region of the period (per) gene in natural populations of Drosophila melanogaster. DNA comparison of two alleles of identical lengths gave a high number of s...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02342746
更新日期：1991-03-01 00:00:00
abstract：:Seven new Italian and two new British HTLV-II isolates were obtained from injecting drug users and the entire long terminal repeat (LTR) region was sequenced. Restriction analysis showed that all the Italian isolates are of the IIb subtype, whereas the British isolates are of the IIa subtype. To understand whether the...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006340
更新日期：1998-05-01 00:00:00
