Synonymous Groups Research Articles

Model of Overlapping Messages with Degenerate Coding

Superposition of signals in DNA molecule is a sufficiently general principle of information coding. The necessary re-quirement for such superposition is the degeneracy of the code, which allows placing different messages on the same DNA fragment. Code words that are equivalent in the informational sense (i.e., synonyms) form synonymous group and the entire set of code words is partitioned into synonymous groups. This paper is dedicated to constructing and analyzing the model of synonymous coding. We evaluate some characteristics of synonymous coding as applied to code words of length two although many definitions may be extended for words of arbitrary length.

Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers (SSR)

Pomegranate ( Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In the present study, we report the development of 4 new polymorphic SSR markers. They have been used in addition to 11 SSRs previously published to investigate molecular diversity of 33 P. granatum ecotypes. Based on the multi-locus profiles, twenty-two distinctive genotypes were identified. Globally, quite low genetic diversity has been revealed, as measured by allele richness (2.83 per locus) and heterozygosity (He = 0.245; Ho = 0.243), reflecting the narrow genetic background of the plant material. Four synonymous groups could be detected involving 15 accessions. Results of ordination and cluster analysis suggested that almost all the Tunisian cultivars share similar genetic background, and are likely derived from a small number of introductions in ancient times. Results issued from this study provide essential information to project a pomegranate core-collection without plant material duplication and for sustainable management of pomegranate landraces at national and international level. Furthermore, these SSR markers are powerful tool for marker assisted selection (MAS) program and for QTL studies.

Evolutionary analysis of human-origin influenza A virus (H3N2) genes associated with the codon usage patterns since 1993

This study investigated genetic variations in eight major genes (hemagglutinin, HA; neuraminidase, NA; matrix protein, MP; non-structural protein, NS; nucleoprotein, NP; polymerase, PA; PA basic protein 1, PB1; and PA basic protein 2, PB2) of the influenza A virus subtype H3N2 (A/H3N2) to determine the evolutionary pattern in codon bias. A total of 6,881 sequences isolated between 1993 and 2010 were used. The relative synonymous codon usage (RSCU) and G+C% content at the three codon positions were analyzed by calculating the codon substitution patterns were analyzed by calculating the percentage of synonymously substituted codons (SSCs) and that of codons substituted to the same codon within each synonymous codon group (EMC) between 1993 and subsequent years. In the multivariate analysis of RSCU, we observed directional changes in HA, NA, PB1, and PB2, and these changes were significantly correlated with the variation in the G+C contents at the first (GC(1st)) and second (GC(2nd)) codon positions over time. These directional changes in HA and NA appear to affect their antigenic characteristics by altering their SSCs gradually, and NP, PA, PB1, and PB2 genes also continuously changed their substitution patterns by accumulating the decrements of EMC values over a long term. Our findings suggest that, in human populations, A/H3N2 viruses have gradually changed their SSCs in two external genes, HA and NA, and that these accumulated alteration patterns may result in the antigenic changes over time. Moreover, A/H3N2 viruses also appear to change synonymous codon usage patterns in NP, PA, PB1, and PB2 genes by accumulating decrements in EMCs within synonymous codon groups over time.

Genetic Characterization of Old Slovenian Grapevine Varieties ofVitis viniferaL. by Microsatellite Genotyping

Microsatellite genotyping of 38 local Slovenian varieties was performed using 11 SSR markers that have been shown to be highly polymorphic in European Vitis resources. Combining those data with previous studies, 49 unique genotypes were identified within the varieties currently cultivated in the Slovenian Primorje region. These genotypes were further compared to 161 cultivars from eight European countries to assess their genetic relationships. A high level of genetic diversity among Slovenian grapevines was revealed and some unknown relationships were discovered. Identity analyses revealed 11 groups of synonyms among Slovenian varieties and three matches between a Slovenian variety and a variety from other countries. Several groups of Slovenian varieties with similar names resulted in different SSR profiles. The genetic distances between varieties used in Slovenia and the most popular cultivars used in other European countries revealed the closest relationship with Croatian varieties and the most distant with French varieties.

How a corpus-based study of the factors which influence collocation can help in the teaching of business English

In this paper I use two case studies to show how corpus linguistics can be used to help in the teaching of business English. Senior managers in global companies often find themselves having to do their job in a foreign language. Given that language is one of the key tools of management, the senior managers are normally very keen to develop a sophisticated command of what they perceive to be key lexis. Consequently, the business English teacher may be required to answer searching and demanding questions in a very precise and accurate way. In this paper I show how a corpus-based investigation of the collocational behaviour of key lexis can be used to answer many of these questions. For example, a study of this kind can reveal the different senses of a word and show how it may be associated with a particular semantic prosody. By studying the collocations associated with a group of so-called synonyms it is often possible to identify slight but significant differences in the meaning of the words in the group.

Genetic diversity of Japanese chestnut cultivars assessed by SSR markers

The history of chestnut utilization in Japan is very long. Many cultivars have been preserved without being sufficiently organized and studied with respect to genetic variation. We developed 12 new SSR (simple sequence repeat) markers from Japanese chestnut (Castanea crenata) by using SSR-enriched genomic libraries. All 12 primer pairs selected for SSR analysis successfully amplified fragments in 6 Castanea species. The genetic diversity and relationships among 216 chestnut accessions were assessed by SSR markers, including 142 Japanese chestnuts, 38 Chinese chestnuts (C. mollissima), 2 European chestnuts (C. sativa), 9 American chestnuts (C. dentata), and 23 Japanese–Chinese hybrids. Among the 216 accessions, we identified 21 synonym groups (including 1 bud sport group), and 189 different genotypes. The mean values of observed heterozygosity (HO) and the expected heterozygosity (HE) in the Japanese chestnuts were 0.65 and 0.65, respectively. A phenogram of the 189 genotypes revealed 3 major groups, corresponding to Japanese, Chinese and American chestnuts. Japanese–Chinese hybrid cultivars were mainly included in the Chinese chestnut group. In the present study, genetic backgrounds could be identified for native and cultivated Japanese chestnuts and Japanese–Chinese hybrid cultivars, and many synonyms showing identical SSR genotypes were found. Genetic and geographical relationships of unique characteristics such as “Shidareguri” (weeping) and “Togenashi” (spineless) were also discussed. These results will improve the efficiency of cultivar identification and of chestnut breeding programs.

Molecular characterisation of the national collection of Swiss cherry cultivars

SummaryThis study aimed to assess the genetic diversity present among Swiss cherry accessions using the microsatellite markers (SSRs) proposed by the Prunus working group of the ECPGR-FN (European Collaborative Programme for Genetic Resources-Fruit Network) for varietal identification. We analysed 567 cherry accessions from nationwide collections of the fruit genetic resources inventory, and from the nuclear stock of Agroscope ACW, an archive of healthy, virus-free fruit varieties. Of the 20 SSRs tested, 14 resulted in polymorphic and useful multiplex mixes covering the entire cherry genome. The numbers of alleles per locus ranged from two to 21, which was generally higher than reported in the literature. Several groups of putative synonyms, with up to 16 accessions, were found, reducing the number of individual genetic profiles to 278. This represents a 49% reduction of the total number of genetically different accessions. Our results may therefore lead to making the maintenace of, and breeding from, Swiss cherry collections more cost-effective.

Domain corpus independent vocabulary generation for embedded continuous speech recognition

This paper proposes a domain corpus independent vocabulary generation algorithm in order to improve the coverage of vocabulary for embedded continuous speech recognition (CSR). A vocabulary in CSR is normally derived from a word frequency list. Therefore, the vocabulary coverage is dependent on a domain corpus. We present an improved way of vocabulary generation using part-of-speech (POS) tagged corpus and knowledge base. We investigate 152 POS tags defined in a POS tagged corpus and word-POS tag pairs. We analyze all words paired with 101 among 152 POS tags and decide on a set of words which have to be included in vocabularies of any size. The other 51 POS tags are mainly categorized with noun-related, named entity (NE)-related and verb-related POSs. We introduce a domain corpus independent word inclusion method for noun-, verb-, and NE-related POS tags using knowledge base. For noun-related POS tags, we generate synonym groups and analyze their relative importance using Google search. Then, we categorize verbs by lemma and analyze relative importance of each lemma from a pre-analyzed statistic for verbs. We determine the inclusion order of NEs through Google search. The proposed method shows at least 28.6% relative improvement of coverage for a SMS text corpus when the sizes of vocabulary are 5 K, 10 K, 15 K and 20 K. In particular, the coverage of 15 K size vocabulary generated by the proposed method reaches up to 97.8% with the relative improvement of 44.2%.

Nomenclature and genetic relationships of apples and pears from Terceira Island

Heritage apple (Malus domestica Borkh. hybrids) and pear (Pyrus communis L. hybrid) trees grow in villages throughout Terceira Island, Azores, Portugal. Some of these pears have different names but similar morphology. The objective of this study was to determine synonymy, homology, and phylogeny of apples and pears from Terceira and to examine potential relationships of the island pears with standard apples and pears of Portuguese or American descent. Nine apple microsatellite markers were used to determine genetic relationships. Distance- and parsimony-based cluster analysis grouped these genotypes into separate apple and pear clades. The Terceira apples were divided into two clades: the macā and the reineta-reinette. Among the 17 heritage apple genotypes, seven unique accessions were identified and four groups of synonyms, or possibly clones, were detected including: ‘Reineta Agosto’ and ‘Reineta Verde’ from Altares; ‘Reineta Castanha’ and ‘Reineta Verde Miuda’; ‘Macā Pera,’ ‘Macā Calhau’, ‘Pero Branco’ from Salga and from Terra-Chā and ‘Macā Marmelo’; and the five genotypes ‘Macā Sao Joao’, ‘Malapio Rosa’, ‘Macā Gaspar’, ‘Macā Branca’ and ‘Macā Pato’. In addition, two homonyms were detected. ‘Pero Vermelho’ from Terra Chā was a separate genotype from a tree from Doze Ribeiras of the same name, but Pero Branco from Terra Chā appears to be a clone that can be distinguished by an additional allele at CH1F07a from a tree with that name from Salga. One pair of apple clones, ‘Reineta Agosto’ and ‘Reineta Verde’ from Altares appear to be derived from an unreduced gamete of ‘Golden Delicious.’ Another apple genotype ‘Macā Acida’ could be a sibling of the ‘Macā Pera’ clonal group. Other tested standard apples from the US genebank were unrelated to Terceira genotypes. Of the seven heritage pears, five unique genotypes and one pair of synonyms were detected. ‘Pera Papo Pintassilgo’ from Raminho and ‘Pera Vermelha’ from the nursery of Servico de Desenvolvimento Agario da Terceira (SDAT) were synonyms. ‘Passans du Portugal’ was related to ‘Pera Cabaca’ but other standard pears from the US genebank were unrelated to Terceira genotypes. Future studies will include additional apple and pear cultivars from other Islands of the Azores and continental Portugal, and wild Asian species to further explore genetic relationships.

Microsatellite-based characterization of the Castanea sativa cultivar heritage of southern Switzerland

Southern Switzerland has a long tradition of chestnut cultivation as a staple food. Local inhabitants constantly selected varieties according to the ripening period, the type of use, and the adaptability to the territory. As a result, the panorama of chestnut varieties is very complex, as reflected by more than 120 different variety names in an area of 26,000 ha. Since 1994, 47 varieties have been conserved in the chestnut germplasm of southern Switzerland (CSS), including Marroni, Euro-Japanese, and French varieties. A selection of 164 individuals from the CSS was analysed by 8 SSR markers (4 of which were developed in this study). Microsatellite analysis indicated that the CSS was accurately established, as 86% of the individuals grafted were correctly labeled. The identification of 98 genotypes, 10 clonal chestnut groups, 4 synonym groups, and 12 homonym groups reflected the complex ethnogeographical structure of the chestnut distribution. The 17 Marroni individuals considered clustered in 2 differentiated genetic groups instead of only 1 as expected. The fundamental problem of the frequent cases of homonymy and synonymy is discussed, as is the need for criteria for discriminating between polyclonal varieties and distinct homonymous varieties.

Use of Highly Discriminating Morphological Characters and Isozymes in the Study of Spanish Chestnut Cultivars

Morphological characters (six traits) and isozymes (four systems, five loci) were used to discriminate between Spanish chestnut cultivars (Castanea sativa Mill.) from the Iberian Peninsula. A total of 701 accessions (representing 168 local cultivars) were analyzed from collections made between 1989 and 2003 in the main chestnut growing areas: 31 were from Andalucía (12 cultivars), 293 from Asturias (65 cultivars), 25 from Castilla-León (nine cultivars), four from Extremadura (two cultivars) and 348 from Galicia (80 cultivars). Data were synthesized using multivariate analysis, principal component analysis, and cluster analysis. A total of 152 Spanish cultivars were verified: 58 cultivars of major importance and 94 of minor importance, of which 18 had high intracultivar variation. Thirty-seven cultivars were clustered into 14 synonymous groups. Six of these were from Galicia, one from Castilla-León (El Bierzo), four from Asturias, one from Asturias and Castilla-León (El Bierzo), and two from Asturias, Castilla-León (El Bierzo), and Galicia. The chestnut cultivars from Galicia and Asturias were undifferentiated in genetic terms, indicating that they are not genetically isolated. Overall, chestnut cultivars from southern Spain showed the least variation. Many (58%) of Spanish cultivars produced more than 100 nuts/kg; removing this low market-value character will be a high priority. The data obtained will be of use in chestnut breeding programs in Spain and elsewhere.

Microsatellites are Used to Examine Apple and Pear Identities and Genetic Relationships

Simple Sequence Repeat (SSR) markers developed in apple and pear were used to determine genetic relationships among heritage apple and pear cultivars from Portugal's Azore Islands, and to develop identity fingerprints for European and Asian pear accessions at the USDA–ARS National Clonal Germplasm Repository (NCGR). We used 11 SSR markers (six from apple and five from pear) to examine 18 heritage apple and 9 heritage pear cultivars from the Azores. Eight additional Portuguese and economically important cultivars of apple and eight of pear were used as standards. Cluster analysis separated the apple and pear accessions into two distinct groups. Among apple genotypes, 12 unique accessions and five groups of synonyms were identified, while, in pear, seven unique genotypes and three pairs of synonyms were found. None of the accessions obtained from the Azores corresponded to widely grown standard Portuguese apple or pear cultivars. To examine 144 NCGR pear accessions, we used nine polymorphic SSR loci that were developed from GenBank sequences. Cluster analysis identified five sets of synonyms (four in P. communis L. and one in P. ussuriensis Maxim.) and four pairs of homonyms (three in P. communis and one in P. pyrifolia Burm. f. Nakai), and confirmed three clonal sets. Morphological evaluations and additional SSR markers will be used to confirm these results, and to genetically document the identities of pear genotypes. SSR markers will greatly assist the management of ex situ pome fruit germplasm collections by helping to eliminate duplicate accessions and expanding the genetic diversity represented.

Ways of trying in Russian: clustering behavioral profiles

This article proposes a methodology for addressing three long-standing problems of near synonym research. First, we show how the internal structure of a group of near synonyms can be revealed. Second, we deal with the problem of distinguishing the subclusters and the words in those subclusters from each other. Finally, we illustrate how these results identify the semantic properties that should be mentioned in lexicographic entries. We illustrate our methodology with a case study on nine near synonymous Russian verbs that, in combination with an infinitive, express TRY. Our approach is corpus-linguistic and quantitative: assuming a strong correlation between semantic and distributional properties, we analyze 1,585 occurrences of these verbs taken from the Amsterdam Corpus and the Russian National Corpus, supplemented where necessary with data from the Web. We code each particular instance in terms of 87 variables (a.k.a. ID tags), i. e., morphosyntactic, syntactic and semantic characteristics that form a verb's behavioral profile. The resulting co-occurrence table is evaluated by means of a hierarchical agglomerative cluster analysis and additional quantitative methods. The results show that this behavioral profile approach can be used (i) to elucidate the internal structure of the group of near synonymous verbs and present it as a radial network structured around a prototypical member and (ii) to make explicit the scales of variation along which the near synonymous verbs vary.

Analysis of Apple Germplasm in Northwestern Spain

Spain is the 15th largest apple (Malus ×domestica Borkh.) producer in the world with production depending mainly on foreign cultivars. During the 1970s, a germplasm bank of local cultivars was established in Galicia with the aim of preserving the local resources of northwestern Spain. A total of 408 accessions were studied using 89 morphological characters, with 15 corresponding to phenology, 46 to fruit, 7 to flowers, 11 to leaves, 6 to pests and 4 to diseases. Three variable isoenzymes, PGM E.C.5.3.1.9, PGI E.C.2.7.5.1 and EST E.C.2.7.5.1, were analyzed for 405 accessions and 27 commercial cultivars. The main objectives of this work were 1) to evaluate the inter- and intracultivar variability using morphological characters and isoenzymes, 2) to classify the accessions according to the main sources of variability, and 3) to identify repetitions in the germplasm bank. Principal component analysis (PCA) revealed six main sources of variability in the following order: size of fruit, color of skin, acidity, sweetness, harvest time, and attractiveness. The PCA analysis across 350 accessions produced 42 morphological groups. The 3 isoenzymes produced 190 genotype clusters. Combining morphological classification with the isoenzyme genotypes, we found 31 groups of synonyms involving 82 accessions and 8 more possible groups involving 17 accessions. This result allows the elimination of 53 repetitive accessions from the germplasm bank. Six commercial cultivars were identified as the progenitors of eighteen accessions: `Reineta Blanca' of seven, `Reina de Reinetas' of two, `Reineta de Caux' of eight and `Golden Delicious', `Golden 4187' or `Ozark Gold' of one each. Because inter- and intracultivar variability was high and names given by the growers were not reliable, the suggested selection strategy is to select individual clones among and within cultivars to exploit both the inter- and intracultivar genetic variability.

Codon adaptation and synonymous substitution rate in diatom plastid genes

Diatom plastid genes are examined with respect to codon adaptation and rates of silent substitution (Ks). It is shown that diatom genes follow the same pattern of codon usage as other plastid genes studied previously. Highly expressed diatom genes display codon adaptation, or a bias toward specific major codons, and these major codons are the same as those in red algae, green algae, and land plants. It is also found that there is a strong correlation between Ks and variation in codon adaptation across diatom genes, providing the first evidence for such a relationship in the algae. It is argued that this finding supports the notion that the correlation arises from selective constraints, not from variation in mutation rate among genes. Finally, the diatom genes are examined with respect to variation in Ks among different synonymous groups. Diatom genes with strong codon adaptation do not show the same variation in synonymous substitution rate among codon groups as the flowering plant psbA gene which, previous studies have shown, has strong codon adaptation but unusually high rates of silent change in certain synonymous groups. The lack of a similar finding in diatoms supports the suggestion that the feature is unique to the flowering plant psbA due to recent relaxations in selective pressure in that lineage.

Regularities of context-dependent codon bias in eukaryotic genes.

Nucleotides surrounding a codon influence the choice of this particular codon from among the group of possible synonymous codons. The strongest influence on codon usage arises from the nucleotide immediately following the codon and is known as the N1 context. We studied the relative abundance of codons with N1 contexts in genes from four eukaryotes for which the entire genomes have been sequenced: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. For all the studied organisms it was found that 90% of the codons have a statistically significant N1 context-dependent codon bias. The relative abundance of each codon with an N1 context was compared with the relative abundance of the same 4mer oligonucleotide in the whole genome. This comparison showed that in about half of all cases the context-dependent codon bias could not be explained by the sequence composition of the genome. Ranking statistics were applied to compare context-dependent codon biases for codons from different synonymous groups. We found regularities in N1 context-dependent codon bias with respect to the codon nucleotide composition. Codons with the same nucleotides in the second and third positions and the same N1 context have a statistically significant correlation of their relative abundances.

The Quantifier System: One of the Largest and Least Known Parts of English

The structure of semantics is still largely unknown territory. Semantic fields appear to be the building blocks of semantic structure, but most semantic fields remain unmapped. This paper analyses the structure of one of those, which I call the "quantifier system," although only one small part of it is filled with well known quantifiers. The system is explained in the same way as I explain it to my ESL students. Several ideas in this paper may be of use in analyzing other semantic fields. Firstly, I analyze the field in terms of distinctive features, rather as in phonology. Secondly, the semantic terms are sometimes words and sometimes phrases. Thirdly, each semantic term is a group of synonyms. Fourthly, synonyms and antonyms can be understood not just as lists, but as the building blocks of a larger system. Fifthly, semantic groups in English can include words drawn from different parts of speech.

Small regions of preferential codon usage and their effect on overall codon bias--the case of the plp gene.

Preferential codon usage within synonymous groups (codon bias), is hypothesised to be a consequence of either mutational pressure or translational selection. This paper examines PLP and DM-20, two transcripts differentially spliced from the plp gene, using a variety of previously described indices measuring codon bias as well as a novel index for quantifying the response to directional mutation pressure. The results demonstrate that small regions of extreme codon bias may have appreciable effects on the quantification of total bias, and that this effect may be either an increase or a decrease depending which index is used.

Rates of synonymous substitution do not indicate selective constraints on the codon use of the plant psbA gene.

The psbA gene of the flowering plant chloroplast genome has a pattern of codon bias that differs from all other angiosperm chloroplast genes. In psbA, unlike all other chloroplast genes, the third-codon-position composition does not reflect the general genome compositional bias of a high A+T content. Instead, in specific synonymous groups, the codon use of psbA more closely corresponds to the tRNA population available for translation. Since it requires a composition unlike the genome composition bias, this pattern of codon use is likely to be the result of selection. Selective constraints on codon use are expected to result in decreased rates of synonymous substitution, and it has been observed that psbA has the lowest rate of synonymous substitution among plant chloroplast genes. In the present study, this is examined further by testing whether or not those synonymous groups that specifically have an atypical codon use in psbA have correspondingly low rates of silent substitution. An analysis of synonymous substitution rate, performed separately for different degeneracy classes of amino acids, shows that, contrary to the expectation, those sites that are presumed, based on their codon use, to be under selective constraint in psbA do not show low rates of substitution and are not responsible for the overall low rate of synonymous substitution in this gene. Instead, they actually show increased rates of substitution relative to other chloroplast genes. Two hypotheses concerning the role of selection in psbA are advanced to explain the results.

Selection on the codon bias of Chlamydomonas reinhardtii chloroplast genes and the plant psbA gene.

Plant chloroplast genes have a codon use that reflects the genome compositional bias of a high A+T content with the single exception of the highly translated psbA gene which codes for the photosystem II D1 protein. The codon usage of plant psbA corresponds more closely to the limited tRNA population of the chloroplast and is very similar to the codon use observed in the chloroplast genes of the green alga Chlamydomonas reinhardtii. This pattern of codon use may be an adaptation for increased translation efficiency. A correspondence between codon use of plant psbA and Chlamydomonas chloroplast genes and the tRNAs coded by the chloroplast genome, however, is not observed in all synonymous codon groups. It is shown here that the degree of correspondence between codon use and tRNA population in different synonymous groups is correlated with the second codon position composition. Synonymous groups with an A or T at the second codon position have a high representation of codons for which a complementary tRNA is coded by the chloroplast genome. Those with a G or C at the second position have an increased representation of codons that bind a chloroplast tRNA by wobble. It is proposed that the difference between synonymous groups in terms of codon adaptation to the tRNA population in plant psbA and Chlamydomonas chloroplast genes may be the result of differences in second position composition.