Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species

Repeated motifs of amino acids within proteins are an abundant feature of eukaryotic sequences and may catalyze the rapid production of genetic and even phenotypic variation among organisms. The completion of the genome sequencing projects of 12 distinct Drosophila species provides a unique dataset to study these intriguing sequence features on a phylogeny with a variety of timescales. We show that there is a higher percentage of proteins containing repeats within the Drosophila genus than most other eukaryotes, including non-Drosphila insects, which makes this collection of species particularly useful for the study of protein repeats. We also find that proteins containing repeats are overrepresented in functional categories involving developmental processes, signaling, and gene regulation. Using the set of 1-to-1 ortholog alignments for the 12 Drosophila species, we test the ability of repeats to act as reliable phylogenetic signals and find that they resolve the generally accepted phylogeny despite the noise caused by their accelerated rate of evolution. We also determine that in general the position of repeats within a protein sequence is non-random, with repeats more often being absent from the middle regions of sequences. Finally we find evidence to suggest that the presence of repeats is associated with an increase in evolutionary rate upon the entire sequence in which they are embedded. With additional evidence to suggest a corresponding elevation in positive selection we propose that some repeats may be inducing compensatory substitutions in their surrounding sequence.     

The distribution and frequency of microsatellite loci in Drosophila melanogaster

We report the results of a comprehensive search of Drosophila melanogaster DNA sequences in GenBank for di-, tri-, and tetranucleotide repeats of more than four repeat units, and a DNA library screen for dinucleotide repeats. Dinucleotide repeats are more abundant (66%) than tri- (30%) or tetranucleotide (4%) repeats. We estimate that 1917 dinucleotide repeats with 10 or more repeat units are present in the euchromatic D. melanogaster genome and, on average, they occur once every 60 kb. Relative to many other animals, dinucleotide repeats in D. melanogaster are short. Tri- and tetranucleotide repeats have even fewer repeat units on average than dinucleotide repeats. Our WorldWide Web site (http://www.bio.cornell.edu/genetics/aquadro/aquadro.html) posts the complete list of 1298 microsatellites (≥ five repeat units) identified from the GenBank search. We also summarize assay conditions for 70 D. melanogaster microsatellites characterized in previous studies and an additional 56 newly characterized markers.     

Assessing the genetic diversity of Panicum coloratum var. makarikariense using agro‐morphological traits and microsatellite‐based markers

Panicum coloratum var. makarikariense is a perennial C₄ grass native to South Africa with relatively good forage production under limited‐resource conditions. Genetic characterisation and breeding efforts have been scant, thus limiting its use in cattle raising systems. The goal of the present study was to assess the genetic diversity of a collection of P. coloratum var. makarikariense using agro‐morphological traits and molecular markers, in comparison with one accession of var. coloratum and one population of Panicum bergii. Agro‐morphological variability between and within accessions of var. makarikariense in a common garden setting was observed, showing that there is still opportunity for selection. Some accessions performed better than the commercialised material in relation to potential forage production. A total of 117 ISSR bands and 48 SSR alleles allowed the detection of genetic variability between and within accessions. The presence of accession‐specific bands suggested distinctness and limited gene flow. The genetic variability encountered in the commercialised material suggested that it is a stabilised population which has not undergone a strong selection process. Low correlation between agro‐morphologic and molecular variability was observed indicating that both approaches provide complementary information. Both morphological and molecular markers reveal genetic differentiation between varieties and species. This study provides a set of new SSR markers available for diversity assessment and valuable information that can be applied directly in collection management for breeding and conservation programmes.     

Differential distributions of mononucleotide repeat sequences in 256 viral genomes and its potential implications

Mononucleotide repeats (MNRs) have been systematically investigated in the genomes of eukaryotic and prokaryotic organisms. However, detailed information on the distribution of MNRs in viral genomes is limited. In this study, we examined the distributions of MNRs in 256 fully sequenced virus genomes which showed extensive variations across viral genomes, and is significantly influenced by both genome size and CG content. Furthermore, the ratio of the observed to the expected number of MNRs (O/E ratio) appears to be influenced by both the host range and genome type of a particular virus. Additionally, the densities and frequencies of MNRs in genic regions are lower than in non-coding regions, suggesting that selective pressure acts on viral genomes. We also discuss the potential functional roles that these MNR loci could play in virus genomes. To our knowledge, this is the first analysis focusing on MNRs in viruses, and our study could have potential implications for a deeper understanding of virus genome stability and the co-evolution that occurs between a virus and its host.     

芜菁SSR引物的开发及多态性分析

目的:用于芜菁的简单序列重复(SSR)标记数量有限,初步探索多态性较好SSR的结构特性,开发更多的SSR引物,有助于芜菁的研究。方法:开发680对新的SSR引物,以2个芜菁品种为模板进行多态性扩增,筛选出多态性较好的引物。结果:565(83.1%)对引物在2种芜菁之间能够有效扩增,有多态性的引物有141对(20.7%);SSR的长度与其多态性水平之间没有直接的线性关系,但SSR基序碱基数与重复次数和多态性水平之间存在一定的联系,即3碱基为基序、7次重复的SSR多态性较好。结论:SSR的类型与引物的多态性之间有一定的联系。     

Characterization and cross‐species amplification of microsatellite markers in cherimoya (Annona cherimola Mill., Annonaceae)

Fifteen polymorphic microsatellites were developed using a CT/AG‐enriched genomic library of cherimoya cv. Fino de Jete and screened on 23 genotypes from different geographical areas. This is the first set of microsatellites developed in Annonaceae. Fourteen of the microsatellites detected a single locus and only one detected two loci. The number of alleles in the single locus microsatellites ranged from two to six and the observed and expected heterozygosity ranged from 0.17 to 0.61 and from 0.12 to 0.76, respectively. Most of the simple sequence repeats were transferable to other species in the family.     

Tetranucleotide microsatellite loci for Indian major carp

The characterization of five tetranucleotide microsatellite loci in a commercially important Asian cyprinid, Catla catla , is described. The alleles are not prone to stutter artefacts, usually associated with dinucleotide loci, and are readily visualized with a fast silver-staining protocol after electrophoresis in non-denaturing polyacrylamide.     

Amino acid composition and protein dimension

There is indirect evidence that the amino acid composition of proteins depends on their dimension. The amino acid composition of a nonredundant set of about 550,000 proteins was determined and it was observed that, in the range of 50-200 residues, the percentage of occurrence of most of the residue types significantly depends on protein dimension. This result should prove useful in analyzing protein sequences and genomics.     

Characterization of EST derived SSRs from the bay scallop,Argopecten irradians

Interest in bay scallop conservation has resulted in organized stock enhancement efforts and increased attention to fisheries management issues. Genetic markers can facilitate the monitoring of enhancement efforts, characterization of wild populations, and optimize hatchery practices. We have identified eight polymorphic simple sequence repeat markers including one dinucleotide, six trinucleotide and one compound dinucleotide repeats, in expressed sequence tags generated from multiple bay scallop cDNA libraries. The numbers of alleles range from two to five. The expected and observed heterozygosities range from 0.093 to 0.720 and 0.095 to 0.600, respectively.     

On the origins of medfly invasion and expansion in Australia

As a result of their rapid expansion and large larval host range, true fruit flies are among the world's most important agricultural pest species. Among them, Ceratitis capitata has become a model organism for studies on colonization and invasion processes. The genetic aspects of the medfly invasion process have already been analysed throughout its range, with the exception of Australia. Bioinvasion into Australia is an old event: medfly were first captured in Australia in 1895, near Perth. After briefly appearing in Tasmania and the eastern states of mainland Australia, medfly had disappeared from these areas by the 1940s. Currently, they are confined to the western coastal region. South Australia seems to be protected from medfly infestations both by the presence of an inhospitable barrier separating it from the west and by the limited number of transport routes. However, numerous medfly outbreaks have occurred since 1946, mainly near Adelaide. Allele frequency data at 10 simple sequence repeat loci were used to study the genetic structure of Australian medflies, to infer the historical pattern of invasion and the origin of the recent outbreaks. The combination of phylogeographical analysis and Bayesian tests showed that colonization of Australia was a secondary colonization event from the Mediterranean basin and that Australian medflies were unlikely to be the source for the initial Hawaiian invasion. Within Australia, the Perth area acted as the core range and was the source for medfly bioinvasion in both Western and South Australia. Incipient differentiation, as a result of habitat fragmentation, was detected in some localized areas at the periphery of the core range.     

A comparison of fluorescamine and o-phthaldialdehyde as effective blocking reagents in protein sequence analyses by the Beckman sequencer

Use of o-phthaldialdehyde to chemically reduce the newly generated amino termini responsible for the progressively increasing background during an extended amino acid sequence analysis in a liquid phase sequencer has been described. The results have been compared with Fluram blocking using apomyoglobin and rabbit C-reactive protein as standard and unknown samples, respectively.     

Analysis of intra-specific somatic hybrids of potato (Solanum tuberosum) using simple sequence repeats

We have utilised simple sequence repeat (SSR) polymorphism to analyse two sets of potential intra-specific hybrids of potato. Two primer pairs were used and both showed that one set of fusion products could not be true heterokaryons. In the other set, one of the primer pairs showed that unique bands in each of the parents were present in all of the hybrids, unambiguously demonstrating hybridity. This simple and robust, high-resolution assay can be used at the callus level and is amenable to automation, making it possible to reduce greatly the time required to screen a large number of potential somatic hybrids.     

A set of polymorphic microsatellite loci for the bay scallop,Argopecten irradians

The method of creating enriched microsatellite libraries can supply an abundant source of microsatellite sequences at a considerably reduced cost. Here we report the development of 15 polymorphic microsatellite loci from the bay scallop, Argopecten irradians, using enrichment protocol. Polymorphism was assessed in a sample of hatchery population (n = 38) revealing three to seven alleles per locus. The expected and observed heterozygosities ranged from 0.198 to 0.813 and from 0.083 to 0.833, respectively. These markers will be useful for genetic variation monitoring and parentage analysis.     

Characterization of Mononucleotide Repeats in Sequenced Prokaryotic Genomes

The increasing availability of prokaryotic genome sequenceshas shown that simple sequence repeats (SSRs) are widespreadin prokaryotes and that there is extensive variation in theirlength, number and distribution. Considering their potentialimportance in generating genomic diversity, we determined thedistribution of a specific group of SSRs, mononucleotide repeatsof size between 5 and 13 nt, in 157 sequenced prokaryotic genomes.The data obtained in the present study show that (i) a largenumber of mononucleotide SSRs is present in all prokaryoticgenomes investigated, (ii) shorter repeats are much more abundantthan longer repeats, and (iii) in the majority of the genomes,longer mononucleotide SSRs are excluded from coding regionsalthough we identified several organisms where mononucleotideSSRs are not excluded from the coding regions. We also observedthat some genomes contain more mononucleotide SSRs than expected,while others contain significantly less. Bacterial genomes thatcontain much less mononucleotide SSRs than expected are generallylarger and more GC-rich, while bacterial genomes that containmuch more mononucleotide SSRs than expected are in general smallerand more AT-rich. Finally, we also noted that genomes that containa high fraction of horizontally transferred genes have a lowermononucleotide SSR density and that A and T are generally overrepresentedin mononucleotide SSRs.     

EST‐derived polymorphic microsatellites from cultivated strawberry (Fragaria×ananassa) are useful for diversity studies and varietal identification among Fragaria species

Microsatellite or simple sequence repeat markers derived from expressed sequence tags (ESTs) provide genetic markers within potentially functional genes, which could be very useful for breeding programs. To date, the development of microsatellite markers in the genus Fragaria has focused mainly on Fragaria vesca. However, most of the interests of breeding programs relate to specific characteristics of cultivated strawberry. Here, we describe a set of 10 EST‐derived microsatellites from Fragaria × ananassa. These markers showed high levels of polymorphism within strawberry cultivars and among different Fragaria species, indicating their potential for genetic studies not only on strawberry but also in other species within the genus.     

A method to recognize distant repeats in protein sequences

An automated algorithm is presented that delineates protein sequence fragments which display similarity. The method incorporates a selection of a number of local nonoverlapping sequence alignments with the highest similarity scores and a graphtheoretical approach to elucidate the consistent start and end points of the fragments comprising one or more ensembles of related subsequences. The procedure allows the simultaneous identification of different types of repeats within one sequence. A multiple alignment of the resulting fragments is performed and a consensus sequence derived from the ensemble(s). Finally, a profile is constructed form the multiple alignment to detect possible and more distant members within the sequence. The method tolerates mutations in the repeats as well as insertions and deletions. The sequence spans between the various repeats or repeat clusters may be of different lengths. The technique has been applied to a number of proteins where the repeating fragments have been derived from information additional to the protein sequences. © 1993 Wiley-Liss, Inc.     

Limited variability of CTG/CAG repeats in <Emphasis Type="Italic">Lycopersicon</Emphasis> nuclear DNA

Seven clones containing (CTG)_n/(CAG)_n repeats (n ≥ 4) were isolated by screening Lycopersicon esculentum genomic DNA. Four of the clones contained more than one simple sequence repeat (SSR). The SSRs were analyzed in several L. esculentum cultivars after polymerase chain reaction (PCR) amplification. No length variations were observed, suggesting considerable locus stability. Five clones are from transcribed regions, which might explain the lack of cultivar variations. However the conservation of CTG repeats was limited as differences in some transcribed loci were registered between L. pennellii and other Lycopersicon species. It is noted that in Lycopersicon trinucleotide repeat variation might be used for species identification.     

Microsatellite loci for the North American tortoises (genus Gopherus) and their applicability to other turtle species

We describe the development of nine microsatellite loci from the gopher tortoise (Gopherus polyphemus). Screening 270 individuals, we found these loci to be highly variable (from two to 15 alleles per locus) and thus likely to be applicable in parentage and population‐level analyses for G. polyphemus. All nine loci amplified readily in the other three species of Gopherus as well. This observation, together with successful cross amplification of several loci in two additional families (Cheloniidae, Kinosternidae), underscores their potential utility among turtles in general.     

Synthesis of 3-O-acyl esters of serine and threonine

The 3-O-acyl derivatives of serine and threonine have been prepared by reacting oleoyl chloride and palmitoyl chloride with N-t-butoxycarbonyl (N-T-BOC) serine and N-t-BOC threonine. The t-BOC group was removed by treatment with 4 N HCl in dioxane. The products were identified by proton magnetic resonance spectroscopy, infrared spectroscopy, elemental analysis and chromatographic properties. The O-acyl serines and O-acyl threonines were converted to their methyl esters by treatment with boron trifluoride in methanol and were converted to their dinitrophyl derivatives by treatment with dinitrofluorobenzen (DNFB). The yield of the dinitrophenyl derivatives was very high but the yield of methyl esters was low due mainly to methanolysis and loss of the fatty acyl group. The O-acyl serines and O-acyld threonines prepared will provide standards for researchers who are interested in identifying fatty acids esterified to serine and threonine hydroxyl groups in membrane proteins.     

Microsatellite markers developed from Theobroma cacao L. expressed sequence tags

Theobroma cacao L. expressed sequence tags (ESTs) were converted into useful genetic markers for fingerprinting individuals and genetic linkage mapping. Primers were designed to microsatellite‐containing ESTs. Twenty‐two T. cacao accessions, parents of various mapping populations segregating for disease resistance and crop yield characteristics, were tested. Twenty‐seven informative loci were discovered with 26 primer pairs. The number of detected alleles ranged from two to 11 and averaged 4.4 per locus. All 27 markers could be mapped into at least one of the existing F₁ or F₂ populations segregating for agronomically important traits.