Porcine SINE-associated microsatellite markers: evidence for new artiodactyl SINEs

Simple sequence repeats for genetic studies of alpaca

Trace sequences from the 2X alpaca genome sequencing effort were examined to identify simple sequence repeats (microsatellites) for genetic studies. A total of 6,685 repeat-containing sequences were downloaded from GenBank, processed, and assembled into contigs representing an estimated 4,278 distinct sequences. This sequence set contained 2,290 sequences of length > 100 nucleotides that contained microsatellites of length > or = 14 dinucleotide or 10 trinucleotide repeats with purity equal to 100%. An additional 13 sequences contained a GC microsatellite of length > or = 12 repeats (purity = 100%) were also obtained. Primer pairs for amplification of 1,516 putative loci are presented. Amplification of genomic DNA from alpaca and llama by PCR was demonstrated for 14 primer sets including one from each of the microsatellite repeat types. Comparative chromosomal location for the alpaca markers was predicted in the bovine genome by BLAT searches against assembly 4.0 of the bovine whole genome sequence. A total of 634 markers (41.8%) returned BLAT hits with score > 100 and Identity > 85%, with the majority assignable to unique locations. We show that microsatellites are abundant and easily identified within the alpaca genome sequence. These markers will provide a valuable resource for further genetic studies of the alpaca and related species.

Evolutionary dynamics of multilocus microsatellite arrangements in the genome of the butterfly Bicyclus anynana, with implications for other Lepidoptera

The sequences flanking microsatellites isolated from the butterfly Bicyclus anynana display high levels of similarity among different loci. We examined sequence data for evidence of the two mechanisms most likely to generate these similarities, namely recombination mediated events, such as unequal crossing over or gene conversion and through transposition of mobile elements (MEs). Many sequences contained tandemly arranged microsatellites, lending support to recombination as the multiplication mechanism. There is, however, also support for ME-mediated multiplication of microsatellites and their flanking sequences. Homology with a known Lepidopteran ME was found in B. anynana microsatellite regions, and polymorphic microsatellite markers with partial similarities in their flanking sequences were passed on to the next generation independently, indicating that they are not linked. Therefore, the rise of these similarities appears to be mediated through both processes, either as an interaction between the two, or by each being responsible for part of the observations. A large proportion of microsatellites embedded in repetitive DNA is representative for most studied butterflies and moths, and a BLAST survey of the B. anynana sequences revealed four short microsatellite-associated sequences that were present in many species of Lepidoptera. The similarities usually start to deviate beyond these sequences, which suggests that they define the extremes of a repeated unit. Further study of these conserved sequences may help to understand the mechanism underlying the multiplication events, and answer the question of why these redundancies are predominantly found in this insect group.

Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs

Background

The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution.

Results

We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNA^Lys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNA^Lys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the insterspersed repeat. Moreover, microsatellites associated with tRNA^Lys-derived SINEs showed the highest complexity and less potential instability.

Conclusion

Our results suggest that tRNA^Lys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNA^Lys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.

Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNA^Lys-derived SINEs, we recommend avoiding their use as genetic markers.

Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones

Background

In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, biodiversity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP) as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD) than does a di-allelic marker system [1]. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced.

Results

Seventeen porcine microsatellite markers were isolated from eleven PAC clones by targeted oligonucleotide-mediated microsatellite identification (TOMMI), an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT) microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC), average heterozygosity (H_T), and effective allele number (N_E) for the STS-markers were calculated using a sampling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds). Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles) in this heterogeneous sampling. Most of the publicly available (porcine) microsatellite amplicons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger amplicons. Indeed, fourteen of the seventeen STS-marker amplicons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be integrated into multilocus assays covering a broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions.

Conclusion

The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop amplicons greater than 250 bases.

Isolation of 105 microsatellite loci from an ovine genomic library enriched for microsatellites

This paper reports on the development of a small-insert (approximately 700 bp) total-genomic library for sheep specifically designed for enrichment for microsatellite (ms) loci. Four enriched libraries were prepared by amplification of the primary library with CA15, CA11, TG15 and TG11 oligonucleotide primers. A total of 11,020 clones was recovered, screened for dinucleotide repeats and over 500 positive clones sequenced. Sequence analysis indicated low clone redundancy and yielded 105 new ovine ms loci. Seventy-two percent of the new loci were found to be polymorphic in the sires of the AgResearch International Mapping Flock (IMF). The 105 new microsatellite loci increase the number of microsatellites available for sheep by >7%.

Mobile elements and the genesis of microsatellites in dipterans

Factors that influence the genesis and genomic distribution of microsatellite DNA are poorly understood. We have identified a novel class of Dipteran mobile elements, mini-me elements, which help elucidate both of these issues. These retroposons contain two internal proto-microsatellite regions that commonly expand into lengthy microsatellite repeats. These elements are highly abundant, accounting for approximately 1.2% of the Drosophila melanogaster genome, giving them the potential to be a prolific source of microsatellite DNA variation. They also give us the opportunity to observe the outcomes of multiple microsatellite genesis events (initiating from the same proto-microsatellite) at separate mini-me loci. Based on these observations, we determined that the genesis of microsatellites within mini-me elements occurs through two separate mutational processes: the expansion of preexisting tandem repeats and the conversion of sequence with high cryptic simplicity into tandemly repetitive DNA. These modes of microsatellite genesis can be generalized beyond the case of mini-me elements and help to explain the genesis of microsatellites in any sequence region that is not constrained by selection.

Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales

Insertion analysis of short and long interspersed elements is a powerful method for phylogenetic inference. In a previous study of short interspersed element data, it was found that cetaceans, hippopotamuses, and ruminants form a monophyletic group. To further resolve the relationships among these taxa, we now have isolated and characterized 10 additional loci. A phylogenetic analysis of these data was able to resolve relationships among the major cetartiodactyl groups, thereby shedding light on the origin of whales. The results indicated (i) that cetaceans are deeply nested within Artiodactyla, (ii) that cetaceans and hippopotamuses form a monophyletic group, (iii) that pigs and peccaries form a monophyletic group to the exclusion of hippopotamuses, (iv) that chevrotains diverged first among ruminants, and (v) that camels diverged first among cetartiodactyls. These findings lead us to conclude that cetaceans evolved from an immediate artiodactyl, not mesonychian, ancestor.

Microsatellite markers from a microdissected swine chromosome 6 genomic library

To develop additional microsatellite (MS) markers in the region of the porcine skeletal muscle ryanodine receptor gene (RYR1), a microdissected genomic library was generated from the proximal half of the q arm of swine chromosome 6. Purified DNA was restriction enzyme-digested, ligated to oligonucleotide adaptors and amplified by PCR using primers complementary to the adaptor sequences. The purity of the amplified products and boundaries of the microdissected chromosomal region were verified by fluorescence in situ hybridization. (CA)n-containing sequences were then identified in a small insert genomic library generated from the PCR-amplified microdissected DNA. Oligonucleotide primers were developed for the PCR amplification of 30 of the 46 (CA)n repeat-containing clones, which were subsequently used to amplify DNA isolated from unrelated pigs of different breeds to determine the informativeness of these MS markers. Twenty-two of these MS markers were genotyped on the University of Illinois Yorkshire x Meishan swine reference population. These 22 markers were all assigned within a 50.7-CM region of the swine chromosome 6 linkage map, indicating the specificity of the microdissected library.

Artiodactyl interspersed DNA repeats in cetacean genomes

Interspersed repeats that emerged at different evolutionary times are informative in mammalian phylogeny. Here we show that the ancient short interspersed elements (SINEs) ARE1 and ARE2 are abundantly present in the genomes of artiodactyls and cetaceans but not in other mammalian genomes. This supports the classification of the cetaceans with the artiodactyls by a shared character that is unlikely to be the result of convergence.

An integrated genetic and physical map of the bovine X chromosome

Genotypic data for 56 microsatellites (ms) generated from maternal full sib families nested within paternal half sib pedigrees were used to construct a linkage map of the bovine X Chromosome (Chr) (BTX) that spans 150 cM (ave. interval 2.7 cM). The linkage map contains 36 previously unlinked ms; seven generated from a BTXp library. Genotypic data from these 36 ms was merged into an existing linkage map to more than double the number of informative BTX markers. A male specific linkage map of the pseudoautosomal region was also constructed from five ms at the distal end of BTXq. Four informative probes physically assigned by fluorescence in situ hybridization defined the extent of coverage, confirmed the position of the pseudoautosomal region on the q-arm, and identified a 4.1-cM marker interval containing the centromere of BTX.

A chromosome-specific microdissected library increases marker density on bovine chromosome 1

Genetic resolution of bovine chromosome 1 (BTA1) linkage group was significantly increased by screening for microsatellite clones a microdissected library constructed from a bovine cell line carrying a t(1;29) translocation. Eighty-five percent of the microsatellites (ms) (46/54) identified were informative in the USDA/MARC mapping population, and 96% of these ms (44/46) linked to BTA1 (LOD > 3.0). When merged with 40 existing BTA1 markers the genetic map spanned 153.8 cM (sex-averaged interval, 1.9 cM). The fourfold improvement in marker density of BTA1 provides a genetic map that enhances mapping of quantitative trait loci and implementation of marker assisted selection.

The porcine skeletal muscle ryanodine receptor gene structure coding region 1 to 10614 harbouring 71 exons

The skeletal muscle ryanodine receptor (RYR1) belongs to a family of calcium release channels that are expressed in different tissues. The RYR1 gene is one of the largest genes characterized, so far, containing a 15253 nucleotide ORF in swine. To study the genomic organization of the porcine skeletal muscle ryanodine receptor gene we have isolated seven genomic fragments spanning 72.7 kb of chromosomal DNA of chromosome 6q12. This region harbours exons 1 to 71 coding for 3538 amino acids (69.6%) of the ryanodine receptor 1.

Cloning and characterization of 414 polymorphic porcine microsatellites

We report the sequences, sizes, and number of alleles of 414 new porcine microsatellites that were cloned in our laboratory and 21 microsatellites derived from GenBank DNA sequences. We also confirm the usefulness of porcine microsatellite primer pairs derived from short interdispersed elements.

Physical assignments of 68 porcine cosmid and lambda clones containing polymorphic microsatellites

Two lambda phage and 66 cosmids containing informative porcine microsatellites were assigned to 17 of 18 porcine autosomes and the X Chromosome (Chr) by fluorescence in situ hybridization (FISH). These assignments provide additional physically anchored markers to integrate the porcine physical and genetic maps.

A small-insert bovine genomic library highly enriched for microsatellite repeat sequences

A bovine genomic phagemid library was constructed with randomly sheared DNA. Enrichment of this single-stranded DNA library with CA or GT primers resulted in 45% positive clones. The 14% of positive clones with (CA.GT) > 12, and not containing flanking repetitive elements, were sequenced, and the efficiency of marker production was compared with random M13 bacteriophage libraries. Primer sequences and genotyping information are presented for 390 informative bovine microsatellite markers. The genomic frequency for 11 tri- and tetranucleotide repeats was estimated by hybridization to a lambda genomic library. Only GCT, GGT, and GGAT were estimated to have a frequency of > 100 per genome. Enrichment of the phagemid library for these repeats failed to provide a viable source of microsatellite markers in the bovine. Comparison of map interval lengths between 100 markers from the enriched library prepared from randomly sheared DNA and M13 bacteriophage libraries prepared from Mbo1 restriction digests suggested no bias in skeletal genomic coverage based on source of small insert DNA. In conclusion, enrichment of the bovine phagemid library provides a sufficient source of microsatellites so that small repeat lengths and flanking repetitive sequences common in the bovine can be eliminated, resulting in a high percentage of informative markers.