Families of clustered microsatellites in a conifer genome

Elsik, Christine G.; Cg, Williams

doi:10.1007/s004380100443

Cited by 30 publications

(19 citation statements)

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“…Our results found the (AT/TA)n motif to be most prevalent, while previous studies noted that the (AC)n and (AG)n motifs are most common in conifers [76], [79], [80]. The frequency of this motif was, however, less than those computed for Vitis vinifera (42.04%) and Cucumis sativus (55.03%).…”

Section: Discussioncontrasting

confidence: 80%

Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences

et al. 2013

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Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution.

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Section: Discussioncontrasting

confidence: 80%

Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences

et al. 2013

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“…Similar clustering of microsatellites around the centromere has been observed in various plant species like sugarbeet [61], barley [62,63], tomato [64,65] and several other Triticeae species [63]. Several factors are responsible for this clustering of genomic SSRs on genetic linkage maps, major being their non-random physical distribution in plant genomes [66,67], reduced recombination in centromeric regions [68,69] and the genomic origin of DNA sequences used for SSR development [70]. …”

Section: Discussionsupporting

confidence: 60%

Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.)

et al. 2011

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BackgroundChickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites) markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data.ResultsA microsatellite enriched library of chickpea (enriched for (GT/CA)n and (GA/CT)n repeats) was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded) × JG-62 (double podded)] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3%) were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map and the previously published chickpea intraspecific map, integration of maps was performed which revealed improvement of marker density and saturation of the region in the vicinity of sfl (double-podding) gene thereby bringing about an advancement of the current map.ConclusionAn arsenal of 181 new chickpea STMS markers was reported. The developed intraspecific linkage map defined map positions of 138 markers which included 101 new locations.Map integration with a previously published map was carried out which revealed an advanced map with improved density. This study is a major contribution towards providing advanced genomic resources which will facilitate chickpea geneticists and molecular breeders in developing superior genotypes with improved traits.

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“…Simple repeats are difficult to quantify based on WGS coverage, but over 150 were identified among the ten P. taeda BACs (Table 2). Previous studies have shown that simple repeats and microsatellites are found throughout the pine genome [27,38,39]. Using the unmasked MAKER runs, there were also 70 putative ORF elements identified (Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…This very large single-copy fraction could be due to the presence of large complex gene families in pines, as was evidenced by southern hybridizations performed on P. taeda using single-to low-copy gene probes from angiosperms [24,25]. Additionally, the single-copy fraction of the pine genome is enriched for repeats, as it was later shown that at least one fifth of low-copy sequences in P. taeda are retroelements and one third contain microsatellite repeats [26,27]. …”

Section: Introductionmentioning

confidence: 99%

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

et al. 2010

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BackgroundIn today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24). The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda.ResultsWe present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS) sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity) elsewhere in the genome, but only 23% have identical copies (99% identity). The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome.ConclusionsThis study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is a feasible goal.

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Families of clustered microsatellites in a conifer genome

Cited by 30 publications

References 30 publications

Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences

Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences

Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.)

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

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