Abstract
Here, we report the results of next-generation sequencing on the GS Junior system to identify a large number of microsatellites from the epiphytic moss Orthotrichum speciosum. Using a combination of a total (non-enrichment) genomic library and small-scale 454 pyrosequencing, we determined 5382 contigs whose length ranged from 103 to 5445 bp. In this dataset we identified 92 SSR (simple sequence repeats) motifs in 89 contigs. Forty-six of these had flanking regions suitable for primer design. We tested PCR amplification, reproducibility, and the level of polymorphism of 46 primer pairs for Orthotrichum speciosum using 40 individuals from two populations. As a result, the designed primers revealed 35 polymorphic loci with more than two alleles detected. This method is cost- and time-effective in comparison with traditional approaches involving cloning and sequencing.
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Claims 5
Claim · model-written summary
Sequencing produced 5382 contigs, ranging from 103 to 5445 bp.
- Taxon
- Orthotrichum speciosum
Lewinskya speciosae1 - Outcome
- contigse0
- Value
- 5382e0
- Qualifier
- 103 to 5445 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we determined 5382 contigs whose length ranged from 103 to 5445 bp.”
e1“epiphytic moss Orthotrichum speciosum”
Claim · model-written summary
The dataset contained 92 SSR motifs in 89 contigs.
- Taxon
- Orthotrichum speciosumLewinskya speciosae1
- Outcome
- SSR (simple sequence repeats) motifse0
- Value
- 92e0
- Qualifier
- 89 contigse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In this dataset we identified 92 SSR (simple sequence repeats) motifs in 89 contigs.”
e1“epiphytic moss Orthotrichum speciosum”
Claim · model-written summary
Forty-six SSR-bearing contigs had flanking regions suitable for primer design.
- Taxon
- Orthotrichum speciosumLewinskya speciosae1
- Outcome
- flanking regions suitable for primer designe0
- Value
- Forty-sixe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Forty-six of these had flanking regions suitable for primer design.”
e1“epiphytic moss Orthotrichum speciosum”
Claim · model-written summary
Designed primers revealed 35 polymorphic loci with more than two alleles.
- Taxon
- Orthotrichum speciosumLewinskya speciosae1
- Outcome
- polymorphic locie0
- Value
- 35e0
- Qualifier
- more than two allelese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the designed primers revealed 35 polymorphic loci with more than two alleles detected.”
e1“epiphytic moss Orthotrichum speciosum”
Claim · model-written summary
The method was reported as more cost and time effective than traditional cloning and sequencing.
- Taxon
- Orthotrichum speciosumLewinskya speciosae1
- Outcome
- cost- and time-effectivee0
- Comparator
- traditional approaches involving cloning and sequencinge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“This method is cost- and time-effective in comparison with traditional approaches involving cloning and sequencing.”
e1“epiphytic moss Orthotrichum speciosum”