dc.contributor.author |
Ranade, Sonali Sachin
|
|
dc.contributor.author |
Lin, Yao-Cheng
|
|
dc.contributor.author |
Van de Peer, Yves
|
|
dc.contributor.author |
García-Gil, María Rosario
|
|
dc.date.accessioned |
2016-02-24T12:54:55Z |
|
dc.date.available |
2016-02-24T12:54:55Z |
|
dc.date.issued |
2015-12-26 |
|
dc.description |
Additional file 1: Putative primer pairs for the class I and class II SSRs in the coding regions of Norway spruce (Picea abies ) and Loblolly pine ( Pinus taeda ). |
en_ZA |
dc.description.abstract |
BACKGROUND : Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1–6 bp tandem
repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies.
We carried out a comparative study of perfect SSR loci belonging to class I (≥20) and class II (≥12 and <20 bp)
types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to
retrieve SSRs from the full length CDS of predicted genes in both species.
RESULTS : Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and
hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs
followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus
taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was
significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich
motifs, within class II SSRs in both the species (P-values = 10−9 and 0). With reference to class I SSRs, AT-rich and
GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich
motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005).
CONCLUSIONS : Our study gives a comparative overview of the genome SSRs composition based on high confidence
genes in the two recently sequenced and economically important conifers and, also provides information on functional
molecular markers that can be applied in genetic studies in Pinus and Picea species. |
en_ZA |
dc.description.librarian |
am2015 |
en_ZA |
dc.description.sponsorship |
SSR was supported with a stipend from Kempe foundation. Travel cost for
SSR was covered by the travel grant from Foundation Fund for Forestry
Science Research, Faculty of Forest Sciences, SLU, Umeå. We acknowledge
the support from Berzelii Centre of excellence at Umeå Plant Science Centre,
Umeå, Sweden. We also acknowledge the Swedish research Council (VR) and
the Swedish Governmental Agency for Innovation Systems (VINNOVA) for
supporting the infrastructure to maintain P. abies genome assembly as
publically available at Umeå Plant Science Centre (UPSC), Umeå, Sweden.
Authors also acknowledge the support of computational resources from Picea
abies genome consortium (http://congenie.org/) and Dendrome project. |
en_ZA |
dc.description.uri |
http://www.biomedcentral.com/bmcgenet |
en_ZA |
dc.identifier.citation |
Ranade, SS, lin, Y-C, Van de Peer, Y & García-Gil, MR 2015, 'Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)', BMC Genetics, vol. 16, art. 149, pp. 1-9. |
en_ZA |
dc.identifier.issn |
1471-2156 |
|
dc.identifier.other |
10.1186/s12863-015-0304-y |
|
dc.identifier.uri |
http://hdl.handle.net/2263/51519 |
|
dc.language.iso |
en |
en_ZA |
dc.publisher |
BioMed Central |
en_ZA |
dc.rights |
© 2015 Ranade et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License. |
en_ZA |
dc.subject |
Norway spruce |
en_ZA |
dc.subject |
Picea abies |
en_ZA |
dc.subject |
Loblolly pine |
en_ZA |
dc.subject |
Pinus taeda |
en_ZA |
dc.subject |
Simple sequence repeats (SSR) |
en_ZA |
dc.subject |
Microsatellites |
en_ZA |
dc.subject |
High confidence genes |
en_ZA |
dc.title |
Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda) |
en_ZA |
dc.type |
Article |
en_ZA |