2019
DOI: 10.1007/s00468-019-01875-w
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SNP discovery in radiata pine using a de novo transcriptome assembly

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Cited by 6 publications
(5 citation statements)
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“…Prior to NGS technologies becoming available in pines, SNPs were primarily discovered and validated through expressed sequence tag (EST) libraries (Chancerel et al, 2011; Dantec et al, 2004; Eckert et al, 2009). Now, much of the SNP discovery has shifted to reduced representation sequencing approaches such as RNA sequencing (RNA‐seq) and targeted capture sequencing including exome capture (Durán et al, 2019; Liu et al, 2016; Lu et al, 2016; Neves et al, 2013; Suren et al, 2016; Telfer et al, 2019). This focus on reduced representation methods stems from the massive size (>20 Gbp) and repetitive nature of pine genomes, which makes whole genome sequencing costly and computationally inefficient for SNP discovery.…”
Section: Introductionmentioning
confidence: 99%
“…Prior to NGS technologies becoming available in pines, SNPs were primarily discovered and validated through expressed sequence tag (EST) libraries (Chancerel et al, 2011; Dantec et al, 2004; Eckert et al, 2009). Now, much of the SNP discovery has shifted to reduced representation sequencing approaches such as RNA sequencing (RNA‐seq) and targeted capture sequencing including exome capture (Durán et al, 2019; Liu et al, 2016; Lu et al, 2016; Neves et al, 2013; Suren et al, 2016; Telfer et al, 2019). This focus on reduced representation methods stems from the massive size (>20 Gbp) and repetitive nature of pine genomes, which makes whole genome sequencing costly and computationally inefficient for SNP discovery.…”
Section: Introductionmentioning
confidence: 99%
“…The newly generated reference transcriptome sequence ( MUS assembly ) builds on published transcriptome data (Wachowiak et al, 2015) but extends the available reference by including the two mountain pines. In the new assembly, the number of raw gene models reconstructed is considerably higher as compared to the original P. sylvestris raw assembly and to single‐species studies in other pines (Parchman et al, 2010; Pinosio et al, 2014; Duran et al, 2019). On the other hand, at 14 666, the number of successfully annotated protein‐coding genes is lower than previously reported from P. sylvestris (19 659; Wachowiak et al, 2015) or from better‐studied relatives like P. lambertiana (26 568; Gonzales‐Ibeas et al, 2016) or Picea abies (28 354; Nystedt et al, 2013), and the model species of Arabidopsis thaliana (about 27 500; Cheng et al, 2017; Proost et al, 2015).…”
Section: Discussionmentioning
confidence: 95%
“…Due to their large size and complexity, the assembly of pine genomes is particularly challenging, and has only been satisfactorily achieved for loblolly pine ( Pinus taeda ; Zimin et al, 2014 ) and sugar pine ( Pinus lambertiana ; Stevens et al, 2016 ), which are among the largest genomes ever sequenced and assembled. However, thousands of polymorphic regions potentially suitable for use in genotyping in pine species have already been discovered using high‐throughput sequencing methods such as whole transcriptome studies (Blanca et al, 2012 ; Chancerel et al, 2011 ; Durán et al, 2019 ; Geraldes et al, 2011 ; Liu et al, 2014 ; Parchman et al, 2010 ; Trick et al, 2009 ; Wachowiak et al, 2015 ).…”
Section: Introductionmentioning
confidence: 99%