459
provided 1343 articles (after filtering data), considering the relevance of each article
to the focus of the literature search. This literature search revealed that scientific
research includes a high number of tree species families, although families of model
and worldwide cultivated species, such as Salicaceae, Pinaceae, Rosaceae, Fagaceae
and Fabaceae, prevailed (Fig. 17.1a). Major research themes involving both HTS
technologies and forest tree species included (1) the genetic bases of response to
biotic and abiotic factors and quantitative trait variation, (2) marker development
and characterization, (3) chloroplast characterization and phylogenetic analyses, (4)
population genomics and evolutionary studies, (5) transcriptome characterization
and (6) genome draft development (Fig. 17.1b). Illumina technology dominates
high-throughput sequencing in forest tree species (Fig. 17.1c), with targeted
sequencing being homogenously distributed among nuclear genome, organelle
genome and transcriptome (Fig. 17.1d). Reduced genome sequencing has been less
applied than whole-genome sequencing (Fig. 17.1e), with RADSeq and GBS representing around 50% of the applied reduced sequencing methods. The literature
searches also revealed that both SSR and SNP markers have been developed from
high-throughput sequencing in a similar percentage (around 50%) (Fig. 17.1f).
When considering genetic determinism studies of biotic and abiotic phenotypic
responses that generate relevant information for breeding programmes, it can be
noted that transcriptome sequencing (also called RNA-sequencing or RNA-Seq)
prevailed (28 out of 39 articles). The transcriptome is an efficient tool for generating
enormous sequence collections of expressed genes, in particular for forest tree species, which can have large or repetitive genome. It provides a valuable starting point
for characterizing functional genetic variation and discovering functional molecular
markers. Developments of gene database collections and bioinformatics tools have
been crucial for the annotation of transcriptome sequences and the assignation of
their putative biological functions.
Up to date, several transcriptomic studies on tree species have been carried out
by means of Roche/454-technology strategies, mainly for the development of
genomics resources of unexplored species and for secondary metabolic products
discovery: in Quercus spp. (Ueno et al. 2010; Torre et al. 2014; Lesur et al. 2015),
Pinus contorta (Parchman et al. 2010), Pinus pinaster (Canales et al. 2014), Khaya
senegalensis (Karan et al. 2012), Azadirachta indica (Krishnan et al. 2012; Wang
et al. 2016), Nothofagus alpina (Torales et al. 2012), Prosopis alba (Torales et al.
2013), Carapa guianensis (Brousseau et al. 2014), Melia azedarach (Wang et al.
2016), Cedrela balansae (Torales et al. 2018) and Dalbergia odorifera (Liu et al.
2019) between others. On the other hand, a review carried out by Parent et al. (2015)
showed the species and approaches that were applied in order to find forest gene
differential expression in wood formation, stress response among other conditions,
through microarray and RNA-Seq analysis. They also highlighted the application of
RNA-Seq analysis in many species without genome reference and strategies used to
“native tree”)). Strategy B: (TITLE-ABS-KEY (“transcriptome” OR “genome” AND sequencing)
AND TITLE-ABS-KEY (“forest tree” OR “tree species” OR “native tree”)). Search date:
04-04-2019.
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…
provided 1343 articles (after filtering data), considering the relevance of each article
to the focus of the literature search. This literature search revealed that scientific
research includes a high number of tree species families, although families of model
and worldwide cultivated species, such as Salicaceae, Pinaceae, Rosaceae, Fagaceae
and Fabaceae, prevailed (Fig. 17.1a). Major research themes involving both HTS
technologies and forest tree species included (1) the genetic bases of response to
biotic and abiotic factors and quantitative trait variation, (2) marker development
and characterization, (3) chloroplast characterization and phylogenetic analyses, (4)
population genomics and evolutionary studies, (5) transcriptome characterization
and (6) genome draft development (Fig. 17.1b). Illumina technology dominates
high-throughput sequencing in forest tree species (Fig. 17.1c), with targeted
sequencing being homogenously distributed among nuclear genome, organelle
genome and transcriptome (Fig. 17.1d). Reduced genome sequencing has been less
applied than whole-genome sequencing (Fig. 17.1e), with RADSeq and GBS representing around 50% of the applied reduced sequencing methods. The literature
searches also revealed that both SSR and SNP markers have been developed from
high-throughput sequencing in a similar percentage (around 50%) (Fig. 17.1f).
When considering genetic determinism studies of biotic and abiotic phenotypic
responses that generate relevant information for breeding programmes, it can be
noted that transcriptome sequencing (also called RNA-sequencing or RNA-Seq)
prevailed (28 out of 39 articles). The transcriptome is an efficient tool for generating
enormous sequence collections of expressed genes, in particular for forest tree species, which can have large or repetitive genome. It provides a valuable starting point
for characterizing functional genetic variation and discovering functional molecular
markers. Developments of gene database collections and bioinformatics tools have
been crucial for the annotation of transcriptome sequences and the assignation of
their putative biological functions.
Up to date, several transcriptomic studies on tree species have been carried out
by means of Roche/454-technology strategies, mainly for the development of
genomics resources of unexplored species and for secondary metabolic products
discovery: in Quercus spp. (Ueno et al. 2010; Torre et al. 2014; Lesur et al. 2015),
Pinus contorta (Parchman et al. 2010), Pinus pinaster (Canales et al. 2014), Khaya
senegalensis (Karan et al. 2012), Azadirachta indica (Krishnan et al. 2012; Wang
et al. 2016), Nothofagus alpina (Torales et al. 2012), Prosopis alba (Torales et al.
2013), Carapa guianensis (Brousseau et al. 2014), Melia azedarach (Wang et al.
2016), Cedrela balansae (Torales et al. 2018) and Dalbergia odorifera (Liu et al.
2019) between others. On the other hand, a review carried out by Parent et al. (2015)
showed the species and approaches that were applied in order to find forest gene
differential expression in wood formation, stress response among other conditions,
through microarray and RNA-Seq analysis. They also highlighted the application of
RNA-Seq analysis in many species without genome reference and strategies used to
“native tree”)). Strategy B: (TITLE-ABS-KEY (“transcriptome” OR “genome” AND sequencing)
AND TITLE-ABS-KEY (“forest tree” OR “tree species” OR “native tree”)). Search date:
04-04-2019.
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…