469
SSR markers were also transferred to other Nothofagus species contributing to
the generation of a panel of SSRs for these species. This panel includes neutral and
functional markers, located in coding and non-coding regions of nuclear and extranuclear genomes (chloroplast and mitochondrion), presenting polymorphism and
species-specific alleles (high divergence between species). This genomic information is useful to investigate demographic, adaptive and hybridizing events in
Nothofagus species, taking advantage of their remarkable eco-physiological differences, and also to assist conservation, management and breeding programmes.
17.4.2 Transcriptome Sequencing of Prosopis alba
Prosopis alba is a multipurpose native tree of great economic value adapted to arid
and semi-arid regions of Northwestern Argentina. However, this species had few
genomic resources: 6 microsatellites from Prosopis chilensis (Mottura et al. 2005)
and 12 from a bulk sample of several species of Prosopis (Bessega et al. 2013).
Therefore, RNA-Seq was performed to identify genes controlling important traits
and to develop functional markers (Torales et al. 2013). Assembled and annotated
unigenes (Table 17.1 and Fig. 17.2) indicated a good proportion of the P. alba gene
catalogue, considering the average number of genes encoded in a plant nuclear
genome (Logacheva et al. 2011). The remaining sequences (32%), without significant identity to any other protein sequences in the existing databases, could be novel
genes and may still be informative for identifying putative biological functions,
which may be considered as P. alba-specific ones. Furthermore, the limited set of
molecular markers currently available in this species was significantly increased
with the thousands of new markers identified (Table 17.1).
The SSRs developed in P. alba were easily transferred to other Prosopis species
(P. denudans, P. hassleri, P. flexuosa, P. chilensis) and the interspecific hybrids
(P. flexuosa x P. chilensis), which did not have functional markers (Pomponio et al.
2015). In addition, high-confidence nuclear SNPs were identified, some of them
related to the production of cellulose, together with the lignin biosynthetic pathway
and with abiotic stress, among others. These markers will be useful for breeding
programmes. On the other hand, contigs/isotigs of chloroplast reads composed of
59,040 bp were identified through alignment analyses to related chloroplast
sequences. The partial Prosopis cp genome represents ~40% of the total cp genome
of Vigna radiata (151,271 bp) (Tangphatsornruang et al. 2010). In addition, there
were 55 intra scaffold gaps in P. alba cp genome.
The development of genomics resources represents a starting point for functional
genetic studies in natural and cultivated populations of Prosopis denudans and
P. alba (see below). It also represents useful tools to conduct comparative genomics
studies with other Prosopis species, taking advantage of their remarkable ecophysiological differences. This work highlights the utility of transcriptome highperformance sequencing as a fast and cost-effective way of obtaining rapid
information on the coding genetic variation in Prosopis genus.
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…
SSR markers were also transferred to other Nothofagus species contributing to
the generation of a panel of SSRs for these species. This panel includes neutral and
functional markers, located in coding and non-coding regions of nuclear and extranuclear genomes (chloroplast and mitochondrion), presenting polymorphism and
species-specific alleles (high divergence between species). This genomic information is useful to investigate demographic, adaptive and hybridizing events in
Nothofagus species, taking advantage of their remarkable eco-physiological differences, and also to assist conservation, management and breeding programmes.
17.4.2 Transcriptome Sequencing of Prosopis alba
Prosopis alba is a multipurpose native tree of great economic value adapted to arid
and semi-arid regions of Northwestern Argentina. However, this species had few
genomic resources: 6 microsatellites from Prosopis chilensis (Mottura et al. 2005)
and 12 from a bulk sample of several species of Prosopis (Bessega et al. 2013).
Therefore, RNA-Seq was performed to identify genes controlling important traits
and to develop functional markers (Torales et al. 2013). Assembled and annotated
unigenes (Table 17.1 and Fig. 17.2) indicated a good proportion of the P. alba gene
catalogue, considering the average number of genes encoded in a plant nuclear
genome (Logacheva et al. 2011). The remaining sequences (32%), without significant identity to any other protein sequences in the existing databases, could be novel
genes and may still be informative for identifying putative biological functions,
which may be considered as P. alba-specific ones. Furthermore, the limited set of
molecular markers currently available in this species was significantly increased
with the thousands of new markers identified (Table 17.1).
The SSRs developed in P. alba were easily transferred to other Prosopis species
(P. denudans, P. hassleri, P. flexuosa, P. chilensis) and the interspecific hybrids
(P. flexuosa x P. chilensis), which did not have functional markers (Pomponio et al.
2015). In addition, high-confidence nuclear SNPs were identified, some of them
related to the production of cellulose, together with the lignin biosynthetic pathway
and with abiotic stress, among others. These markers will be useful for breeding
programmes. On the other hand, contigs/isotigs of chloroplast reads composed of
59,040 bp were identified through alignment analyses to related chloroplast
sequences. The partial Prosopis cp genome represents ~40% of the total cp genome
of Vigna radiata (151,271 bp) (Tangphatsornruang et al. 2010). In addition, there
were 55 intra scaffold gaps in P. alba cp genome.
The development of genomics resources represents a starting point for functional
genetic studies in natural and cultivated populations of Prosopis denudans and
P. alba (see below). It also represents useful tools to conduct comparative genomics
studies with other Prosopis species, taking advantage of their remarkable ecophysiological differences. This work highlights the utility of transcriptome highperformance sequencing as a fast and cost-effective way of obtaining rapid
information on the coding genetic variation in Prosopis genus.
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…