472
are currently being transferred to other species of the genus (Pomponio et al. 2019).
Functional annotation of both transcriptomes is reported in Table 17.1.
17.5.2 Genome Sequencing of Austrocedrus chilensis
In gymnosperm native species, partial genome sequencing has only been performed
on A. chilensis using 454 GS FLX Titanium technology (El Mujtar, unpublished
data; Table 17.1). Genomic resources were assembled, classified and annotated
using a procedure that combined several local and online bioinformatics tools
(Fig. 17.3). A total of 89,562 contigs (including 34,581 singletons) was generated,
representing nuclear and organelle (1418 contigs) genomes. Annotation was only
possible for 14.5% of the contigs, with a high proportion corresponding to repetitive
sequences (e.g. transposon, gag-protease poly, gag-pol poly). This is not surprising
however for partial sequencing of species with large and complex genomes (high
proportion of repetitive sequences) such as gymnosperms (Pellicer et al. 2018).
Contigs assigned to cpDNA genome were realigned using Cunninghamia lanceolata chloroplast genome as reference, allowing the reconstruction of seven consensus contigs coding for 116 annotated chloroplast genes. Genomic resources were
also used to identify SSRs markers located in 33.4%, 16.2% and 1.4% of nuclear,
chloroplast and mitochondrial contigs, respectively. These genome resources
expand the -omic resources for Austrocedrus chilensis.
17.5.3 Transcriptome Sequencing of Nothofagus alpina
and N. obliqua Under Water Stress Conditions
Nothofagus alpina and N. obliqua, as stated previously in this chapter, are two
closely related species which occur in sympatry in part of their Argentinian natural
range. Particularly, in the Lake Lácar basin (Lanín National Park), both species are
present along the pluviometrical gradient from west to east. Given their physiological differences in drought tolerance (see, e.g. Varela et al. 2010) and Global Climate
Change predictions of higher temperature and lower precipitation for the region
(Barros et al. 2015), a drought stress assay was performed in order to gain insight
into the global, transcriptomic responses of these species to water stress (Marchelli,
Arana, Varela, et al. unpublished data). The experiment was performed in a greenhouse with two contrasting provenances of each species, one humid and one drier,
and was repeated with different plants in a different season. The experiment setting
was periodically measured for soil humidity, air temperature, leaf stomatal conductance and pre-dawn water potential in order to ensure proper water stress at the time
of harvesting the stressed plants.
S. L. Torales et al.
are currently being transferred to other species of the genus (Pomponio et al. 2019).
Functional annotation of both transcriptomes is reported in Table 17.1.
17.5.2 Genome Sequencing of Austrocedrus chilensis
In gymnosperm native species, partial genome sequencing has only been performed
on A. chilensis using 454 GS FLX Titanium technology (El Mujtar, unpublished
data; Table 17.1). Genomic resources were assembled, classified and annotated
using a procedure that combined several local and online bioinformatics tools
(Fig. 17.3). A total of 89,562 contigs (including 34,581 singletons) was generated,
representing nuclear and organelle (1418 contigs) genomes. Annotation was only
possible for 14.5% of the contigs, with a high proportion corresponding to repetitive
sequences (e.g. transposon, gag-protease poly, gag-pol poly). This is not surprising
however for partial sequencing of species with large and complex genomes (high
proportion of repetitive sequences) such as gymnosperms (Pellicer et al. 2018).
Contigs assigned to cpDNA genome were realigned using Cunninghamia lanceolata chloroplast genome as reference, allowing the reconstruction of seven consensus contigs coding for 116 annotated chloroplast genes. Genomic resources were
also used to identify SSRs markers located in 33.4%, 16.2% and 1.4% of nuclear,
chloroplast and mitochondrial contigs, respectively. These genome resources
expand the -omic resources for Austrocedrus chilensis.
17.5.3 Transcriptome Sequencing of Nothofagus alpina
and N. obliqua Under Water Stress Conditions
Nothofagus alpina and N. obliqua, as stated previously in this chapter, are two
closely related species which occur in sympatry in part of their Argentinian natural
range. Particularly, in the Lake Lácar basin (Lanín National Park), both species are
present along the pluviometrical gradient from west to east. Given their physiological differences in drought tolerance (see, e.g. Varela et al. 2010) and Global Climate
Change predictions of higher temperature and lower precipitation for the region
(Barros et al. 2015), a drought stress assay was performed in order to gain insight
into the global, transcriptomic responses of these species to water stress (Marchelli,
Arana, Varela, et al. unpublished data). The experiment was performed in a greenhouse with two contrasting provenances of each species, one humid and one drier,
and was repeated with different plants in a different season. The experiment setting
was periodically measured for soil humidity, air temperature, leaf stomatal conductance and pre-dawn water potential in order to ensure proper water stress at the time
of harvesting the stressed plants.
S. L. Torales et al.