467
Annotation against the Arabidopsis thaliana proteome resulted in 36,371 contigs
(44.48% of the total) with a name and function assigned. On the other hand, preliminary differential expression (DE) analysis revealed more than 1000 contigs differentially expressed between temperatures, regardless of the moment of the day
(FDR-corrected p-value <0.05). This first step in the -omic study of N. pumilio will
be of great help to current and future studies related to functional genomics, local
genetic variation and adaptation and gene discovery and characterization in this
important native species.
In angiosperm native species, genome sequencing has also only been performed
on N. alpina and N. obliqua using Roche/454 technology (El Mujtar et al. 2014;
Table 17.1 see also SeqQual pipeline, available at https://github.com/garniergere/
SeqQual). Several local and online bioinformatics tools were combined for the
assembly, annotation and classification of produced genomic resources (Fig. 17.3).
Although it was a partial genome sequencing of low coverage (13.4 Mb of
Table 17.1 Summary of HTS results obtained for the Argentinean native tree species
Species
System
# Raw reads
#
Unigenes # SSRs
#
SNPs
#
BLAST
matches
# GO
terms
Nothofagus
alpina
Transcriptome
(454
GS-FLX)
146,267
(408)
a
24,886
3,048
(2,517)
b
ND
15,497 11,834
N. alpina-N.
obliqua
Genome (454
GS-FLX)
361,438
(313)
a
32,595
2,274 (769)
b 8,669 5,134
4,750
N. pumilio
Transcriptome
(IonTorrent
Proton dev.)
222,828,783
(133)
a
81,761
8,456
ND
36,371 6,153
Prosopis alba Transcriptome
(454
GS-FLX)
1,103,231
(421)
a
54,814
5,992
(4,593)
b
6,236 37,563 22,095
Cedrela
balansae
Transcriptome
(454
GS-FLX)
212,589
(434)
a
27,111
2,663
(1,932)
b
1,243 20,953 19,029
Austrocedrus
chilensis
Transcriptome
(454
GS-FLX)
C: 395,835 32,255
(C+S)
1,450(C+S)
b C:253 ND
c
12,382
(C+S)
S: 421,884
S:186
Austrocedrus
chilensis
Genome (454
GS-FLX)
358,803
(378)
a
ND
3,563
(2,056)
b
ND
11,032 ND
Handroanthus
impetiginosus
Transcriptome
(454
GS-FLX)
318,156
(408)
a
44,263
9,745
(7,324)
b
ND
c
31,958 8,792
Cordia
trichotoma
Transcriptome
(454
GS-FLX)
413,968
(465)
a
14,700
1,500 (903)
b ND
c
ND
c
ND
c
C control, S stress, ND no data
a
Mean length (bp)
b
SSRs with designed primers
c
Not yet analysed
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…
Annotation against the Arabidopsis thaliana proteome resulted in 36,371 contigs
(44.48% of the total) with a name and function assigned. On the other hand, preliminary differential expression (DE) analysis revealed more than 1000 contigs differentially expressed between temperatures, regardless of the moment of the day
(FDR-corrected p-value <0.05). This first step in the -omic study of N. pumilio will
be of great help to current and future studies related to functional genomics, local
genetic variation and adaptation and gene discovery and characterization in this
important native species.
In angiosperm native species, genome sequencing has also only been performed
on N. alpina and N. obliqua using Roche/454 technology (El Mujtar et al. 2014;
Table 17.1 see also SeqQual pipeline, available at https://github.com/garniergere/
SeqQual). Several local and online bioinformatics tools were combined for the
assembly, annotation and classification of produced genomic resources (Fig. 17.3).
Although it was a partial genome sequencing of low coverage (13.4 Mb of
Table 17.1 Summary of HTS results obtained for the Argentinean native tree species
Species
System
# Raw reads
#
Unigenes # SSRs
#
SNPs
#
BLAST
matches
# GO
terms
Nothofagus
alpina
Transcriptome
(454
GS-FLX)
146,267
(408)
a
24,886
3,048
(2,517)
b
ND
15,497 11,834
N. alpina-N.
obliqua
Genome (454
GS-FLX)
361,438
(313)
a
32,595
2,274 (769)
b 8,669 5,134
4,750
N. pumilio
Transcriptome
(IonTorrent
Proton dev.)
222,828,783
(133)
a
81,761
8,456
ND
36,371 6,153
Prosopis alba Transcriptome
(454
GS-FLX)
1,103,231
(421)
a
54,814
5,992
(4,593)
b
6,236 37,563 22,095
Cedrela
balansae
Transcriptome
(454
GS-FLX)
212,589
(434)
a
27,111
2,663
(1,932)
b
1,243 20,953 19,029
Austrocedrus
chilensis
Transcriptome
(454
GS-FLX)
C: 395,835 32,255
(C+S)
1,450(C+S)
b C:253 ND
c
12,382
(C+S)
S: 421,884
S:186
Austrocedrus
chilensis
Genome (454
GS-FLX)
358,803
(378)
a
ND
3,563
(2,056)
b
ND
11,032 ND
Handroanthus
impetiginosus
Transcriptome
(454
GS-FLX)
318,156
(408)
a
44,263
9,745
(7,324)
b
ND
c
31,958 8,792
Cordia
trichotoma
Transcriptome
(454
GS-FLX)
413,968
(465)
a
14,700
1,500 (903)
b ND
c
ND
c
ND
c
C control, S stress, ND no data
a
Mean length (bp)
b
SSRs with designed primers
c
Not yet analysed
17 Application of High-Throughput Sequencing Technologies in Native Forest Tree…