0000000000016499
AUTHOR
Josefa Gómez-maldonado
showing 23 related works from this author
Additional file 12: Table S5. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Primers used in PCR for validation of positive BAC clones in the BAC library screening. (DOCX 39 kb)
Additional file 14: of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Detailed description of the GeneAssembler pipeline (DOCX 124 kb)
Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Background In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. Results In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were design…
Additional file 4: Table S3. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Exon length comparison between the XET BAC clone from P. pinaster and two XET genes from Arabidopsis thaliana. The two gene capture models closest to the BAC clone are also included. (DOCX 18 kb)
Additional file 4: Table S3. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Exon length comparison between the XET BAC clone from P. pinaster and two XET genes from Arabidopsis thaliana. The two gene capture models closest to the BAC clone are also included. (DOCX 18 kb)
Additional file 3: Table S2. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Intron length comparisons between Susy BAC clone from P. pinaster and Susy from two angiosperm plants. The intron I8 in the BAC clone contains a gap. The gene capture model is also included (DOCX 20 kb)
Additional file 5: Table S4. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Intron length comparison between the XET BAC clone from P. pinaster and two XET genes from Arabidopsis thaliana. The two gene capture models closest to the BAC clone are also included. (DOCX 17 kb)
Additional file 2: Table S1. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Exon length comparison between SuSy BAC clone from P. pinaster and SuSy from two angiosperm plants. The first exon is lacking in the BAC clone. The gene capture model is also included (DOCX 19 kb)
Additional file 3: Table S2. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Intron length comparisons between Susy BAC clone from P. pinaster and Susy from two angiosperm plants. The intron I8 in the BAC clone contains a gap. The gene capture model is also included (DOCX 20 kb)
Additional file 2: Table S1. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Exon length comparison between SuSy BAC clone from P. pinaster and SuSy from two angiosperm plants. The first exon is lacking in the BAC clone. The gene capture model is also included (DOCX 19 kb)
Additional file 5: Table S4. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Intron length comparison between the XET BAC clone from P. pinaster and two XET genes from Arabidopsis thaliana. The two gene capture models closest to the BAC clone are also included. (DOCX 17 kb)
Additional file 13: Figure S7. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Functional categories by GO terms for the full-length unigenes used in the capture approach (TIF 269 kb)
Additional file 7: Figure S3. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Alignment of the PAL gene promoter [GenBank:HE866754], to the gene capture PAL gene 5´upstream region (TIF 389 kb)
Additional file 11: Table S6. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Summary of AS contigs obtained in the gene capture and used to build the AS model. (XLS 138 kb)
Additional file 9: Figure S5. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Nucleotide alignment of maritime pine AS cDNAs. (TIF 533 kb)
Additional file 6: Figure S2. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Alignment of the GS1a gene promoter [GenBank:AJ225121], to the gene capture GS1a gene 5´upstream region (TIF 245 kb)
Additional file 6: Figure S2. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Alignment of the GS1a gene promoter [GenBank:AJ225121], to the gene capture GS1a gene 5´upstream region (TIF 245 kb)
Additional file 8: Figure S4. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Alignment of the PAT gene promoter [GenBank:HE866755], to the gene capture PAT gene 5´upstream region. (TIF 332 kb)
Additional file 7: Figure S3. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Alignment of the PAL gene promoter [GenBank:HE866754], to the gene capture PAL gene 5´upstream region (TIF 389 kb)
Additional file 8: Figure S4. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Alignment of the PAT gene promoter [GenBank:HE866755], to the gene capture PAT gene 5´upstream region. (TIF 332 kb)
Additional file 10: Figure S6. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Amino acid alignment of maritime pine AS protein (TIF 460 kb)
Additional file 9: Figure S5. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Nucleotide alignment of maritime pine AS cDNAs. (TIF 533 kb)
Additional file 1: Figure S1. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
2016
Workflow overview followed to isolate and sequence maritime pine BAC clones. (A) Primary PCR screening of pools of the BAC library using specific oligonucleotides against XET cDNA. (B) Plating of cells of the positive pools on 24.2 X 24.2 cm plates. (C) The single clones of the pool were individualized in 36 X 384 plates using a QPix and grown orderly gridded in high-density filters. (D) The replica filters containing the ordered single clones of each pool were hybridized with cDNA 32P-labeled specific probes and exposed to a phosphorimaging screen. (E) Secondary PCR screening was performed on single clones to isolate positives. (F) BAC DNA isolation of positives to prepare a 454 library ei…