TEAM LEADER: Tyler Alioto

POSTDOCTORAL FELLOWS: Fernando Cruz

TECHNICIANS: Jèssica Gómez

SUMMARY

The assembly and annotation team carries out genome projects — sequencing, assembling and annotating genomes de novo. Because we specialize in large eukaryotic genomes and transcriptomes, genome sequence assembly is challenging, not only because of the sheer size of the data and computational requirements, but also due to repetitive elements, polyploidy and variation (single-nucleotide, insertions/deletions, and larger structural variants). We aim to meet these challenges by developing new computational protocols as each project demands. In particular, we are focusing our efforts on the adoption of nanopore-based single molecule long-read sequencing technology for both genomic DNA and messenger RNA sequencing. This year we have successfully applied hybrid assembly methods to the sequencing of a number of species including birds, amphibians, fish, insects, plants, fungi. Our rapid and robust annotation pipeline, which we are constantly improving, helps us understand these genomes by automatically integrating statistical models of coding DNA with evidence such as transcribed sequences and protein homology. In the last year, we have incorporated nanopore-based sequencing of RNA (direct RNA or dRNA) into our annotation pipeline.

Assembly QC. Problematic or variable regions in genome assemblies can be easily identified by alignment of Oxford Nanopore Technologies MinION reads back to the assembly.

Fig. 1

Assembly QC. Problematic or variable regions in genome assemblies can be easily identified by alignment of Oxford Nanopore Technologies MinION reads back to the assembly.

RESEARCH PROJECTS

  • Genome sequence assembly
  • Gene prediction/genome annotation
  • Transcriptome reconstruction
  • Functional annotation
  • Identification and quantification of genomic variation

SELECTED PUBLICATIONS

Alioto T, Blanco E, Parra G, Guigó R.
“Using geneid to Identify Genes.”
Curr Protoc Bioinformatics, e56, 2018.

Chaves-Pozo E, Bandín I, Olveira JG, Esteve-Codina A, Gómez-Garrido J, Dabad M, Alioto T, Ángeles Esteban M, Cuesta A.
“European sea bass brain DLB-1 cell line is susceptible to nodavirus: A transcriptomic study.”
Fish Shellfish Immunol, 86:14–24, 2018.

Puerma E, Orengo DJ, Cruz F, Gómez-Garrido J, Librado P, Salguero D, Papaceit M, Gut M, Segarra C, Alioto TS, et al.
“The High-Quality Genome Sequence of the Oceanic Island Endemic Species Drosophila guanche Reveals Signals of Adaptive Evolution in Genes Related to Flight and Genome Stability.”
Genome Biol Evol, 10:1956–1969, 2018.