ena-STUDY-Stazione Zoologica Anton Dohrn-20-05-2015-17:49:30:521-10
Genome sequencing and annotation of the diatom Pseudo-nitzschia multistriata
Pseudo-nitzschia multistriata is a marine planktonic diatom that is able to produce the neuro-toxin domoic acid. The life cycle of this species includes a sexual phase and its genetics is controllable. To produce the genome sequence, we used an axenic offspring of two F1 siblings obtained by crossing two wild type strains isolated in the Gulf of Naples (Italy). The genome was assembled from a total of 172 million 101 bp overlapping paired end reads with ~175 bp inserts, 117 million 100 bp paired end reads with ~450 bp inserts, 72 million ~68 bp (after trimming) mate pair reads with ~1.2 KBp inserts and 5.4 million ~156 bp (after trimming) mate pair reads with ~4.5 Kbp inserts. The final size of the assembled Psuedo-nitzschia multistriata genome is 59.3 Mbp including ambiguous bases. Ab-initio gene prediction supported by genomic alignments of proteins from other species and RNAseq reads from multiple samples resulted in prediction of 12152 transcripts in 12008 genes. The availability of a sequenced genome for Pseudo-nitzschia multistriata will contribute to consolidate it as a model species for diatoms. Pseudo-nitzschia multistriata can be transformed, therefore functional genomics approaches to study gene function are possible. These tools will allow to explore the mechanisms of toxin production and other molecular processes specific to diatoms, one of the major and most important groups of unicellular microalgae.
Pseudo-nitzschia multistriata is a marine planktonic diatom that is able to produce the neuro-toxin domoic acid. The life cycle of this species includes a sexual phase and its genetics is controllable. To produce the genome sequence, we used an axenic offspring of two F1 siblings obtained by crossing two wild type strains isolated in the Gulf of Naples (Italy). The genome was assembled from a total of 172 million 101 bp overlapping paired end reads with ~175 bp inserts, 117 million 100 bp paired end reads with ~450 bp inserts, 72 million ~68 bp (after trimming) mate pair reads with ~1.2 KBp inserts and 5.4 million ~156 bp (after trimming) mate pair reads with ~4.5 Kbp inserts. The final size of the assembled Psuedo-nitzschia multistriata genome is 59.3 Mbp including ambiguous bases. Ab-initio gene prediction supported by genomic alignments of proteins from other species and RNAseq reads from multiple samples resulted in prediction of 12152 transcripts in 12008 genes. The availability of a sequenced genome for Pseudo-nitzschia multistriata will contribute to consolidate it as a model species for diatoms. Pseudo-nitzschia multistriata can be transformed, therefore functional genomics approaches to study gene function are possible. These tools will allow to explore the mechanisms of toxin production and other molecular processes specific to diatoms, one of the major and most important groups of unicellular microalgae.