Insights into a dinoflagellate genome through expressed sequence tag analysis

Abstract

Background: Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids) that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging.

Progress in Understanding Harmful Algal Blooms: Paradigm Shifts and New Technologies for Research, Monitoring, and Management

“…Although the EST analysis is restricted by the fact that only a fraction of the transcribed genome is surveyed and only when the corresponding mRNA is expressed, this approach has been effectively used to identify gene transcripts, discover new genes and determine sequence homology for various HAB taxa. EST databases are now extensive and representative of a wide diversity of organisms, including the HAB species Alexandrium fundyense (Hackett et al 2005), A. catenella (Uribe et al 2008), A. ostenfeldii (Jaeckisch et al 2008), A. minutum (Yang et al 2010), Karenia brevis (Lidie et al 2005), Chrysochromulina polylepis (John et al 2010) and Prymnesium parvum (La Claire 2006), with more in the pipeline awaiting further annotation and verification.…”

The Mechanism of Diarrhetic Shellfish Poisoning Toxin Production in Prorocentrum spp.: Physiological and Molecular Perspectives

“…The expression of translation-associated genes, intracellular signalling and selfish genetic element genes in dinflagellates can be characterised using microarrays to study the genetic properties and alterations in gene expression under nutritional and environmental stress [95,97,98,99,100,101,102,103,104,105]. …”

“…Because of the lack of complete genome data, only a limited amount of expressed genes can be identified (e.g., 27%–28% in A. minutum [94,96], 15% in A. ostenfeldii [100], 25% in A. catenella [101], 20% in A. tamarense [103], and 29% in K. brevis ) [108]. In addition, dinoflagellates usually regulate RNA splicing and may affect the constitution and expression of RNA [92,114,115,116,117].…”

Genomic Insights into Processes Driving the Infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp

“…To date, not much is known about the energy metabolism of Amoebophrya. A comparison with their sister lineage, apicomplexa (diverging ϳ800 to 900 million years ago), may help efforts to understand the nutritional mode of these parasites (2,60,61). The apicomplexa include many human and animal pathogens such as Plasmodium (causative agent of malaria) (62), Toxoplasma (parasitic toxoplasmosis disease) (63), and Cryptosporidium (diarrhea in mammals).…”