Limits...
Insights into a dinoflagellate genome through expressed sequence tag analysis.

Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D - BMC Genomics (2005)

Bottom Line: We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X.We speculate this histone may be retained for its role in DNA double-strand break repair.These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA. jeremiah-hackett@uiowa.edu

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.

Results: Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair.

Conclusion: This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

Show MeSH

Related in: MedlinePlus

Putative dinoflagellate-specific proteins. Amino acid sequence alignments of putative dinoflagellate-specific proteins. A) putative plastid protein that was highly represented in the A. tamarense cDNA library (cluster size = 22). A. tamarense sequences 1, 2, and 3 correspond to clones GC1-aba-e-13, GC1-abh-e14, and GC1-abd-o-22, respectively, and are aligned with highly similar ESTs from the dinoflagellates L. polyedrum (CD809498) and P. lunula (BU582532). The boxed region indicated a possible plastid targeting sequence. B) Putative dinoflagellate specific protein with significant blast hits only to other dinoflagellate ESTs. The Alexandrium sequence corresponds to clone UI-D-GC1-abh-f-23-0-UI.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1173104&req=5

Figure 1: Putative dinoflagellate-specific proteins. Amino acid sequence alignments of putative dinoflagellate-specific proteins. A) putative plastid protein that was highly represented in the A. tamarense cDNA library (cluster size = 22). A. tamarense sequences 1, 2, and 3 correspond to clones GC1-aba-e-13, GC1-abh-e14, and GC1-abd-o-22, respectively, and are aligned with highly similar ESTs from the dinoflagellates L. polyedrum (CD809498) and P. lunula (BU582532). The boxed region indicated a possible plastid targeting sequence. B) Putative dinoflagellate specific protein with significant blast hits only to other dinoflagellate ESTs. The Alexandrium sequence corresponds to clone UI-D-GC1-abh-f-23-0-UI.

Mentions: The collection of 11,171 ESTs comprised of single-pass 3'-reads (483 from the start library and 10,688 from the normalized library) from A. tamarense was assembled into 6,723 clusters. The normalized library showed a high degree of complexity, with a novelty rate of 60.18% and about 52% of the sequenced clones contained inserts that were longer than the single sequence read (ca. 750 bp). Clustering of the total EST set showed that most of the reads were singletons (4,618 sequences) and the largest cluster was comprised of 46 ESTs that are closely related to HLPs (Table 1). Other highly represented transcripts were those encoding luciferin-binding protein (a protein involved in the regulation of bioluminescence) and several photosynthetic proteins (e.g., Rubisco, ATP synthase C chain, light harvesting proteins). Several large clusters were transcripts that lacked a similarity (e-value < e-5) to known proteins. One of these ESTs has an open reading frame that encodes a protein with a potential plastid-targeting signal (Figure 1A). Interestingly, database searches against NCBI's nr and dbEST returned hits only to other dinoflagellate ESTs. Another of the largest clusters only had hits to ESTs from other dinoflagellates (Figure 1B). These two proteins are therefore candidates for dinoflagellate-specific proteins.


Insights into a dinoflagellate genome through expressed sequence tag analysis.

Hackett JD, Scheetz TE, Yoon HS, Soares MB, Bonaldo MF, Casavant TL, Bhattacharya D - BMC Genomics (2005)

Putative dinoflagellate-specific proteins. Amino acid sequence alignments of putative dinoflagellate-specific proteins. A) putative plastid protein that was highly represented in the A. tamarense cDNA library (cluster size = 22). A. tamarense sequences 1, 2, and 3 correspond to clones GC1-aba-e-13, GC1-abh-e14, and GC1-abd-o-22, respectively, and are aligned with highly similar ESTs from the dinoflagellates L. polyedrum (CD809498) and P. lunula (BU582532). The boxed region indicated a possible plastid targeting sequence. B) Putative dinoflagellate specific protein with significant blast hits only to other dinoflagellate ESTs. The Alexandrium sequence corresponds to clone UI-D-GC1-abh-f-23-0-UI.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1173104&req=5

Figure 1: Putative dinoflagellate-specific proteins. Amino acid sequence alignments of putative dinoflagellate-specific proteins. A) putative plastid protein that was highly represented in the A. tamarense cDNA library (cluster size = 22). A. tamarense sequences 1, 2, and 3 correspond to clones GC1-aba-e-13, GC1-abh-e14, and GC1-abd-o-22, respectively, and are aligned with highly similar ESTs from the dinoflagellates L. polyedrum (CD809498) and P. lunula (BU582532). The boxed region indicated a possible plastid targeting sequence. B) Putative dinoflagellate specific protein with significant blast hits only to other dinoflagellate ESTs. The Alexandrium sequence corresponds to clone UI-D-GC1-abh-f-23-0-UI.
Mentions: The collection of 11,171 ESTs comprised of single-pass 3'-reads (483 from the start library and 10,688 from the normalized library) from A. tamarense was assembled into 6,723 clusters. The normalized library showed a high degree of complexity, with a novelty rate of 60.18% and about 52% of the sequenced clones contained inserts that were longer than the single sequence read (ca. 750 bp). Clustering of the total EST set showed that most of the reads were singletons (4,618 sequences) and the largest cluster was comprised of 46 ESTs that are closely related to HLPs (Table 1). Other highly represented transcripts were those encoding luciferin-binding protein (a protein involved in the regulation of bioluminescence) and several photosynthetic proteins (e.g., Rubisco, ATP synthase C chain, light harvesting proteins). Several large clusters were transcripts that lacked a similarity (e-value < e-5) to known proteins. One of these ESTs has an open reading frame that encodes a protein with a potential plastid-targeting signal (Figure 1A). Interestingly, database searches against NCBI's nr and dbEST returned hits only to other dinoflagellate ESTs. Another of the largest clusters only had hits to ESTs from other dinoflagellates (Figure 1B). These two proteins are therefore candidates for dinoflagellate-specific proteins.

Bottom Line: We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X.We speculate this histone may be retained for its role in DNA double-strand break repair.These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences and Roy J, Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA. jeremiah-hackett@uiowa.edu

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.

Results: Approximately 20% of the 6,723 unique (11,171 total 3'-reads) ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP) and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair.

Conclusion: This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

Show MeSH
Related in: MedlinePlus