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Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis.

Pallavicini A, Canapa A, Barucca M, Alfőldi J, Biscotti MA, Buonocore F, De Moro G, Di Palma F, Fausto AM, Forconi M, Gerdol M, Makapedua DM, Turner-Meier J, Olmo E, Scapigliati G - BMC Genomics (2013)

Bottom Line: The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy.The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species.

Results: The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.

Conclusion: Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.

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Related in: MedlinePlus

Graphic summary of the combined de novo assembly strategy and filtering steps applied to generate the final high quality transcripts set comprising 66,308 sequences.
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Related In: Results  -  Collection

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Figure 1: Graphic summary of the combined de novo assembly strategy and filtering steps applied to generate the final high quality transcripts set comprising 66,308 sequences.

Mentions: A total of 105,653 contigs was obtained following the combination of the data generated by the two de novo assemblers. Finally, the filtering step applied to remove poorly covered sequences, resulting from the fragmentation of transcripts expressed at particularly low levels, reduced the contig number to a final high quality set of 66,308 sequences. A detailed graphical summary of the strategy used and of the results obtained by the de novo assembly of L. menadoensis transcriptome is shown in Figure 1.


Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis.

Pallavicini A, Canapa A, Barucca M, Alfőldi J, Biscotti MA, Buonocore F, De Moro G, Di Palma F, Fausto AM, Forconi M, Gerdol M, Makapedua DM, Turner-Meier J, Olmo E, Scapigliati G - BMC Genomics (2013)

Graphic summary of the combined de novo assembly strategy and filtering steps applied to generate the final high quality transcripts set comprising 66,308 sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750513&req=5

Figure 1: Graphic summary of the combined de novo assembly strategy and filtering steps applied to generate the final high quality transcripts set comprising 66,308 sequences.
Mentions: A total of 105,653 contigs was obtained following the combination of the data generated by the two de novo assemblers. Finally, the filtering step applied to remove poorly covered sequences, resulting from the fragmentation of transcripts expressed at particularly low levels, reduced the contig number to a final high quality set of 66,308 sequences. A detailed graphical summary of the strategy used and of the results obtained by the de novo assembly of L. menadoensis transcriptome is shown in Figure 1.

Bottom Line: The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy.The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species.

Results: The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.

Conclusion: Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.

Show MeSH
Related in: MedlinePlus