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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.

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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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Venn diagram depicting the overlap between liver, testis and muscle transcriptomes. The overlap is evaluated on the 1,000 most expressed transcripts in each tissue (modified from supplementary materials of Amemiya et al. [38]). The values between brackets indicate the number of highly tissue-specific genes (found among the 1,000 most expressed in one tissue but displaying a FPKM value lower than 1 in the other two).
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Figure 8: Venn diagram depicting the overlap between liver, testis and muscle transcriptomes. The overlap is evaluated on the 1,000 most expressed transcripts in each tissue (modified from supplementary materials of Amemiya et al. [38]). The values between brackets indicate the number of highly tissue-specific genes (found among the 1,000 most expressed in one tissue but displaying a FPKM value lower than 1 in the other two).

Mentions: The overlap between liver, testis and muscle transcriptomes was further investigated by analyzing how many common genes were found among the 1,000 most expressed in each tissue. A schematic representation of transcriptomes overlap is given in the Venn diagram in Figure 8. 172 sequences, likely representing housekeeping genes, whose expression at rather elevated levels is important in all tissues, were found in all the 3 sets. In all the three organs analyzed, about 2/3 of the transcripts were identified as tissue specific, highlighting once again the strong link between the biological function of different tissues and gene expression.


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)

Venn diagram depicting the overlap between liver, testis and muscle transcriptomes. The overlap is evaluated on the 1,000 most expressed transcripts in each tissue (modified from supplementary materials of Amemiya et al. [38]). The values between brackets indicate the number of highly tissue-specific genes (found among the 1,000 most expressed in one tissue but displaying a FPKM value lower than 1 in the other two).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Venn diagram depicting the overlap between liver, testis and muscle transcriptomes. The overlap is evaluated on the 1,000 most expressed transcripts in each tissue (modified from supplementary materials of Amemiya et al. [38]). The values between brackets indicate the number of highly tissue-specific genes (found among the 1,000 most expressed in one tissue but displaying a FPKM value lower than 1 in the other two).
Mentions: The overlap between liver, testis and muscle transcriptomes was further investigated by analyzing how many common genes were found among the 1,000 most expressed in each tissue. A schematic representation of transcriptomes overlap is given in the Venn diagram in Figure 8. 172 sequences, likely representing housekeeping genes, whose expression at rather elevated levels is important in all tissues, were found in all the 3 sets. In all the three organs analyzed, about 2/3 of the transcripts were identified as tissue specific, highlighting once again the strong link between the biological function of different tissues and gene expression.

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