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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

Scatter plot depicting the expression levels (calculated as FPKM, Fragments Per Kilobase per Million fragments mapped) in liver and testis. Genes whose expression levels are identical in the two organs are located on the bisector. For graphical representation convenience, only genes whose expression was lower than 1,000 FPKM in both tissues are shown (therefore 79 genes are not shown in the graph).
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Figure 6: Scatter plot depicting the expression levels (calculated as FPKM, Fragments Per Kilobase per Million fragments mapped) in liver and testis. Genes whose expression levels are identical in the two organs are located on the bisector. For graphical representation convenience, only genes whose expression was lower than 1,000 FPKM in both tissues are shown (therefore 79 genes are not shown in the graph).

Mentions: The RNA-seq mapping revealed that a higher number of transcripts were expressed in testis in respect to liver, since the expression of 55,975 contigs (84.42%) was found in liver, whereas the expression of 61,633 sequences (92.95%) was detected in testis. The comparison between the two organs highlighted that 51,302 contigs (77.37%) were expressed in both. Nevertheless, the two transcriptomes resulted to be remarkably divergent when comparing expression levels, which for most genes were largely divergent as shown by the expression scatter plot in Figure 6. The list of the 20 most expressed transcripts in liver and testis is reported in Tables 6 and 7, respectively. With a few exceptions (most notably the elongation factor 1 α and the ATP synthase F0 subunit 6, whose expression is important for the correct maintenance of all cell types) the 20 genes characterizing the two tissues show great differences in 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)

Scatter plot depicting the expression levels (calculated as FPKM, Fragments Per Kilobase per Million fragments mapped) in liver and testis. Genes whose expression levels are identical in the two organs are located on the bisector. For graphical representation convenience, only genes whose expression was lower than 1,000 FPKM in both tissues are shown (therefore 79 genes are not shown in the graph).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Scatter plot depicting the expression levels (calculated as FPKM, Fragments Per Kilobase per Million fragments mapped) in liver and testis. Genes whose expression levels are identical in the two organs are located on the bisector. For graphical representation convenience, only genes whose expression was lower than 1,000 FPKM in both tissues are shown (therefore 79 genes are not shown in the graph).
Mentions: The RNA-seq mapping revealed that a higher number of transcripts were expressed in testis in respect to liver, since the expression of 55,975 contigs (84.42%) was found in liver, whereas the expression of 61,633 sequences (92.95%) was detected in testis. The comparison between the two organs highlighted that 51,302 contigs (77.37%) were expressed in both. Nevertheless, the two transcriptomes resulted to be remarkably divergent when comparing expression levels, which for most genes were largely divergent as shown by the expression scatter plot in Figure 6. The list of the 20 most expressed transcripts in liver and testis is reported in Tables 6 and 7, respectively. With a few exceptions (most notably the elongation factor 1 α and the ATP synthase F0 subunit 6, whose expression is important for the correct maintenance of all cell types) the 20 genes characterizing the two tissues show great differences in 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