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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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Transcriptomic richness of L. menadoensis liver and testis and of L. chalumnae muscle. Data are shown as the cumulative FPKM values of the 1,000 most expressed transcripts per each tissue, normalized on the total expression (y-axis). Modified from supplementary materials of Amemiya et al. [38].
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Figure 7: Transcriptomic richness of L. menadoensis liver and testis and of L. chalumnae muscle. Data are shown as the cumulative FPKM values of the 1,000 most expressed transcripts per each tissue, normalized on the total expression (y-axis). Modified from supplementary materials of Amemiya et al. [38].

Mentions: The transcriptome richness was further graphically inspected in Figure 7 comparing L. menadoensis liver and testis transcriptomes to the RNA-seq of L. chalumnae muscle. A steep curve, that reaches quickly the asymptote (corresponding to the 100% of the transcription observed in each tissue), means that a low number of genes are expressed at high levels in a specific tissue. On the contrary, the later the curve approaches the asymptote, the more genes are expressed, indicating higher transcriptome richness. Among the 3 tissues, muscle is the one characterized by the steepest curve, as the 50% of the total gene expression in this organ is given by just 22 genes, consistently with observations previously collected in other organisms [44]. The two tissues used for the deep RNA-seq of L. menadoensis were both richer than muscle, although testis resulted to be, by far, the one expressing a broader range of transcripts. In this tissue 325 genes contributed to 50% of gene expression, while in liver the same number of genes accounted for about 65%. The 1,000 most expressed genes in liver and muscle contributed to about 75% of total transcription, whereas the same number of genes in testis just contributed to 61%.


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)

Transcriptomic richness of L. menadoensis liver and testis and of L. chalumnae muscle. Data are shown as the cumulative FPKM values of the 1,000 most expressed transcripts per each tissue, normalized on the total expression (y-axis). Modified from supplementary materials of Amemiya et al. [38].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Transcriptomic richness of L. menadoensis liver and testis and of L. chalumnae muscle. Data are shown as the cumulative FPKM values of the 1,000 most expressed transcripts per each tissue, normalized on the total expression (y-axis). Modified from supplementary materials of Amemiya et al. [38].
Mentions: The transcriptome richness was further graphically inspected in Figure 7 comparing L. menadoensis liver and testis transcriptomes to the RNA-seq of L. chalumnae muscle. A steep curve, that reaches quickly the asymptote (corresponding to the 100% of the transcription observed in each tissue), means that a low number of genes are expressed at high levels in a specific tissue. On the contrary, the later the curve approaches the asymptote, the more genes are expressed, indicating higher transcriptome richness. Among the 3 tissues, muscle is the one characterized by the steepest curve, as the 50% of the total gene expression in this organ is given by just 22 genes, consistently with observations previously collected in other organisms [44]. The two tissues used for the deep RNA-seq of L. menadoensis were both richer than muscle, although testis resulted to be, by far, the one expressing a broader range of transcripts. In this tissue 325 genes contributed to 50% of gene expression, while in liver the same number of genes accounted for about 65%. The 1,000 most expressed genes in liver and muscle contributed to about 75% of total transcription, whereas the same number of genes in testis just contributed to 61%.

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