Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis.
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.


CONCLUSIONS
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.
Alberto
A
Pallavicini
Adriana
A
Canapa
Marco
M
Barucca
Jessica
J
Alfőldi
Maria Assunta
MA
Biscotti
Francesco
F
Buonocore
Gianluca
G
De Moro
Federica
F
Di Palma
Anna Maria
AM
Fausto
Mariko
M
Forconi
Marco
M
Gerdol
Daisy Monica
DM
Makapedua
Jason
J
Turner-Meier
Ettore
E
Olmo
Giuseppe
G
Scapigliati
D000818:Animals; D005075:Biological Evolution; D020451:Contig Mapping; D005399:Fishes / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D007214:Indonesia; D008099:Liver / Q000378:metabolism; D008297:Male; D017423:Sequence Analysis, RNA; D013737:Testis / Q000378:metabolism; D059467:Transcriptome