A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator).
Mol Phylogenet Evol
; 53(3): 826-34, 2009 Dec.
Article
de En
| MEDLINE
| ID: mdl-19695333
ABSTRACT
In recent years, phylogenetic tree reconstructions that rely on multiple gene alignments that had been deduced from expressed sequence tags (ESTs) have become a popular method in molecular systematics. Here, we present a 454 pyrosequencing approach to infer the transcriptome of the Emperor scorpion Pandinus imperator. We obtained 428,844 high-quality reads (mean length=223+/-50 b) from total cDNA, which were assembled into 8334 contigs (mean length 422+/-313 bp) and 26,147 singletons. About 1200 contigs were successfully annotated by BLAST and orthology search. Specific analyses of eight distinct hemocyanin sequences provided further proof for the quality of the 454 reads and the assembly process. The P. imperator sequences were included in a concatenated alignment of 149 orthologous genes of 67 metazoan taxa that covers 39,842 amino acids. After removal of low-quality regions, 11,168 positions were employed for phylogenetic reconstructions. Using Bayesian and maximum likelihood methods, we obtained strongly supported monophyletic Ecdysozoa, Arthropoda (excluding Tardigrada), Euarthropoda, Pancrustacea and Hexapoda. We also recovered the Myriochelata (Chelicerata+Myriapoda). Within the chelicerates, Pycnogonida form the sister group of Euchelicerata. However, Arachnida were found paraphyletic because the Acari (mites and ticks) were recovered as sister group of a clade comprising Xiphosura, Scorpiones and Araneae. In summary, we have shown that 454 pyrosequencing is a cost-effective method that provides sufficient data and coverage depth for gene detection and multigene-based phylogenetic analyses.
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Phylogenèse
/
Scorpions
/
Analyse de séquence d'ADN
Type d'étude:
Prognostic_studies
Limites:
Animals
Langue:
En
Journal:
Mol Phylogenet Evol
Sujet du journal:
BIOLOGIA
/
BIOLOGIA MOLECULAR
Année:
2009
Type de document:
Article
Pays d'affiliation:
Allemagne