2024-03-28T11:55:16Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1034392021-12-28T16:28:02Zcom_10261_132com_10261_8col_10261_385
Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea)
Pons, Joan
Bauzà-Ribot, Maria M.
Jaume, Damià
Juan, Carlos
CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)
Ministerio de Ciencia e Innovación (España)
Crustacea
Amphipoda
Metacrangonyx
Mitogenome evolution
Mitochondrial RNA secondary structure
Abstract. Background: Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the
Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012).
Results: We present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived
gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand
bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure.
Conclusions: Next-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic
evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan
mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition
displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (−) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to
those of the few crustaceans studied at present
This work wsa supported by Spanish MCINN grants CGL2009-08256 and CGL2012-33597 partially financed with EU FEDER funds. MMBR was supported by a Spanish FPI fellowship
We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI)
Peer reviewed
2014-10-16T11:11:21Z
2014-10-16T11:11:21Z
2014-07-06
artículo
http://purl.org/coar/resource_type/c_6501
BMC Genomics 15: 566 (2014)
http://hdl.handle.net/10261/103439
10.1186/1471-2164-15-566
1471-2164
http://dx.doi.org/10.13039/501100004837
24997985
en
Publisher's version
http://www.biomedcentral.com/1471-2164/15/566
http://dx.doi.org/10.1186/1471-2164-15-566
Sí
open
BioMed Central