TY  - JOUR
AU  - Hamon, P.
AU  - Duroy, P.-O.
AU  - Dubreuil-Tranchant, C.
AU  - Mafra D'Almeida Costa, P.
AU  - Duret, C.
AU  - Razafinarivo, N.J.
AU  - Couturon, E.
AU  - Hamon, S.
AU  - De Kochko, A.
AU  - Poncet, V.
AU  - Guyot, R.
PY  - 2011//
TI  - Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae)
T2  - Mol. Genet. Genomics
JO  - Molecular Genetics and Genomics
SP  - 447
EP  - 460
VL  - 285
IS  - 6
KW  - Coffea
KW  - Evolution
KW  - Genetic diversity
KW  - LTR-retrotransposons
KW  - article
KW  - coffee
KW  - controlled study
KW  - Divo
KW  - gene amplification
KW  - gene dosage
KW  - gene expression
KW  - gene insertion
KW  - gene locus
KW  - gene sequence
KW  - genetic identification
KW  - genetic polymorphism
KW  - genetic variability
KW  - molecular cloning
KW  - Nana
KW  - nonhuman
KW  - nucleotide sequence
KW  - phylogeny
KW  - plant evolution
KW  - plant gene
KW  - priority journal
KW  - Psilanthus
KW  - random amplified microsatellite
KW  - retroposon
KW  - Rubiaceae
KW  - species differentiation
KW  - tree
KW  - Ty1 copia gene
KW  - Genes
KW  - Plant
KW  - Genome
KW  - Retroelements
N2  - In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution. © 2011 Springer-Verlag.
SN  - 16174615 (Issn)
UR  - http://www.scopus.com/inward/record.url?eid=2-s2.0-79958144966&partnerID=40&md5=c48ec642536ea72c098c032e4ea383c3
N1  - Export Date: 21 October 2011; Source: Scopus; Coden: Mggoa; doi: 10.1007/s00438-011-0617-0; PubMed ID: 21505885; Language of Original Document: English; Correspondence Address: Hamon, P.; IRD, UMR DIADE, BP 64501, Montpellier Cedex 5, France; email: perla.hamon@ird.fr; Molecular Sequence Numbers: GENBANK: DV666936, HM755952, HM755953;; Chemicals/CAS: Retroelements
ID  - Hamon_etal2011
ER  -