A novel microsatellite locus isolated from an AFLP fragment in the mangrove species Kandelia obovata (Rhizophoraceae)

Abstract

The study of AFLP analysis in Kandelia obovata, one of the major mangrove species in Japan, revealed the existence of a unique fragment showing stuttered peaks. We cloned this fragment and found a novel microsatellite locus. We report the method used for isolation and the polymorphic nature of this locus among the populations on Iriomote Island.

Characterization of 95 novel microsatellite markers for Zhikong scallop Chlamys farreri using FIASCO-colony hybridization and EST database mining

“…Alternatively, mining public databases, especially the EST database, is now a viable option for new marker development. Bioinformatic analysis of the EST database has been very popular for microsatellite marker development in species with abundant EST sequences 12,13,19,21 . However, as a by‐product of the EST project, it is well known that the feasibility of this strategy depends on the development of ESTs, which makes it either not possible or inefficient for many marine bivalves lacking EST sequences.…”

“…Among the three basic methods, the second and third are efficient and low-cost approaches to obtaining new microsatellite markers for species of interest. 12,13,[19][20][21] However, the low crossamplification ratio among scallop species makes the third method inefficient for marker development in the Zhikong scallop. 12,13,[19][20][21] Alternatively, mining public databases, especially the EST database, is now a viable option for new marker development.…”

“…Bioinformatic analysis of the EST database has been very popular for microsatellite marker development in species with abundant EST sequences. 12,13,19,21 However, as a by-product of the EST project, it is well known that the feasibility of this strategy depends on the development of ESTs, which makes it either not possible or inefficient for many marine bivalves lacking EST sequences. For the Zhikong scallop, only 3467 sequences were registered in GenBank and 1.9% of EST sequences contained microsatellites.…”

“…The low frequency of microsatellites in the genome makes the isolation of robust SSRs challenging. However, the FIASCO method, which was tested on and confirmed by different marine organisms, 16,21 may provide a good choice for isolation of microsatellite DNA in scallop species. In this study, we combined and optimized the methods of FIASCO and colony hybridization for isolation of microsatellites in the Zhikong scallop.…”