In silico mining of SSR markers from Expressed Sequence Tags of bamboo species

Abstract

With the ever increasing number of Expressed Sequence Tags (ESTs) from various sequencing projects, ESTs have become valuable and first-hand source of in-silico mining of simple sequence repeats (SSR) markers. We examined a total of 3419 EST sequences from three bamboo species, namely, Phyllostachys edulis, Bambusa oldhamii and Dendrocalamus sinicus for the presence of di- to hexa- microsatellites. The frequency of SSR containing ESTs varied from 5.36% in B. oldhamii to 13.05% in P. edulis. No SSRs were found in D. sinicus. Tri-nucleotide repeats (49.34%) were most frequent in P. edulis, while not much comparable difference in repeats was found in B. oldhamii. Flanking primer pairs were also designed in-silico for the sequences containing SSRs and their position on the genome hypothesized using similarity searching. SSRs located in open reading frame (ORF) were given functional annotation using Gene Ontology. Polymorphic SSRs were also detected using new pipeline- polySSR. Polymorphism level was very low (2.43%) and the position of the polymorphic SSRs was determined. The development of SSRs and the study of polymorphism will help in the further study of intra- and inter- gene flow, genetic structure, variability, linkage mapping and evolutionary relationships in bamboo

Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

“…There is a chance of occurrence of redundancy in the EST sequences. In order to remove the redundancy, CAP3 assembler [ 18 , 19 ] was used for sequence assembly. The resulting non-redundant sequences are contigs and singletons.…”

Development and crosstransferability of functionally relevant microsatellite markers in Dendrocalamus latiflorus and related bamboo species

“…Microsatellite markers are used as tools for assessing genetic variation and dissecting complex traits. Nevertheless, such marker resource is severely limited in bamboo (Sharma et al 2009;Lu et al 2009;Ramalakshmi and Piramanayagam 2010) and nonexistent in D. latiflorus. Genic microsatellites derived from publicly available expressed sequence tag (EST) database have gained considerable importance because they are inexpensive to develop, ubiquitously dispersed in genome, codominantly inherited and often a putative function can be assigned (Provan et al 2001;Chung et al 2006).…”

Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

“…Fifteen EST-SSRs from Bambusa edulis and B. oldhamii were shown to be ~60% transferable to moso bamboo (Dong, Wu, Lin, Zhou, & Tang, 2011). Subsequently, more bamboo-based EST-SSRs were also reported by Ramalakshmi and Piramanayagam (2010) and Cai et al (2019). Dong, Zhang, and Yang (2012) used sixteen bamboo-specific SSRs for assessing the genetic structure of D. sinicus.…”