Development of ESTs and data mining of pineapple EST-SSRs

Abstract

Improving the quality of the non-climacteric fruit, pineapple, is possible with information on the expression of genes that occur during the process of fruit ripening. This can be made known though the generation of partial mRNA transcript sequences known as expressed sequence tags (ESTs). ESTs are useful not only for gene discovery but also function as a resource for the identification of molecular markers, such as simple sequence repeats (SSRs). This paper reports on firstly, the construction of a normalized library of the mature green pineapple fruit and secondly, the mining of EST-SSRs markers using the newly obtained pineapple ESTs as well as publically available pineapple ESTs deposited in GenBank. Sequencing of the clones from the EST library resulted in 282 good sequences. Assembly of sequences generated 168 unique transcripts (UTs) consisting of 34 contigs and 134 singletons with an average length of ≈500 bp. Annotation of the UTs categorized the known proteins transcripts into the three ontologies as: molecular function (34.88%), biological process (38.43%), and cellular component (26.69%). Approximately 7% (416) of the pineapple ESTs contained SSRs with an abundance of trinucleotide SSRs (48.3%) being identified. This was followed by dinucleotide and tetranucleotide SSRs with frequency of 46 and 57%, respectively. From these EST-containing SSRs, 355 (85.3%) matched to known proteins while 133 contained flanking regions for primer design. Both the ESTs were sequenced and the mined EST-SSRs will be useful in the understanding of non-climacteric ripening and the screening of biomarkers linked to fruit quality traits.

Development and Characterization of EST-SSR Markers in Taxodium ‘zhongshansa’

“…The highest proportion of mononucleotide repeat sequences in Taxodium 'zhongshansa' is in accordance with the results from J. curcas L. (Kumari et al 2013) and wheat (Asadi and Monfared 2014), but in contrast to those from citrus (Chen et al 2006), lily (Du et al 2014), pineapple (Ong et al 2012), and arabidopsis (Cardle et al 2000), in which trinucleotides were identified as the most numerous repeats. A potential explanation for the high ratio of mononucleotide SSR loci in this study was that mononucleotide SSRs would be amplified rapidly after interspecific hybridization (Gao et al 2011).…”

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

“…In the present research, a total of 8,769 potential EST-SSRs were identified in 7,732 unigenes, and the frequency of the occurrence of EST-SSRs was one SSR in every 6.59 kb, which is much higher than those obtained for tree peony (1/9.24 kb) 12 , alfalfa (1/12.06 kb) 13 , pineapple (1/13 kb) 38 , and lotus (1/13.04 kb) 39 . However, this frequency is lower than those obtained in Levant cotton (1/2.4 kb) 40 , castor bean (1/1.77 kb) 41 , radish (1/3.45 kb) 42 , and gerbera (1/5.6 kb) 43 .…”

Peer Review #1 of "Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia) (v0.1)"

“…In this study, a total of 6,752 potential EST-SSRs were identified in the 77,764 unigenes. The frequency of EST-SSRs was one SSR per 4.35-kb sequence, which is much higher than what was reported for pineapple (1 in 13 kb) (Ong et al, 2012), and lotus (1 in 13.04 kb) (Pan et al, 2010). However, this frequency is lower than what was reported for Levant cotton (1 in 2.4 kb) (Jena et al, 2012), castor bean (1 in 1.77 kb) (Qiu et al, 2010), and radish (1 in 3.45 kb) (Wang et al, 2012).…”