An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry

Abstract

The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs). Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS), which also provides a web service API (Application Programming Interface) for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae

“…It is well recognized that variations in the coding regions can lead to the identification of functional markers linked with specific traits of interest. Towards enriching this repository of SSR markers, a set of EST database comprising of over 10000 sequences were analyzed (NCBI-SRA SRP047446) [ 10 ] to identify 1469 ESTs which harbored 2028 microsatellite regions. For a repeat motif to be developed into a marker, the repeat motif should be ≥15 bp with a total amplicon size of ≥150 bp [ 19 ].…”

“…In an earlier study, we generated a large number of Expressed Sequence Tags (ESTs) from the leaf tissue of a mulberry genotype (Dudia white) exposed to drought stress by global transcriptome analysis [ 10 ]. The transcriptome data used in this study is available at the National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (SRA) with the study accession number of SRP047446 [ 10 ]. A set of 10,169 EST sequences formed the basis for the development of genic SSR markers.…”

“…Polymorphism in the genic regions, though less, has a greater likelihood of identifying functional variability among genotypes. In this paper, we report development of more than 200 genic SSR markers identified by analyzing a set of mulberry transcriptome generated using a germplasm accession of mulberry with superior drought adaptive traits, viz., Dudia white [ 10 ].…”

OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis

“…Even though Arabidopsis has been the subject of intensive functional genetics studies, ;30% of the proteins encoded by the genome remain uncharacterized according to the latest version of the Arabidopsis Information Resource database (TAIR; Dhanyalakshmi et al, 2016). Some of these unknown genes can be expected to be involved in processes which are essential for cellular life, and such essential genes can be postulated to be evolutionarily conserved in the green lineage.…”

Mulberry (Morus spp.) has the features to treat as a potential perennial model system

“…During their perennial growth habit, trees have integrated multiple unique traits. In mulberry, unique traits such as rapid growth and biomass production, 31,32 leaf quality traits,- 13,33,34 plant insect/microbe interacting traits, [35][36][37][38][39][40][41] abiotic stress tolerance traits 42,43 and the traits associated with nutritional and medicinal values [44][45][46][47][48][49][50] have been studied. Mulberrysilkworm food chain also exhibits phytoremediation potential.…”