Genomic Insights into Guava: De novo Transcriptome Assembly Using Illumina Sequencing Data and SSR Markers Exploration and Discovery
Niveditha R Patil
Department of Fruit Science, College of Horticulture, UHS Campus, GKVK, Bengaluru, Karnataka, India.
Venkata Rao *
Department of Fruit Science, College of Horticulture, UHS Campus, GKVK, Bengaluru, Karnataka, India.
B Fakrudin
Department of Biotechnology and Crop Improvement, College of Horticulture, UHS Campus, GKVK, Bengaluru, Karnataka, India.
Raghunatha Reddy R L
Department of SS&AC, RHREC, College of Horticulture, UHS Campus, GKVK, Bengaluru, Karnataka, India.
Mohan Kumar S
Department of Biotechnology and Crop Improvement, College of Horticulture, UHS Campus, GKVK, Bengaluru, Karnataka, India.
*Author to whom correspondence should be addressed.
Abstract
Guava (Psidium guajava L.) is one of the nutritionally and commercially important fruit crops which belongs to family Myrtaceae, and the genus Psidium having diploid chromosome number of 2n = 22. Despite its economic importance genomic resources in guava are scarce and genetics of useful horticultural traits are poorly understood. In the present study, we performed de novo transcriptomic analysis of guava through Illumina technology. We obtained 211432 transcripts as well as 76764 unigenes, with an average length of 1087 bp, minimum length of 499 bp, maximum length of 23,043, N50 value of 1204 bp and average GC content of 44.40 percent. Total of 41,254 unigenes (53.74% of all unigenes) were annotated with UniPort, and 33,005 sequences annotated with Gene Ontology terms (about 42.99%), and 17,270 sequences annotated with enzyme codes (22.49%) respectively. Regarding the KEGG database, 9,885 sequences were linked to 441 identified Furthermore, 29,360 simple sequence repeats (SSRs) were identified and 30 pairs of primers were selected to evaluate the validity and universality in four genotypes of guava, and 27 pairs generated clear and abundant bands and were found to be polymorphic in nature. These data could be used as an important resource for studying the genetics and molecular biology for guava in future work.
Keywords: De novo, transcriptome, unigenes, SSR, amplification, polymorphism