AUTHOR=Singh Nripendra Vikram , Patil Prakash Goudappa , Sowjanya Roopa P. , Parashuram Shilpa , Natarajan Purushothaman , Babu Karuppannan Dhinesh , Pal Ram Krishna , Sharma Jyotsana , Reddy Umesh K. 

TITLE=Chloroplast Genome Sequencing, Comparative Analysis, and Discovery of Unique Cytoplasmic Variants in Pomegranate (Punica granatum L.)

JOURNAL=Frontiers in Genetics

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.704075

DOI=10.3389/fgene.2021.704075

ISSN=1664-8021

ABSTRACT=Here we report comprehensive chloroplast (cp) genome analysis of 16 pomegranate (Punica granatum L.) genotypes representing  commercial cultivars, ornamental and wild types through large-scale sequencing and assembling using next-generation sequencing (NGS) technology. Comparative genome analysis revealed that the size of cp genomes varied from 158,593 bp (in wild,  ‘1201’ & ‘1181’) to 158,662 bp (cultivar, ‘Gul-e-Shah Red’) among the genotypes, with characteristic quadripartite structures separated by a pair of inverted repeats (IRs). The higher conservation for the total number of coding and non-coding genes (rRNA and tRNA) and their sizes, and  inverted repeats (IR-A and IR-B) were observed across all the cp genomes. Interestingly,  high variations were observed in sizes of large single copy (LSC)  (88976 to 89044 bp) and  small single copy (SSC, 18682 to 18684) regions. Although, the structural organisation of newly assembled cp genomes were comparable to that of previously reported cp genomes of pomegranate (‘Helow’, ‘Tunisia’ and ‘Bhagawa’), the striking differences were observed with the Lagerstroemia lines viz., Lagerstroemia intermedia (NC_0346620) and L. speciosa (NC_031414), which clearly confirmed  previous findings. Further, phylogenetic analysis also revealed that members outside the genus Punica were clubbed into a separate clade. The contraction and expansion analysis revealed that the structural variations in IRs, LSC and SSC have significantly accounted for evolution of cp genomes of Punica and L. intermedia over the periods. Microsatellite survey across cp genomes resulted into identification of a total 233 to 234 SSRs, with majority of them were mono- (A/T or C/G, 164-165 numbers), followed by di- (AT/AT or AG/CT, 54),  tri- (6), tetra- (8) and penta-nucleotides (1). Further, the comparative structural variant analyses across cp genomes resulted in identification of many varietal specific SNP/ Indel markers . In summary our study has offered a successful development of large scale cp genomics resources to leverage future genetic, taxonomical and phylogenetic studies in pomegranate.