The chloroplast genome of black pepper (Piper nigrum L.) and its comparative analysis with related Piper species

Abstract

Piper nigrum, also known as black pepper, is an economically and ecologically important crop of the genus Piper. It has been titled as the king of spices due to its wide consumption throughout the world. In the present investigation, the chloroplast genome of P. nigrum has been assembled from a whole genome sequence by integrating the short and long reads generated through Illumina and PacBio platforms, respectively. The chloroplast genome was observed to be 161,522 bp in size, having a quadripartite structure with a large single copy (LSC) region of 89,153 bp and a small single copy (SSC) region of 18,255 bp separated by a copy of inverted repeats (IRs), each 27,057 bp in length. Taking into consideration all the duplicated genes, a total of 131 genes were observed, which included 81 protein-coding genes, 37 tRNAs, 4 rRNAs, and 1 pseudogene. Individually, the LSC region consisted of 83 genes, the SSC region had 13 genes, and 18 genes were present in each IR region. Additionally, 216 SSRs were detected and 11 of these were validated through amplification in 12 species of Piper. The features of the chloroplast genome have been compared with those of the genus Piper. Our results provide useful insights into evolutionary and molecular studies of black pepper which will contribute to its further genetic improvement and breeding.

Molecular Structure and Variation Characteristics of the Plastomes from Six Malus baccata (L.) Borkh. Individuals and Comparative Genomic Analysis with Other Malus Species

“…Chloroplasts exist in the cytoplasm and are relatively independent and semi-autonomous with maternally inherited elements (cp genome) [ 41 ]. The chloroplast genome has a double-chained structure, and its size and composition are stable [ 42 ].…”

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

“…Variations in the lengths of large single copy (LSC), small single copy (SSC), and inverted repeat (IR) regions were the main contributors to the size variation in the chloroplast genome in the evolution of plants ( Xiao-Ming et al, 2017 ). The black pepper chloroplast genome, about 161,522 bp long and quadripartite, offers insights into evolutionary and molecular studies, aiding in genetic development and breeding ( Gaikwad et al, 2023 ). Tabulation of organelles genomic resources and their utilization for various spices growth and developments have been presented as Supplementary Table 8 .…”