The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA .

Cannabis sativa has a complex history reflected in both selection on naturally occurring compounds and historical trade routes among humans. Iran is a rich resource of natural populationswhich hold the promise to characterize historical patterns of population structure and genetic diversity within Cannabis. Recent advances in high-throughput DNA sequencing technologies have dramatically increased our ability to produce information to the point that it is now feasible to inexpensively obtain population level genotype information at a large scale. In the present investigation, we have explored the use of Genotyping-By-Sequencing (GBS) in Iranian cannabis. We genotyped 98 cannabis samples 36 from Iranian locations and 26 accessions from two germplasm collections. In total, 24,710 high-quality Single Nucleotide Polymorphisms (SNP) were identified. Clustering analysis by Principal Component Analysis (PCA) identified two genetic clusters among Iranian populations and fineSTRUCTURE analysis identified 19 populations with some geographic partitioning. We defined Iranian cannabis in two main groups using the results of the PCA and discovered some strong signal to define some locations as population according to fineSTRUCTURE analyses. However, single nucleotide variant analysis uncovered a relatively moderate level of variation among Iranian cannabis.

The genus Teucrium (Lamiaceae) comprises approximately 250 species with significant medicinal and ecological importance. Despite extensive phytochemical studies, molecular data, particularly on chloroplast (cp.) genomes, remain limited for many species, especially those native to Iran. In this study, we sequenced and analyzed the complete cp. genomes of three Iranian Teucrium species, T. chamaedrys, T. flavum, and T. polium, to investigate genome structure, variation, and phylogenetic relationships within the genus. Using high-throughput sequencing, we assembled and annotated the cp. genomes, revealing typical quadripartite structures with sizes ranging from 149,913 bp to 150,026 bp. Comparative genomic analyses, including IR boundary shifts, codon usage, repeat elements, and nucleotide diversity, highlighted structural variations. Sequence divergence analysis using mVISTA revealed several genes, including rpoC2, ycf1, ycf2, ndhF, rpl32, rps16, and accD, displayed notable sequence variation, making them potential phylogenetic markers. Additionally, highly variable intergenic regions, such as trnH-GUG-psbA, rps16-trnQ-UUG, and petG-trnW-CCA, were identified as potential hotspots for species differentiation. Codon usage analysis revealed a strong preference for A/U-ending codons, while nucleotide diversity (Pi) analysis identified highly variable intergenic regions such as trnH-GUG-psbA and rpl32-trnL-UAG. Phylogenetic reconstruction based on cp. genome sequences placed T. chamaedrys, T. flavum, and T. polium in well-supported clades, clarifying evolutionary relationships within Teucrium. This study provides the first complete cp. genome sequences for these Iranian Teucrium species, expanding genomic resources and offering valuable insights into their genetic diversity, evolutionary history, and medicinal potential.

The genus Salvia, a prominent member of the Lamiaceae family, is renowned for its ecological, medicinal, and economic significance. Despite its importance, molecular data, particularly chloroplast (cp.) genome information, remain scarce for many native Iranian Salvia species. In this study, we sequenced and analyzed the complete cp. genomes of five Iranian Salvia species (S. aethiopis, S. sclarea, S. glutinosa, S. verticillata, and S. officinalis) to elucidate their genomic structure, evolutionary relationships, and potential for biotechnological applications. The cp. genomes of the five Salvia species exhibited a conserved quadripartite structure, with sizes ranging from 151,163 to 151,662 bp, and a GC content of 38%. Each genome contained 132 or 131 genes, comprising 86 or 87 protein-coding, 8 rRNA, and 37 tRNA genes, with duplications in rpl2, rpl23, and rps12. Minor variations in gene content were observed, such as the absence of trnS-CGA in S. glutinosa. Comparative analysis of IR boundaries showed subtle expansions in S. officinalis and S. sclarea, while S. glutinosa remained stable. Trans-splicing of the rps12 gene was observed in all species, with complex structures in S. glutinosa and S. sclarea. Codon usage analysis revealed a preference for A/U-ending codons, with S. verticillata displaying unique patterns. Nucleotide diversity (Pi) identified highly variable regions, such as rpl14-rpl16 and psbK-psbI, as potential molecular markers. Phylogenetic analysis resolved distinct clades, with S. aethiopis and S. sclarea forming a close group, S. glutinosa clustering with S. chanryoenica, and S. officinalis showing genetic homogeneity with Mediterranean species. S. verticillata exhibited an earlier divergence, highlighting the genus’s evolutionary complexity. This study provides critical genomic resources for species identification, phylogenetic studies, and the development of molecular markers, facilitating the conservation of native Salvia species and their utilization in breeding programs for medicinal and aromatic traits.

Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado ‘Hass’ draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan × Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community.