Background: Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes ofPrimula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding ofPrimulamitogenomic diversity and evolution. The present study reported and compared threePrimulamitogenomes and discussed the size expansion of mitogenomes in Ericales.Results: Mitogenome master circles were sequenced and successfully assembled for threePrimulataxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. ThePrimulamitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found amongPrimulaspecies between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop inatp6caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships withinPrimulacould be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence ofPrimulaand its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall.Conclusions: The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation inPrimulamitogenomes. Relatively high nucleotide diversity was found in thePrimulamitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs inPrimulawas complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.

The Myrsinaceae s.str. clade is a tropical woody representative in Myrsinoideae of Primulaceae and has ca. 1300 species. The generic limits and alignments of this clade are unclear due to the limited number of genetic markers and/or taxon samplings in previous studies. Here, the chloroplast (cp) genomes of 13 taxa within the Myrsinaceae s.str. clade are sequenced and characterized. These cp genomes are typical quadripartite circle molecules and are highly conserved in size and gene content. Three pseudogenes are identified, of which ycf15 is totally absent from five taxa. Noncoding and large single copy region (LSC) exhibit higher levels of nucleotide diversity (Pi) than other regions. A total of ten hotspot fragments and 796 chloroplast simple sequence repeats (SSR) loci are found across all cp genomes. The results of phylogenetic analysis support the notion that the monophyletic Myrsinaceae s.str. clade has two subclades. Non-synonymous substitution rates (d_N) are higher in housekeeping (HK) genes than photosynthetic (PS) genes, but both groups have a nearly identical synonymous substitution rate (d_S). The results indicate that the PS genes are under stronger functional constraints compared with the HK genes. Overall, the study provides hypervariable molecular markers for phylogenetic reconstruction and contributes to a better understanding of plastid gene evolution in Myrsinaceae s.str. clade.

Musa ornata and Musa velutina are members of the Musaceae family and are indigenous to the South and Southeast Asia. They are very popular in the horticultural market, but the lack of genomic sequencing data and genetic studies has hampered efforts to improve their ornamental value. In this study, we generated the first chromosome-level genome assemblies for both species by utilizing Oxford Nanopore long reads and Hi-C reads. The genomes of M. ornata and M. velutina were assembled into 11 pseudochromosomes with genome sizes of 427.85 Mb and 478.10 Mb, respectively. Repetitive sequences comprised 46.70% and 50.91% of the total genomes for M. ornata and M. velutina, respectively. Differentially expressed gene (DEG) and Gene Ontology (GO) enrichment analyses indicated that upregulated genes in the mature pericarps of M. velutina were mainly associated with the saccharide metabolic processes, particularly at the cell wall and extracellular region. Furthermore, we identified polygalacturonase (PG) genes that exhibited higher expression level in mature pericarps of M. velutina compared to other tissues, potentially being accountable for pericarp dehiscence. This study also identified genes associated with anthocyanin biosynthesis pathway. Taken together, the chromosomal-level genome assemblies of M. ornata and M. velutina provide valuable insights into the mechanism of pericarp dehiscence and anthocyanin biosynthesis in banana, which will significantly contribute to future genetic and molecular breeding efforts.

Pogostemon Desf., the largest genus of the tribe Pogostemoneae (Lamiaceae), consists of ca. 80 species distributed mainly from South and Southeast Asia to China. The genus contains many patchouli plants, which are of great economic importance but taxonomically difficult. Therefore, it is necessary to characterize more chloroplast (cp) genomes for infrageneric phylogeny analyses and species identification of Pogostemon, especially for patchouli plants. In this study, we newly generated four cp genomes for three patchouli plants (i.e., Pogostemon plectranthoides Desf., P. septentrionalis C. Y. Wu et Y. C. Huang, and two cultivars of P. cablin (Blanoco) Benth.). Comparison of all samples (including online available cp genomes of P. yatabeanus (Makino) Press and P. stellatus (Lour.) Kuntze) suggested that Pogostemon cp genomes are highly conserved in terms of genome size and gene content, with a typical quadripartite circle structure. Interspecific divergence of cp genomes has been maintained at a relatively low level, though seven divergence hotspot regions were identified by stepwise window analysis. The nucleotide diversity (Pi) value was correlated significantly with gap proportion (indels), but significantly negative with GC content. Our phylogenetic analyses based on 80 protein-coding genes yielded high-resolution backbone topologies for the Lamiaceae and Pogostemon. For the overall mean substitution rates, the synonymous (d_S) and nonsynonymous (d_N) substitution rate values of protein-coding genes varied approximately threefold, while the d_N values among different functional gene groups showed a wider variation range. Overall, the cp genomes of Pogostemon will be useful for phylogenetic reconstruction, species delimitation and identification in the future.

We report the complete chloroplast genome of Primula obconica, a popular house-plant all over the world. The complete chloroplast genome of P. obconica was sequenced using an Illumina Miseq platform. The circular genome is 153,694 bp in length and comprises a large single copy (LSC, 84,485 bp) region and a small single copy (SSC, 17,689 bp) region, which are separated by a pair of inverted repeats (IRa and IRb, 25,760 bp each). The overall GC content is 37.2%. The P. obconica chloroplast genome encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Phylogenetic analysis based on 18 chloroplast genomes indicates that P. obconica is closely related to the clade of Primula sect. Carolinella, sect. Corusoides and sect. Monocarpicae.