The plastome of non-photosynthetic plants often undergoes gene loss (Mohanta et al., 2020), pseudogenic transformation, and rearrangement. Orchidacea is a typical taxonomic group, and their plastomes underwent gene loss and gene pseudogenization (Kim et al., 2020). Zhou et al. decoded the plastome of Galeola lindleyana in the Vanilloideae subfamily, a heterotrophic orchid plant, and compared it with previously published photosynthetic and heterotrophic orchid plastomes. The length of the G. lindleyana plastome has been reduced to 100,749 bp, while still retaining its typical quadripartite structure. In half-heterotrophs, the reduced photosynthetic function begins with the loss of non-essential or stress-related genes, such as ndh genes, followed by pseudogenization and the loss of major photosynthesis-related genes (such as pet, psa and psb genes) and plastid-encoded polymerases.

In this Research Topic, there are eight research articles that present comparative analysis of plastomes of plants such as Solanum lycopersicum L., Pseudostellaria heterophylla (Miq.) Pax, Corydalis platycarpa (Maxim. ex Palib.) Makino, Aristolochia L., Phyllanthus L., Kandelia Wight & Arn., Artemisia L., and Paraboea (Clarke) Ridley. These articles provide valuable information for molecular identification and phylogenetic analysis.

Plastomes can provide distinguishing features and more molecular markers to help identify closely related species and even as super barcodes for accurate identification of plants and germplasm resources (Gao et al., 2023). Lan et al. analyzed 15 plastomes from 5 Artemisia species, including 12 newly sequenced genomes. Four hotspot regions and 189-192 SSR molecular markers were identified, which can serve as potential DNA barcodes for further studies on Artemisia species. Fang et al. de novo assembled and characterized the complete plastomes of nine species of the genus Phyllanthus. The authors highlighted three highly variable regions (trnS-GCU-trnG-UCC, trnT-UGU-trnL-UAA, and petA-psbJ) that may be useful as potential molecular markers for identifying P. urinaria and its adulterants. Wang et al. sequenced and analyzed the plastomes of 29 tomato germplasm lines. Among the screened SNP markers, those localized to segments of the ndhH gene and the ndhK-ndhC-trnV-UAC gene spacer region could be used for interspecific identification. The developed SNP markers can be used to analyze genetic diversity and population structure at the plastome level and to develop functional markers associated with traits such as male sterility. Bai et al. sampled 11 species of Aristolochia collected from distinct habitats in China and sequenced their complete plastomes. Their analysis of simple sequence repeats (SSRs) was able to identify potential molecular polymorphic markers for analyzing the genetic diversity and structure of Aristolochia populations in the future. Highly variable regions would provide candidate markers for Aristolochia species identification studies. Zhang et al. collected 17 P. heterophylla plant samples with remarkable phenotypic characteristics and obtained their plastome sequences. The authors verified that plastomes could elucidate the relationship among closely related cultivated materials and provide useful information for the development of new, highly polymorphic, and informative molecular makers.

In addition, other articles provide important insights into adaptive evolution and phylogeny, and offer significant guidance for future research on plant evolution and conservation. Raman et al. sequenced the plastome of C. platycarpa and conducted wide-scale comparative studies using publicly available data from 20 Corydalis plastomes. The results revealed extensive genome rearrangement and IR expansion, events that evolved independently in the Corydalis species. The divergence time of the ndh gene in the Corydalis sub-clade species (44.31-15.71 mya) is consistent with the uplift of the Qinghai-Tibet Plateau in the Oligocene and Miocene, and may have triggered the radiation of the Corydalis species during this period. In 2003, Kandelia obovata was identified as a new mangrove species distinct from Kandelia candel. Xu et al. sequenced the 25 whole plastomes of K. obovata (18 samples) and K. candel (Seven samples) for comparison. A comparative molecular simulation study of the homologous NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A) proteins of K. candel and K. obovata predicted that the functions of photosynthetic electron transport and ATP generation were significantly different. The results suggest that energy demand is a pivotal factor in their adaptation to different environments geographically separated by the South China Sea. Wang et al. sequenced and compared the complete plastomes of 12 Paraboea species from China and Vietnam. The study presents several important findings:

Genome comparison of multiple plastomes involves many software, including some popular tools, such as mVISTA, Mauve, IRscope, etc. However, these tools are separate from each other and lack a unifying interface, making comparison analysis a time-consuming and labor-intensive task. An automated workflow for fast and accurate assembly and annotation of plastome sequences from raw whole (nuclear) genome sequencing data is needed. Chen et al. developed Plastaumatic-an automated pipeline for both the assembly and annotation of plastomes, with the ability to load whole genome sequence data with minimal manual input and, therefore a faster run time. The pipeline was demonstrated on two sets of plant sequence data: three soybean accessions and 12 potato accessions. It showed substantially faster completion than manual assembly. This automated pipeline, which includes plastid assembly and annotation is an efficient tool. In their article, Zhou et al., used the GetOrganelle (V1.7.7.0) assembly toolkit which provides fast and accurate de novo assembly of the organelle genome. They also used the CPGAVAS2 web server, which automatically annotates the plastome.