The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.

Rosa lucieae is one of the famous wild ancestors of cultivated roses and plays a very important role in horticultural research, but there is still a lack of research on the R. lucieae chloroplast genome. In this study, we used the Illumina MiSeq platform for sequencing, assembly, and annotation to obtain the R. lucieae chloroplast genome sequencing information and compared genomics, selection stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of Rosa. The R. lucieae cpDNA sequence has a total length of 156,504 bp, and 130 genes are annotated. The length of all 13 studied chloroplast genomes is 156,333~157,385 bp. Their gene content, gene sequence, GC content, and IR boundary structure were highly similar. Five kinds of large repeats were detected that numbered 100~116, and SSR sequences ranged from 78 to 90 bp. Four highly differentiated regions were identified, which can be used as potential genetic markers for Rosa. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of R. lucieae and R. cymose, R. maximowicziana, R. multiflora, and R. pricei showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of Rosa.

Eriobotrya (Rosaceae) is an economically important genus with around 30 species. It is widely distributed in tropical and warm temperate regions of Asia, with most of its species in China, Myanmar, and Vietnam. However, Eriobotrya is often confused with the smaller genus Rhaphiolepis, and the phylogenetic relationships between the two genera are controversial. Here we present phylogenetic analyses of 38 newly generated Eriobotrya and Rhaphiolepis nrDNA together with 16 sequences of nrDNA and 28 sequences of ITS obtained from GenBank, representing 28 species of Eriobotrya and 12 species of Rhaphiolepis, in order to reconstruct highly supported relationships for the two genera. Contrary to previous research based on limited sampling, our results highlight the monophyly of Eriobotrya as well as Rhaphiolepis. The topology recovered here is consistent with key morphological synapomorphies such as the persistent sepals in Eriobotrya. Our findings show that increased sampling of taxa can provide a more robust phylogeny through reducing phylogenetic error and increasing overall phylogenetic accuracy.

Neocinnamomum plants are considered a promising feedstock for biodiesel in China, due to the richness in long-chain fatty acids (LCFAs) found in their seeds. However, the mitochondrial genome (mitogenome) of this genus has not yet been systematically described, and the exploration of species relationships within this genus using mitogenome sequences is also an uncharted territory. This has hindered our understanding of mitogenome diversity and the evolutionary relationships within Neocinnamomum. In this study, a total of 24 individuals representing seven distinct taxa from the genus Neocinnamomum were subjected to Illumina sequencing, and the species N. delavayi was sequenced using Oxford Nanopore sequencing technology. We successfully assembled the mitogenome of N. delavayi, which is 778,066 bp in size and exhibits a single circular structure. The analysis identified 659 dispersed repeats, 211 simple sequence repeats (SSRs), and 30 tandem repeats within the mitogenome. Additionally, 37 homologous fragments, totaling 9929 bp, were found between the mitogenome and the plastid genome (plastome). The codons of 41 protein-coding genes (PCGs) had a preference for ending in A/T, and the codon usage bias of the majority of these genes was influenced by natural selection pressures. Comparative genomic analysis revealed low collinearity and significant gene rearrangements between species. Phylogenetic analysis resulted in the classification of Neocinnamomum into six distinct clades, contradicting previous findings which based on complete plastomes and nuclear ribosomal cistron (nrDNA). In the PCGs of 24 individuals, 86 mutation events were identified, which included three indels and 83 SNPs. Notably, the ccmC gene underwent positive selection in pairwise comparisons of three species pairs. Furthermore, 748 RNA editing sites were predicted within the PCGs of the N. delavayi mitogenome. This study enriches our knowledge of the mitogenomes in the family Lauraceae, and provides valuable data and a foundation for genomic evolution research, genetic resource conservation, and molecular breeding in Neocinnamomum.

Mangifera plants are tropical fruits that have high economic value and scientific utility. However, the chloroplast genome characteristics and phylogenetic relationships among Mangifera species remain unclear. In this work, we reconstructed maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees using 11 newly sequenced chloroplast genomes as well as six existing genomes obtained from the National Center for Biotechnology Information (NCBI) database. The chloroplast genomes all had a typical quadripartite structure, with lengths ranging from 157,368 to 158,942 bp. The GC-content in the genomes ranged from 37.8% to 37.9%. We found conserved boundaries comprised of two inverted repeats (IRs), large single-copy (LSC) regions, and small single-copy (SSC) regions. Nucleotide polymorphism analysis revealed three hypervariable regions (ycf4-cemA, rps18-rpl20, and rpl32-ndhF) in the LSC and SSC regions, which could potentially be used as DNA barcodes for Mangifera species. According to our phylogenetic analysis, Mangifera plants were clustered into three clades. Among them, all five samples of M. indica formed a monophyletic group in Clade Ⅰ. Clade Ⅱ included seven Mangifera species and could be further divided into five subclades with 100% branch support values. Clade Ⅲ included two M. persiciforma samples that formed a monophyletic group. Taken together, these results provide a theoretical basis for species determination, in addition to shedding light on the evolution of Mangifera.

Brassaiopsis angustifoliaK.M. Feng belongs to the family Araliaceae, and is an endangered shrub species in southwest China. Despite the importance of this species, the plastid genome has not been sequenced and analyzed. In this study, the complete plastid genome ofB.angustifoliawas sequenced, analyzed, and compared to the eight species in the Araliaceae family. Our study reveals that the complete plastid genome ofB.angustifoliais 156,534 bp long, with an overall GC content of 37.9%. The chloroplast genome (cp) encodes 133 genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. Five highly divergent regions were successfully identified that could be used as potential genetic markers ofBrassaiopsisand Asian Palmate group. Phylogenetic analysis of 47 plastomes, representing 19 genera of Araliaceae and two related families, was performed to reconstruct highly supported relationships for the Araliaceae, which highlight four well-supported clades of theHydrocotylegroup, GreaterRaukauagroup,Aralia-Panaxgroup, and Asian Palmate group. The genusBrassaiopsiscan be divided into four groups using internal transcribed spacer (ITS) data. The results indicate that plastome and ITS data can contribute to investigations of the taxonomy, and phylogeny ofB.angustifolia. This study provides a theoretical basis for species identification and future biological research on resources of the genusBrassaiopsis.