Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus (Rhamnaceae).

Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01331-7.

Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin.

The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA-psbE, ndhF-rpl32, and psbM-trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.

Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships.

Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species of the genus are widely used for a wide range of medicinal and industrial aspects. At present, most studies related to the gene resources of Litsea are restricted to morphological analyses or features of individual genomes, and currently available studies of select molecular markers are insufficient. In this study, we assembled and annotated the complete chloroplast genomes of nine species in Litsea, carried out a series of comparative analyses, and reconstructed phylogenetic relationships within the genus. The genome length ranged from 152,051 to 152,747 bp and a total of 128 genes were identified. High consistency patterns of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) were discovered across the genus. Variations in gene length and the presence of the pseudogene ycf1Ψ, resulting from IR contraction and expansion, are reported. The hyper-variable gene rpl16 was identified for its exceptionally high Ka/Ks and Pi values, implying that those frequent mutations occurred as a result of positive selection. Phylogenetic relationships were recovered for the genus based on analyses of full chloroplast genomes and protein-coding genes. Overall, both genome sequences and potential molecular markers provided in this study enrich the available genomic resources for species of Litsea. Valuable genomic resources and divergent analysis are also provided for further research of the evolutionary patterns, molecular markers, and deeper phylogenetic relationships of Litsea.

The complete mitochondrial genome sequence and annotation of Tylopilus plumbeoviolaceoides T.H. Li, B. Song & Y.H. Shen, 2002 (Boletaceae, Boletoideae).

Tylopilus plumbeoviolaceoides T.H. Li, B. Song & Y.H. Shen, 2002 is a species of basidiomycete in the family Boletaceae and is mainly found in Yunnan and Guangdong provinces in China. In this study, the mitochondrial genome of T. plumbeoviolaceoides was reported for the first time. The total length of the mitochondrial genome of T. plumbeoviolaceoides was 37,242 bp, with GC content of 23.0%. The mitochondrial genome of T. plumbeoviolaceoides contained 14 conserved protein-coding genes, 25 transfer RNA genes, and 2 ribosomal RNA genes. The phylogenetic tree indicated that T. plumbeoviolaceoides was closely related to Xerocomus impolitus and Butyriboletus roseoflavus. The complete mitochondrial genome of T. plumbeoviolaceoides will be useful for future research on basidiomycetes.

Complete chloroplast genome sequence and annotation of Machilus salicina Hance, 1885 (lauraceae).

Machilus salicina Hance, 1885 is a species of flowering plant in the family Lauraceae and is mainly found at low altitudes in southern China. In this study, we assembled and annotated the complete chloroplast genome of M. salicina for the first time. We analyzed the general features of M. salicina and constructed a phylogenetic tree based on 15 Lauraceae species. The chloroplast genome of M. salicina had a total length of 153,943 bp. The length of a large single copy region, a small single copy region, and two inverted repeat regions were 93,689 bp, 20,070 bp, and 20,092bp, respectively. A total of 128 genes were detected, which included 84 protein-coding genes, 36 tRNAs and 8 rRNAs. The GC content of M. salicina complete chloroplast genome was 39.1%. The phylogenetic tree indicated that M. salicina was closely related to M. yunnanensis.

Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla).

BACKGROUND: Macadamia is a true dicotyledonous plant that thrives in a mild, humid, low wind environment. It is cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects and scientific research value. However, information on the genetic resources of Macadamia spp. remains scanty. RESULTS: The mitochondria (mt) genomes of three economically important Macadamia species, Macadamia integrifolia, M. ternifolia and M. tetraphylla, were assembled through the Illumina sequencing platform. The results showed that each species has 71 genes, including 42 protein-coding genes, 26 tRNAs, and 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, and analysis of genes migrating from chloroplast (cp) to mt were performed in the mt genomes of the three Macadamia species. Phylogenetic analysis based on the mt genome of the three Macadamia species and 35 other species was conducted to reveal the evolution and taxonomic status of Macadamia. Furthermore, the characteristics of the plant mt genome, including genome size and GC content, were studied through comparison with 36 other plant species. The final non-synonymous (Ka) and synonymous (Ks) substitution analysis showed that most of the protein-coding genes in the mt genome underwent negative selections, indicating their importance in the mt genome. CONCLUSION: The findings of this study provide a better understanding of the Macadamia genome and will inform future research on the genus.

Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications.

Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU-atpA and atpH-atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.

Fire-prone Rhamnaceae with South African affinities in Cretaceous Myanmar amber.

The rapid Cretaceous diversification of flowering plants remains Darwin's 'abominable mystery' despite numerous fossil flowers discovered in recent years. Wildfires were frequent in the Cretaceous and many such early flower fossils are represented by charcoalified fragments, lacking complete delicate structures and surface textures, making their similarity to living forms difficult to discern. Furthermore, scarcity of information about the ecology of early angiosperms makes it difficult to test hypotheses about the drivers of their diversification, including the role of fire in shaping flowering plant evolution. We report the discovery of two exquisitely preserved fossil flower species, one identical to the inflorescences of the extant crown-eudicot genus Phylica and the other recovered as a sister group to Phylica, both preserved as inclusions together with burned plant remains in Cretaceous amber from northern Myanmar (~99 million years ago). These specialized flower species, named Phylica piloburmensis sp. nov. and Eophylica priscastellata gen. et sp. nov., exhibit traits identical to those of modern taxa in fire-prone ecosystems such as the fynbos of South Africa, and provide evidence of fire adaptation in angiosperms.

Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications.

Musa (family Musaceae) is monocotyledonous plants in order Zingiberales, which grows in tropical and subtropical regions. It is one of the most important tropical fruit trees in the world. Herein, we used next-generation sequencing technology to assemble and perform in-depth analysis of the chloroplast genome of nine new Musa plants for the first time, including genome structure, GC content, repeat structure, codon usage, nucleotide diversity and etc. The entire length of the Musa chloroplast genome ranged from 167,975 to 172,653 bp, including 113 distinct genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In comparative analysis, we found that the contraction and expansion of the inverted repeat (IR) regions resulted in the doubling of the rps19 gene. The several non-coding sites (psbI-atpA, atpH-atpI, rpoB-petN, psbM-psbD, ndhf-rpl32, and ndhG-ndhI) and three genes (ycf1, ycf2, and accD) showed significant variation, indicating that they have the potential of molecular markers. Phylogenetic analysis based on the complete chloroplast genome and coding sequences of 77 protein-coding genes confirmed that Musa can be mainly divided into two groups. These genomic sequences provide molecular foundation for the development and utilization of Musa plants resources. This result may contribute to the understanding of the evolution pattern, phylogenetic relationships as well as classification of Musa plants.

The complete chloroplast genome sequence of Duranta erecta (Verbenaceae).

In this study, the complete chloroplast (cp) genome of Duranta erecta was assembled using Illumina sequencing data. The complete cp genome is 149,869 bp in length, including a pair of invert repeats (IRA and IRB) regions of 22,839 bp, large single-copy (LSC) region of 86,201 bp, and small single-copy (SSC) region of 17,990 bp. The G + C content of this cp genome was 38.26%. A total of 128 genes were predicted in the genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis confirmed the phylogenetic relationship between D. erecta and other representative species of Verbenaceae.

The complete chloroplast genome sequence of Ehrharta erecta Lam. (Poaceae).

The complete chloroplast (cp) genome of Ehrharta erecta was sequenced and assembled for the first time. In this study, The total genome size is 134,511 bp in length and demonstrates a typical quadripartite structure containing a large single copy (LSC, 95,227 bp) and a small single copy (SSC, 12,306 bp), separated by a pair of inverted repeats (IRa, IRb) of 13,489 bp. The G + C content of this chloroplast genome was 38.76%. Gene annotation analysis identified 130 genes including 84 protein-coding genes, 38 transfer RNA, and 8 ribosomal RNA genes. The maximum-likelihood phylogenetic analysis result showed that E. erecta was closely related to O. sativa in the phylogenetic relationship.

The complete chloroplast genome sequence of Oryza sativa Temperate japonica.

In this study, the complete chloroplast genome of O. sativa Temperate Japonica YunJing-24 was assembled using Illumina sequencing data. The complete chloroplast (cp) genome is 134,556 bp in length, including a pair of invert repeats (IRA and IRB) regions of 20,797 bp, large single-copy (LSC) region of 80,615 bp, and small single-copy (SSC) region of 12,347 bp. A total of 129 genes were predicted in the genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the phylogenetic relationship between O. sativa Temperate Japonica and other representative species.