Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'

Characterization of the complete chloroplast genome and development of molecular markers of Salix

Salix, an economically and ecologically multifunctional tree species widely distributed in China, encompasses five ornamental species sequenced in this study, which are highly beneficial for plant phytoremediation due to their ability to absorb heavy metals. This research utilized high-throughput sequencing to acquire chloroplast genome sequences of Salix, analyzing their gene composition and structural characteristics, identifying potential molecular markers, and laying a foundation for Salix identification and resource classification. Chloroplast DNA was extracted from the leaves of Salix argyracea, Salix dasyclados, Salix eriocephala, Salix integra 'Hakuro Nishiki', and Salix suchowensis using an optimized CTAB method. Sequencing was conducted on the Illumina NovaSeq PE150 platform, and bioinformatics tools were employed to compare the structural features and variations within the chloroplast genomes of the Salix. Analysis revealed high similarity among the chloroplast genome sequences of the five Salix species, with a subsequent examination identifying 276, 269, 270, 273, and 273 SSR loci, respectively, along with unique simple repeat sequences in each variety. Comparison of chloroplast genomes across 22 Salix highlighted variations in regions such as matK-trnQ, ndhC-trnV, psbE-petL, rpl36-rps8, and ndhB-rps7, which may serve as valuable molecular markers for willow resource classification studies. In this study, chloroplast genome sequencing and structural analysis of Salix not only enhances the genetic resources of Salix but also forms a critical basis for the development of molecular markers and the exploration of interspecific phylogeny in the genus.

The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers

BACKGROUND

While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts.

RESULTS

Poor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family.

CONCLUSIONS

This study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research.

The complete chloroplast genome of Philodendron hederaceum (Jacq.) Schott 1829 (Alismatales: Araceae)

Philodendron hederaceum (Jacq.) Schott 1829, a species of the Araceae family, is a foliage plant of ornamental value. The complete chloroplast genome sequence of Philodendron hederaceum was obtained by the de novo assembly of NovaSeq 6000 (Illumina Co., San Diego, CA) paired-end short reads and Oxford Nanopore long reads. The complete chloroplast genome of P. hederaceum was 168,609 bp in length, with a large single-copy (LSC) region of 94,393 bp, a small single-copy (SSC) region of 25,774 bp, and a pair of identical inverted repeat regions (IRs) of 24,221 bp. The genome contained a total of 129 genes, including 85 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis of P. hederaceum with 19 related species and two outgroup species revealed the closest taxonomical relationship with Philodendron lanceolatum in the Araceae family.

The complete chloroplast genome sequence of Rosa 'Limoncello' (Rosales: Rosaceae)

Rosa 'Limoncello' finds applications in gardening and landscaping. In this study, we assembled and annotated the complete chloroplast genome of this variety for the first time. The length of its chloroplast genome was 156,493 bp, containing two short inverted repeat regions of 26,052 bp, each separated by a large single-copy region of 85,649 bp and a small single-copy region of 18,740 bp. The chloroplast DNA of R. 'Limoncello' consisted of 135 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. On comparing the complete chloroplast sequence of R. 'Limoncello' with that of other Rosa species, R. 'Limoncello' was found to be closely related to Rosa cymosa. Thus, information on the chloroplast genome sequence of this rose variety can facilitate phylogenetic studies of the genus Rosa.

Comparative chloroplast genome analysis of four Polygonatum species insights into DNA barcoding, evolution, and phylogeny

The Polygonatum genus represents a perennial herb with the Liliaceae family, boasting substantial economic and medicinal significance. The majority of Polygonatum plants exhibit notable similarity while lacking distinctive identifying characteristics, thus resulting in the proliferation of adulterated medicinal materials within the market. Within this study, we conducted an in-depth analysis of the complete chloroplast (cp) genomes of four Polygonatum plants and compared them with four closely akin species. The primary objectives were to unveil structural variations, species divergence, and the phylogenetic interrelations among taxa. The cp genomes of the four Polygonatum species were typified by a conventional quadripartite structure, incorporating a large single copy region (LSC), a small single copy region (SSC), and a pair of inverted repeat regions. In total, we annotated a range of 131 to 133 genes, encompassing 84 to 86 protein-coding genes, 38 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 0 to 2 pseudogenes (ycf1, infA). Our comparative analyses unequivocally revealed a remarkable consistency in gene order and GC content within the Polygonatum genus. Furthermore, we predicted a potential 59 to 64 RNA editing sites distributed across 22 protein-coding genes, with the ndhB gene exhibiting the most prominent propensity for RNA editing sites, boasting a tally of 15 sites. Notably, six regions of substantial potential variability were ascertained, characterized by elevated Pi values. Noteworthy, molecular markers for species identification, population genetic scrutiny, and phylogenetic investigations within the genus were identified in the form of the psaJ-rpl33 and trnS + trnT-psaD barcodes. The resultant phylogenetic tree unequivocally depicted the formation of a monophyletic clade comprising species within the evolutionary framework of Liliaceae, demonstrating closer evolutionary affinities with Maianthemum, Dracaeneae, and Asparageae. This comprehensive compendium of findings collectively contributes to the advancement of molecular species identification, elucidation of phylogenetic interrelationships, and the establishment of DNA barcodes tailored to the Polygonatum species.

Sequencing and analysis of the complete mitochondrial genomes of Toona sinensis and Toona ciliata reveal evolutionary features of Toona

BACKGROUND

Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives.

RESULTS

(1) T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other.

CONCLUSIONS

This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.

Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae)

Hippeastrum is a genus of ornamental plants with large, brightly colored flowers. Due to the very high seed-setting rate of the hybridization of Hippeastrum, the large population of hybrid progeny and the existence of superparent inheritance, it is difficult to trace the origin of the varieties collected from the market during breeding. In this study, we analyzed the chloroplast genomes of Hippeastrum ‘Milady’, H. alberti, and H. reticulatum using the Illumina NovaSeq sequencing platform and generated full-length sequences of 158,067, 158,067, and 158,522 bp, respectively. All three genomes had the typical tetrad structure. The large single copy, small single copy, and inverted repeat regions of H. reticulatum were observed to be respectively 277, 138, and 20 bp longer than the corresponding regions of H. ‘Milady’ and H. alberti. The results of comparative analysis of simple sequence repeats (SSRs), Ka/Ks ratios, codon preferences, and complete sequences of chloroplasts of these three taxa and 14 other plant species were as follows. First, the chloroplast genomes of H. ‘Milady’, H. alberti, and H. reticulatum contain 209, 209, and 211 SSR sites, respectively, most of which (123, 123, and 122, respectively) are single nucleotide repeats. Second, leucine, arginine, and serine are the most frequently used amino acids in the three chloroplast genomes. Third, H. ‘Milady’, H. alberti, and H. reticulatum are more closely related to Lycoris and Narcissus than to Allium and Agapanthus. Our results will provide information on the study of origins or relatedness of native species, and the identification of cultivars.

Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution

Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.

Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae

Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

Complete chloroplast genome sequence of Pithecellobium clypearia (Jack) Benth

Pithecellobium clypearia (Jack) Benth. 1844 belongs to the genus Pithecellobium in the family Fabaceae. The complete chloroplast genome of P. clypearia was sequenced and analyzed by Illumina sequencing in this study. The full length of the complete chloroplast genome is 176,770 bp, containing a pair of inverted repeat regions of 39,693 bp (IRa and IRb) separated by a large single-copy (LSC) region of 92,500 bp and a small single-copy (SSC) region of 4,884 bp. The P. clypearia chloroplast genome encodes 137 genes, comprising 92 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on complete chloroplast genomes revealed that P. clypearia is closely related to Archidendron lucyi and Pithecellobium flexicaule. This study provides useful resources for further study and development of this species.

Complete Chloroplast Genomes of Three Salix Species: Genome Structures and Phylogenetic Analysis

High genetic diversity and low differentiation present challenges in taxonomy and systematics of Salix. Chloroplast (cp) genome sequencing is efficient for providing new genomic information and elucidating phylogenetic relationships. Salix spathulifolia Seemen, S. cupularis Rehder, and S. annulifera C.Marquand & Airy Shaw are three shrubby willows spread in high-altitude regions in western China. In this study, the integrated circular cp genomes were sequenced and analyzed, and a phylogeny of Salix was constructed on the basis of the cp genomes. The results of chloroplast assembly and annotation information were used to characterize genome feature and interspecific variation. The phylogenetic position of the three willows was evaluated using phylogenetic analysis. Full-length cp genomes were 155,566–155,680 bp with a typical double-stranded circular quadripartite structure, containing one large single-copy region (LSC, 84,431–4552 bp), one small single-copy region (SSC: 16,206–16,221 bp), and two inverted repeats (IR: 27,453–27,461 bp). The cp genomes encoded 130 genes, including 8 rRNA genes, 37 tRNA genes, and 85 protein-coding genes. The guanine-cytosine (GC) content of the overall genome was 36.7%. Comparison among the three willows’ cp genomes revealed high similarity. Phylogenetic analysis indicated that S. spathulifolia was a basal taxon of clade I, while S. annulifera formed a monophyletic group with S. rorida Laksch.; S. cupularis was sister to S. suchowensis W.C. Cheng and S. psammophila Z. Wang & Chang Y. Yang. The complete chloroplast genomes of the three willows provides an additional sequence-based resource for studying the phylogeny and evolutionary history of Salicaceae.

The complete chloroplast genome sequence of Camellia chuongtsoensis

Camellia chuongtsoensis is an evergreen shrub with a single-petaled flower and golden yellow color. The complete chloroplast genome of C. chuongtsoensis was sequenced and analyzed in this study by Illumina sequencing. The chloroplast genome is 156,504 bp in length with a quadripartite structure containing a large single copy (LSC) region of 86,215 bp, a small single copy (SSC) region of 18,253 bp, and a pair of inverted repeat regions of 26,018 bp (IRa and IRb). The chloroplast genome of C. chuongtsoensis encodes 135 genes, comprising 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes.

Complete chloroplast genome sequence of Camellia rhytidophylla, comparative and phylogenetic analysis

Camellia rhytidophylla is an endangered plant with economic value. Using Illumina sequencing, the chloroplast genome of C. rhytidophylla was sequenced and analyzed in this study. The complete chloroplast genome is 157,073 bp in length, which consisted of a pair of inverted repeat regions of 26,055 bp (IRa and IRb) separated by a large single-copy region (LSC) of 86,680 bp and a small single-copy region (SSC) of 18,283 bp. The C. rhytidophylla chloroplast genome encodes 135 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes. Sequence comparison analysis with the chloroplast sequences of 28 other Camellia plants found that C. rhytidophylla had the closest relationship with C. szechuanensis. This study provides a theoretical basis for the analysis of the distant relationship of Camellia.

Development of a Specific Mini-Barcode From Plastome and its Application for Qualitative and Quantitative Identification of Processed Herbal Products Using DNA Metabarcoding Technique: A Case Study on Senna

Herbal products play an important role globally in the pharmaceutical and healthcare industries. However, some specific groups of herbal products are easily adulterated by confused materials on the market, which seriously reduces the products’ quality. Universal conventional DNA barcodes would function poorly since the processed herbal products generally suffer from varying degrees of DNA degradation and DNA mixing during processing or manufacturing. For quality control purposes, an accurate and effective method should be provided for species identification of these herbal products. Here, we provided a strategy of developing the specific mini-barcode using Senna as an example, and by coupling with the metabarcoding technique, it realized the qualitative and quantitative identification of processed herbal products. The plastomes of Senna obtusifolia (L.) H.S.Irwin & Barneby and Senna occidentalis (L.) Link were newly assembled, and the hypervariable coding-regions were identified by comparing their genomes. Then, the specific mini-barcodes were developed based on the identified hypervariable regions. Finally, we applied the DNA metabarcoding technique to the developed mini-barcodes. Results showed that the lengths of plastomes of S. obtusifolia and S. occidentalis were 162,426 and 159,993 bp, respectively. Four hypervariable coding-regions ycf1, rpl23, petL, and matK were identified. Two specific mini-barcodes were successfully developed from matK, and the mini-barcode of primer 647F-847R was proved to be able to qualitatively and quantitatively identify these two processed Senna seeds. Overall, our study established a valuable way to develop the specific mini-barcode, which may provide a new idea for the quality control of processed herbal products.

Complete chloroplast genome sequence and phylogenetic analysis of Camellia fraterna

Camellia fraterna belongs to the genus Camellia in the family Theaceae. We sequenced and analyzed the complete chloroplast genome of C. fraterna by Illumina sequencing in this study. The full length of the complete chloroplast genome is 156,902 bp, containing a pair of inverted repeat regions of 26,030 bp (IRa and IRb) separated by a large single-copy (LSC) region of 86,583 bp and a small single-copy (SSC) region of 18,259 bp. The C. fraterna chloroplast genome encodes 135 genes, comprising 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and three pseudogenes. This study will be useful for further study on genetic diversity and molecular breeding.

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Research Highlights: For the first time, the complete chloroplast (cp) genome of Carya illinoinensis cv. ‘Pawnee’ was de novo assembled. Comprehensive analysis the cp genome of C. illinoinensis revealed potential cpDNA markers for intraspecies identification, genes involved in adaptation, and its phylogenetic position. Background and Objectives: C. illinoinensis is an economically important nut tree in the family Juglandaceae. Cp-derived markers are helpful for genetic research, but they still need to be developed in C. illinoinensis. Additionally, the adaptation and phylogenetic relationships of C. illinoinensis have not been revealed based on the complete cp genome. Materials and Methods: Chloroplast genomic DNA of C. illinoinensis cv. ‘Pawnee’ was extracted and subjected to Illumina sequencing. Results: The cp genome is 160,819 bp in size, exhibiting a typical quadripartite structure with a large single copy (LSC) of 90,022 bp, a small single copy (SSC) of 18,791 bp, and a pair of inverted repeats (IRA and IRB) regions of 26,003 bp each. The genome was predicted to encode 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 19 duplicates in the IR regions. In total, 213 SSRs and 44 long repeats were identified in the cp genome. A comparison of two different C. illinoinensis genotypes, ‘Pawnee’ and 87MX3-2.11, obtained 143 SNPs and 74 indels. The highly variable regions such as atpF, clpP, and ndhA genes, and matK-rps16, trnS-trnG, and trnT-psbD intergenic spacers might be helpful for future intraspecific identification. Positive selection was acting on the ccsA and rps12 cp genes based on the Ka/Ks ratios. Phylogenetic analysis indicated that C. illinoinensis forms a sister clade to Asian Carya species, represented by C. kweichowensis and Annamocarya sinensis. Conclusions: The genome information in our study will have significance for further research on the intraspecies identification and genetic improvement of C. illinoinensis.