Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications.

Based on Sima and Lu's system of the family Magnoliaceae, the genus Lirianthe Spach s. l. includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and are protected due to their endangered status. The limited knowledge of species within this genus and the absence of research on its chloroplast genome have greatly impeded studies on the relationship between its evolution and systematics. In this study, the chloroplast genomes of eight species from the genus Lirianthe were sequenced and analyzed, and their phylogenetic relationships with other genera of the family Magnoliaceae were also elucidated. The results showed that the chloroplast genome sizes of the eight Lirianthe species ranged from 159,548 to 159,833 bp. The genomes consisted of a large single-copy region, a small single-copy region, and a pair of inverted repeat sequences. The GC content was very similar across species. Gene annotation revealed that the chloroplast genomes contained 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, totaling 130 genes. Codon usage analysis indicated that codon usage was highly conserved among the eight Lirianthe species. Repeat sequence analysis identified 42-49 microsatellite sequences, 16-18 tandem repeats, and 50 dispersed repeats, with microsatellite sequences being predominantly single-nucleotide repeats. DNA polymorphism analysis revealed 10 highly variable regions located in the large single-copy and small single-copy regions, among which rpl32-trnL, petA-psbJ, and trnH-psbA were the recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. The result of phylogenetic analysis confirmed that the genus Lirianthe s. l. is a monophyletic taxon and the most affinal to the genera, Talauma and Dugandiodendron, in Sima and Lu's system and revealed that the genus Lirianthe s. s. is paraphyletic and the genus Talauma s. l. polyphyletic in Xia's system, while Magnolia subsection Gwillimia is paraphyletic and subsection Blumiana polyphyletic in Figlar and Nooteboom's system. Morphological studies found noticeable differences between Lirianthe species in aspects including leaf indumentum, stipule scars, floral orientation, tepal number, tepal texture, and fruit dehiscence. In summary, this study elucidated the chloroplast genome evolution within Lirianthe and laid a foundation for further systematic and taxonomic research on this genus.

Adsorption and diffusion of lithium in a graphene/blue-phosphorus heterostructure and the effect of an external electric field.

The adsorption and diffusion behaviors of lithium (Li) in a graphene/blue-phosphorus (G/BP) heterostructure have been investigated using a first principles method based on density functional theory (DFT). The effect of an external electric field on the adsorption and diffusion behaviors has also been investigated. The results show that the adsorption energy of Li on the graphene side of the G/BP heterostructure is higher than that on monolayer graphene, and Li adsorption on the BP side of the G/BP/Li system is slightly stronger than that on monolayer BP (BP/Li). The adsorption energy of Li reaches 2.47 eV, however, the energy barriers of Li diffusion decrease in the interlayer of the G/BP heterostructure. The results mentioned above suggest that the rate performance of the G/BP heterostructure is better than that of monolayer graphene. Furthermore, the adsorption energies of Li atoms in the three different most stable sites, i.e., HG, TP and H1 sites, increase by about 0.49 eV, 0.26 eV, and 0.13 eV, respectively, as the electric field intensity reaches 0.6 V Å-1. The diffusion energy barrier is significantly decreased by an external electric field. It is demonstrated that the external electric field can not only enhance the adsorption but can also modulate the diffusion barriers of Li atoms in the G/BP heterostructure.

Transcriptome analysis reveals key genes and pathways for prickle development in Zanthoxylumarmatum.

Zanthoxylum armatum is an economically important tree species. However, well-developed prickles on its stems and leaves pose serious challenges in terms of management and harvesting. To investigate the molecular mechanism underlying prickle development, we sequenced different stages of prickle morphological development and transcriptomes of different tissues in the root tips (Gen), leaf buds (Ya), and fruits of Z. armatum. The results revealed that proteins related to cell division and genes related to the growth hormone signaling pathway were highly expressed in the prickle just protrusion (PC1). In addition, a high expression of lignin biosynthesis genes was observed during the developmental onset of lignification (PC2) and prickle lignification (PC3). These findings indicate that phenylpropanoid biosynthesis and plant hormone signal transduction are key pathways for the completion of lignification development in the prickle. During prickle development, ZaMYB2 and ZaWRKY3 were significantly upregulated in PC2 and PC3, suggesting their possible involvement in prickle development. Transcriptome and qRT-PCR analyses revealed differential gene expression of zaPAL3, za4CLL1, zaCOMT1, ZaWRKY3, and ZaCCD31 in the Gen, Ya, newly formed fruit (ZaF1), newly oil-spotted fruits (ZaF2), PC1, PC2, and PC3 of Zarmatum. zaCCD31 was highly expressed in leaf buds, whereas Za4CLL1 was highly expressed in root tips. During the lignification of prickles, the relative expression of genes including zaMYB2 increased gradually; however, the relative expression of zaCCD31 decreased during this process. Therefore, we inferred that these genes might be closely related to prickle development. Notably, zaMYB2 was expressed at higher levels in PC2 and PC3 than in PC1 and was not expressed in Gen, Ya, ZaF1, and ZaF2. Therefore, zaMYB2 is a key gene involved in prickle development of Z. armatum that exhibited tissue-specific expression. This study establishes a foundation for future analyses of the molecular mechanism underlying prickle development in Z. armatum.

The complete chloroplast genome sequence of Michelia balansae var. balansae (Aug. Candolle) Dandy, a timber and spices species in Magnoliaceae.

Michelia balansae var. balansae (Aug. Candolle) Dandy is a timber and spices species in Magnoliaceae, native to China and Vietnam. In this paper, the complete chloroplast genome (cpDNA) and basic annotated information were reported and its phylogenetic relationship with other species in Magnoliaceae was analyzed. The size of chloroplast genome of M. balansae var. balansae is 160,134 bp, which exhibited a typical quadripartite structure comprising a large single-copy (LSC) region of 88,161 bp and a small single-copy (SSC) region of 18,845 bp separated by a pair identical inverted repeat regions (IRs) of 26,564 bp each. The chloroplast genome contains 131 genes, including 86 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that M. balansae var. balansae is most affinal to M. montana and they form a nomophyletic group with other 14 Michelia species. This Michelia clade is sister to the Aromadendron clade with high support. All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu.

Complete chloroplast genome sequence of Lirianthe coco (Loureiro) N. H. Xia & C. Y. Wu (Magnoliaceae), a popular ornamental species.

Lirianthe coco (Loureiro) N. H. Xia & C. Y. Wu is a popular ornamental species of Magnoliaceae. In the present study, the complete chloroplast genome (cpDNA) of L. coco was sequenced, assembled, and analyzed. The results indicated that the size of chloroplast genome of L. coco is 159,828 bp, which exhibits a typical quadripartite structure including a large single-copy (LSC) region of 87,958 bp and a small single-copy (SSC) region of 18,768 bp separated by a pair of identical inverted repeat regions (IRs) of 26,551 bp each. The genome contained 131 genes (113 unique), including 86 protein-coding genes (80 unique), 37 tRNA genes (29 unique), and 8 rRNA genes (4 unique). Phylogenetic analysis showed that L. coco is affinal to L. odoratissima and forms a nomophyletic group with the latter and L. delavayi.

Complete chloroplast genome sequence of Michelia champaca var. champaca Linnaeus, an ornamental tree species of Magnoliaceae.

Michelia champaca var. champaca is an ornamentally important tree in Magnoliaceae. The paper reported the complete chloroplast genome (cpDNA) of M. champaca var. champaca and its basic annotated information. The size of cpDNA is 160,008 bp, with a typical quadripartite structure of a large single-copy (LSC) region of 88,037 bp and a small single-copy (SSC) region of 18,809 bp separated by a pair identical inverted repeat regions (IRs) of 26,581 bp each. The genome contained 131 genes (113 unique), including 86 protein-coding genes (80 unique), 37 tRNA genes (29 unique), and eight rRNA genes (four unique). Phylogenetic analysis showed that M. champaca var. champaca is affinal to M. baillonii and they form a nomophyletic group with other eight Michelia species. This Michelia clade is sister to the Aromadendron cathcartii clade with high support. All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu.

The complete chloroplast genome sequence of Lirianthe hodgsonii, a tree species of Magnoliaceae as least concern.

Lirianthe hodgsonii is a tree species of Magnoliaceae as least concern. In the present paper, the complete chloroplast genome (cpDNA) and basic annotated information of L. hodgsonii were reported and its phylogenetic relationship with other species in Magnoliaceae was analyzed. The size of its complete cpDNA is 159,693 bp, with a typical quadripartite structure comprising a pair of inverted repeat (IR) regions of 26,546 bp, a large single-copy (LSC) region of 87,848 bp and a small single-copy (SSC) region of 18,753 bp. The genome contains 131 unique genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that L. hodgsonii is affinal to Lirianthe bidoupensis and they form a monophyletic group with other seven Lirianthe species. This Lirianthe clade is sister to the Dugandiodendron and Talauma clade with high support. All genera mentioned in this analysis are monophyletic under the system of Magnoliaceae by Sima and Lu.

The complete chloroplast genome sequence of Canarium album.

The first complete chloroplast genome (cpDNA) sequence of Canarium album was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,347 bp in length, contains a large single-copy (LSC) region of 87,838 bp and a small single-copy (SSC) region of 13,935 bp, which were separated by a pair of inverted repeats (IRs) regions of 30,787 bp. The genome contains 129 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall guanine-cytosine (GC) content of the whole genome is 37.5%, and the corresponding values of the LSC, SSC, and IR regions are 35.8%, 32.6%, and 41.1%, respectively. Further, phylogenomic analysis showed that C. album clustered together with Boswellia sacra.

The complete chloroplast genome sequence of Zanthoxylum armatum.

The first complete chloroplast genome sequences of Zanthoxylum armatum were reported in this study. The cpDNA of Z. armatum is 158,579 bp in length, contains a large single copy region (LSC) of 85,780 bp and a small single copy region (SSC) of 17,598 bp, which were separated by a pair of inverted repeat (IR) regions of 27,598 bp. The genome contains 133 genes, including 88 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 38.5%. Phylogenetic analysis of 18 chloroplast genomes within the family Rutaceae suggests that Z. armatum is closely related to Zanthoxylum schinifolium.

The complete chloroplast genome sequence of Olea ferruginea.

The first complete chloroplast genome sequences of Olea ferruginea were reported in this study. The cpDNA of O. ferruginea is 155,531 bp in length, contains a large single-copy region (LSC) of 86,279 bp and a small single-copy region (SSC) of 17,790 bp, which were separated by a pair of inverted repeat (IR) regions of 25,731 bp. The genome contains 129 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 37.8%. Phylogenetic analysis of six chloroplast genomes within the genus Olea suggests that O. ferruginea is closely related to Olea europaea subsp. cuspidate.

The complete chloroplast genome sequence of Ziziphus incurva.

The first complete chloroplast genome sequences of Ziziphus incurva were reported in this study. The complete chloroplast genome (cpDNA) sequence of Z. incurva was determined from Illumina HiSeq pair-end sequencing data. The cpDNA is 160,920 bp in length, contains a large single-copy region (LSC) of 88,778 bp and a small single-copy region (SSC) of 19,172 bp, which were separated by a pair of inverted repeat (IR) regions of 26,477 bp. The genome contains 129 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.8% and the corresponding values of the LSC, SSC, and IR regions are 34.6, 30.8, and 42.7%, respectively. Further, the phylogenomic analysis showed that Z. incurva clustered together with Z. jujube, Z. mauritiana, and Z. spina-christi.