Juglans sigillata, or iron walnut, belonging to the order Juglandales, is an economically important tree species in Asia, especially in the Yunnan province of China. However, little research has been conducted on J. sigillata at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to its plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be useful. To construct a high-quality reference genome for J. sigillata, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50-Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed 1 Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored ∼93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heat map. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated an estimated divergence time between J. sigillata and Juglans regia of 49 million years ago on the basis of single-copy orthologous genes. We provide the first chromosome-level genome for J. sigillata. It will lay a valuable foundation for future research on the genetic improvement of J. sigillata.

The whole chloroplast (cp) genome sequence of Toxicodendron griffithii has been characterized from Illumina pair-end sequencing. The complete cp genome was 159,613 bp in length, containing a large single-copy region (LSC) of 87,722 bp and a small single-copy region (SSC) of 18,911 bp, which were separated by a pair of 26,490 bp inverted repeat regions (IRs). The genome contained 132 genes (113 unique), including 87 protein-coding genes (80 unique), 37 tRNA genes (29 unique), and 8 rRNA genes (4 unique). The overall GC content of T. griffithii cp genome is 37.94%. Phylogenetic analysis of 14 chloroplast genomes within the family Anacardiaceae suggests that T. griffithii is closely related to genus Rhus and genus Pistacia.

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.

Chimonobambusa angustifolia is a famous ornamental and edible bamboo species. Here, the complete chloroplast (cp) genome of C. angustifolia was assembled and annotated. The cp genome is 139,611 bp in size, consisting of two copies of inverted repeat (IR) regions of 21,799 bp, one large single-copy (LSC) region of 83,202 bp, and one small single-copy (SSC) region of 12,811 bp. It encodes 133 genes (110 unique), including 86 protein-coding genes (77 unique), 39 tRNA genes (29 unique), and 8 rRNA genes (4 unique). Phylogenetic analysis based on 21 cp genome sequences within four genera of family Poaceae indicated that genus Chimonobambusa were closely related to genus Shibataea, both belong to subtribe Shlbataeinae.

The genus Lirianthe in the family Magnoliaceae includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and 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 8 species from the genus Lirianthe were sequenced and analyzed, their phylogenetic relationships with other genera of the family Magnoliaceae are also elucidated. The results showed that the chloroplast genome sizes of the 8 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 8 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 are recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. Phylogenetic tree analysis confirmed the monophyly of the genus Lirianthe and its closest relationship with the genera, Talauma and Dugandiodendron. 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 of this genus.