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Background Species of Broussonetia (family Moraceae) are commonly used to make textiles and high-grade paper. The distribution of Broussonetia papyrifera L. is considered to be related to the spread and location of humans. The complete chloroplast (cp) genomes of B. papyrifera, Broussonetia kazinoki Sieb., and Broussonetia kaempferi Sieb. were analyzed to better understand the status and evolutionary biology of the genus Broussonetia. Methods The cp genomes were assembled and characterized using SOAPdenovo2 and DOGMA. Phylogenetic and molecular dating analysis were performed using the concatenated nucleotide sequences of 35 species in the Moraceae family and were based on 66 protein-coding genes (PCGs). An analysis of the sequence divergence (pi) of each PCG among the 35 cp genomes was conducted using DnaSP v6. Codon usage indices were calculated using the CodonW program. Results All three cp genomes had the typical land plant quadripartite structure, ranging in size from 160,239 bp to 160,841 bp. The ribosomal protein L22 gene (RPL22) was either incomplete or missing in all three Broussonetia species. Phylogenetic analysis revealed two clades. Clade 1 included Morus and Artocarpus, whereas clade 2 included the other seven genera. Malaisia scandens Lour. was clustered within the genus Broussonetia. The differentiation of Broussonetia was estimated to have taken place 26 million years ago. The PCGs’ pi values ranged from 0.0005 to 0.0419, indicating small differences within the Moraceae family. The distribution of most of the genes in the effective number of codons plot (ENc-plot) fell on or near the trend line; the slopes of the trend line of neutrality plots were within the range of 0.0363–0.171. These results will facilitate the identification, taxonomy, and utilization of the Broussonetia species and further the evolutionary studies of the Moraceae family.

Bombyx mandarina is generally thought to be the wild ancestor nearest to the domesticated silkworm, Bombyx mori. Here, we report the complete mitochondrial genome (mitogenome) of B. mandarina strain Shiquan. The mitogenome contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one A þ T-rich region. Phylogenetic analysis provides solid evidence that B. mandarina Shiquan belongs to Chinese B. mandarina, rather than Japanese B. mandarina. The new mitogenome provides useful information to further explore the origin and domestication of this species.

The complete nucleotide sequence of the Akebia trifoliata chloroplast (cp) genome was reported and characterized in this study. The cp genome is a closed circular molecule of 157 949 bp, composed of a pair of IR regions of 26 149 bp, one LSC region of 86 595 bp, and one SSC region of 19 056 bp. The GC contents of the LSC, SSC, IR regions, and the whole cp genome are 37.11%, 33.62%, 43.08% and 38.66%, respectively. The cp genome contains 130 predicted functional genes, including 85 PCGs, 37 tRNA and 8 rRNA genes. 168 SSRs and 23 long repeats were identified. The results revealed that 21 891 codons characterize the coding capacity of 85 protein-coding genes in Akebia trifoliata, 10.84% and 1.20% of the codons coded for leucine and cysteine respectively. The usage of the start codon exhibited no bias in the A. trifoliata cp genome. Phylogenetic analysis suggest that A. trifoliata is most closely related to S. japonica, which then formed a cluster with N. dormestica and M. saniculifolia to form subgroup of Ranunculales. Our study provides information on mangrove plant species in coastal intertidal zones.