Juglans L. (walnuts and butternuts) is an economically and ecologically important genus in the family Juglandaceae. All Juglans are important nut and timber trees. Juglans regia (Common walnut), J. sigillata (Iron walnut), J. cathayensis (Chinese walnut), J. hopeiensis (Ma walnut), and J. mandshurica (Manchurian walnut) are native to or naturalized in China. A strongly supported phylogeny of these five species is not available due to a lack of informative molecular markers. We compared complete chloroplast genomes and determined the phylogenetic relationships among the five Chinese Juglans using IIumina sequencing. The plastid genomes ranged from 159,714 to 160,367 bp encoding 128 functional genes, including 88 protein-coding genes and 40 tRNA genes each. A complete map of the variability across the genomes of the five Juglans species was produced that included single nucleotide variants, indels (insertions and deletions), and large structural variants, as well as differences in simple sequence repeats (SSR) and repeat sequences. Molecular phylogeny strongly supported division of the five walnut species into two previously recognized sections (Juglans/Dioscaryon and Cardiocaryon) with a 100 % bootstrap (BS) value using the complete cp genomes, protein coding sequences (CDS), and the introns and spacers (IGS) data. The availability of these genomes will provide genetic information for identifying species and hybrids, taxonomy, phylogeny, and evolution in Juglans, and also provide insight into utilization of Juglans plants.

Common walnut (Juglans regia L.) is an economically important hardwood tree species cultivated worldwide for its high quality wood and edible nuts. It is generally accepted that after the last glaciation J. regia survived and grew in almost completely isolated stands in Asia, and that ancient humans dispersed walnuts across Asia and into new habitats via trade and cultural expansion. The history of common walnut in China is a matter of debate, however. We estimated the genetic diversity and spatial genetic structure of 31 walnut populations sampled across its Chinese range using 22 microsatellite markers (13 neutral and 9 non-neutral). Using historical data and population genetic analysis, including approximate Bayesian analysis (ABC), we reconstructed the demographic history of J. regia in China. The genetic data indicated the likely presence of J. regia in glacial refugia in the Xinjiang province (Northwest China), Northeastern China (Beijing, Shandong, and Changbai Mountains), Central China (Qinling and Baishan Mountains and Xi’an), and Southwestern China (Tibet, Yunnan, Guizhou, and Sichuan provinces). Based on DIY-ABC analysis, we identified three ancient lineages of J. regia in China. Two lineages (subpopulation A and subpopulation B+C) diverged about 2.79 Mya, while Southwestern China, and Qinling and Baishan Mountains lineages diverged during the Quaternary glaciations (about 1.13 Mya). Remnants of these once-distinct genetic clusters of J. regia may warrant ecological management if they are to be retained as in situ resources. A population size expansion in Northeastern China was detected in the last five centuries. The present distribution of walnut in China resulted from the combined effects of expansion/contraction from multiple refugia after the Last Glacial Maximum and later human exploitation.

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.

An elucidation of how the selection pressures caused by habitat environments affect plant plastid genomes and lead to the adaptive evolution of plants, is a very intense area of research in evolutionary biology. The genus Paphiopedilum is a predominant group of orchids that includes over 66 species with high horticultural and ornamental value. However, owing to the destructive exploitation and habitat deterioration of wild germplasm resources of Paphiopedilum, it needs more molecular genetic resources and studies on this genus. The chloroplast is cytoplasmically inherited and often used in evolutionary studies. Thus, for this study, we newly sequenced, assembled and annotated five chloroplast genomes of the Paphiopedilum species. The size of these genomes ranged from 155,886 bp (P. henryanum) to 160,503 bp (P. ‘GZSLKY’ Youyou) and they contained 121–122 genes, which consisted of 76 protein coding genes, eight ribosomal RNAs, and 37–38 transfer RNAs. Combined with the other 14 Paphiopedilum species, the characteristics of the repeat sequences, divergent hotspot regions, and the condo usage bias were evaluated and identified, respectively. The gene transfer analysis showed that some fragments of the ndh and ycf gene families were shared by both the chloroplast and nucleus. Although the genomic structure and gene content was conserved, there was a significant boundary shift caused by the inverted repeat (IR) expansion and small single copy (SSC) contraction. The lower GC content and loss of ndh genes could be the result of adaptive evolutionary responses to its unique habitats. The genes under positive selection, including accD, matK, psbM, rpl20, rps12, ycf1, and ycf2 might be regarded as potential candidate genes for further study, which significantly contribute to the adaptive evolution of Paphiopedilum.