Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing.

The evolution of a species depends on multiple forces, such as demography and natural selection. To understand the trajectory and driving forces of evolution of a target species, it is first necessary to uncover that species' population history, such as past and present population sizes, subdivision and gene flow, by using appropriate genetic markers. Cryptomeria japonica is a long-lived monoecious conifer species that is distributed in Japan. There are two main lines (omote-sugi and ura-sugi), which are distinguished by apparent differences in morphological traits that may have contributed to their local adaptation. The evolution of these morphological traits seems to be related to past climatic changes in East Asia, but no precise estimate is available for the divergence time of these two lines and the subsequent population dynamics in this species. Here, we analyzed the nucleotide variations at 120 nuclear genes in 94 individuals by using amplicon sequencing in combination with high-throughput sequencing technologies. Our analysis indicated that the population on Yakushima Island, the southern distribution limit of C. japonica in Japan, diverged from the other populations 0.85 million years ago (MYA). The divergence time of the other populations on mainland Japan was estimated to be 0.32 MYA suggesting that the divergence of omote-sugi and ura-sugi might have occurred before the last glacial maximum. Although we found modest levels of gene flow between the present populations, the long-term isolation and environmental heterogeneity caused by climatic changes might have contributed to the differentiation of the lines and their local adaptation.

Comparative Analysis of the Chloroplast Genomic Information of Cunninghamia lanceolata (Lamb.) Hook with Sibling Species from the Genera Cryptomeria D. Don, Taiwania Hayata, and Calocedrus Kurz.

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an important coniferous tree species for timber production, which accounts for ~40% of log supply from plantations in southern China. Chloroplast genetic engineering is an exciting field to engineer several valuable tree traits. In this study, we revisited the published complete Chinese fir (NC_021437) and four other coniferous species chloroplast genome sequence in Taxodiaceae. Comparison of their chloroplast genomes revealed three unique inversions found in the downstream of the gene clusters and evolutionary divergence were found, although overall the chloroplast genomic structure of the Cupressaceae linage was conserved. We also investigated the phylogenetic position of Chinese fir among conifers by examining gene functions, selection forces, substitution rates, and the full chloroplast genome sequence. Consistent with previous molecular systematics analysis, the results provided a well-supported phylogeny framework for the Cupressaceae that strongly confirms the "basal" position of Cunninghamia lanceolata. The structure of the Cunninghamia lanceolata chloroplast genome showed a partial lack of one IR copy, rearrangements clearly occurred and slight evolutionary divergence appeared among the cp genome of C. lanceolata, Taiwania cryptomerioides, Taiwania flousiana, Calocedrus formosana and Cryptomeria japonica. The information from sequence divergence and length variation of genes could be further considered for bioengineering research.

Genetic differentiation and evolutionary adaptation in Cryptomeria japonica.

Local adaptation of plant species is a central issue for survival during global climate change, especially for long-lived forest trees, with their lengthy regeneration time and spatially limited gene flow. Identification of loci and/or genomic regions associated with local adaptation is necessary for knowledge of both evolution and molecular breeding for climate change. Cryptomeria japonica is an important species for forestry in Japan; it has a broad natural distribution and can survive in a range of different environments. The genetic structure of 14 natural populations of this species was investigated using 3930 SNP markers. Populations on the Pacific Ocean side of Japan are clearly different from those on the Japan Sea side, as discussed in previous studies. Structure analysis and population network trees show that peripheral populations, including the most northerly and southerly ones, have unique features. We found that the genetic differentiation coefficient is low, FST = 0.05, although it must account for the presence of important genes associated with adaptation to specific environments. In total, 208 outlier loci were detected, of which 43 were associated with environmental variables. Four clumped regions of outlier loci were detected in the genome by linkage analysis. Linkage disequilibrium (LD) was quite high in these clumps of outlier loci, which were found in linkage groups (LGs) 2, 7, 10, and 11, especially between populations of two varieties, and when interchromosomal LD was also detected. The LG7 region is characteristic of the Yakushima population, which is a large, isolated, peripheral population occupying a specific environment resulting from isolation combined with volcanic activity in the region. The detected LD may provide strong evidence for selection between varieties.

Variations in insecticidal activity and chemical compositions of leaf essential oils from Cryptomeria japonica at different ages.

The larvicidal effects of the essential oils extracted from the leaves of Cryptomeria japonica at different ages (58, 42, and 26 years old) against 2 mosquito species, Aedes aegypti and Aedes albopictus, were studied. The analysis of major constituents of these essential oils was also investigated. Results obtained from the larvicidal tests, using essential oil from the leaves of 58-year-old C. japonica was found to be most effective against both A. aegypti and A. albopictus larvae, indicating tree age has significant influence on mosquito larvicidal activity. In addition, the eleven pure constituents from C. japonica leaf essential oil were also tested individually against the two mosquito larvae. Among them, alpha-terpinene, gamma-terpinene, p-cymene, 3-carene, terpinolene, and beta-myrcene shows strong larvicidal effect against the two mosquito larvae. Among these pure constituents, 3-carene exhibits the best larvicidal effect against A. aegypti and terpinolene shows an excellent inhibitory action against A. albopictus larvae. The results of this study show that the leaf essential oil and its effective constituents might be considered as a potent source for the production of fine natural larvicides.

Isolation and functional analysis of the CjNdly gene, a homolog in Cryptomeria japonica of FLORICAULA/LEAFY genes.

We report the isolation and characterization of CjNdly, a homolog in Japanese cedar (Cryptomeria japonica D. Don) of the FLORICAULA/LEAFY (FLO/LFY) genes. We determined the entire nucleotide sequence of CjNdly, including short 5'- and 3'-untranslated regions. The deduced amino acid sequence was similar to those of the products of the FLO/LFY genes from other species. The nucleotide sequence showed the closest homology to that of the NEEDLY gene in Pinus radiata D. Don. Although no proline-rich region has been reported previously in homologous gene products from gymnosperms, we found such a region at the amino-terminal end of the deduced amino acid sequence encoded by CjNdly. We detected the expression of CjNdly in both reproductive and vegetative tissues and organs of C. japonica. Heterologous expression of CjNdly in transgenic tobacco plants induced precocious flowering of regenerating shoots on agar-solidified medium and flowers with an abnormal phenotype, namely, petal-like stamens. Our findings suggest that the CjNdly gene may have important roles in flower development in Japanese cedar, resembling those of its angiosperm homologs.