Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Cinnamomum camphora ('Gantong 1')

Cinnamomum camphora is one of the most commonly used tree species in landscaping. Improving its ornamental traits, particularly bark and leaf colors, is one of the key breeding goals. The basic helix-loop-helix (bHLH) transcription factors (TFs) are crucial in controlling anthocyanin biosynthesis in many plants. However, their role in C. camphora remains largely unknown. In this study, we identified 150 bHLH TFs (CcbHLHs) using natural mutant C. camphora 'Gantong 1', which has unusual bark and leaf colors. Phylogenetic analysis revealed that 150 CcbHLHs were divided into 26 subfamilies which shared similar gene structures and conserved motifs. According to the protein homology analysis, we identified four candidate CcbHLHs that were highly conserved compared to the TT8 protein in A. thaliana. These TFs are potentially involved in anthocyanin biosynthesis in C. camphora. RNA-seq analysis revealed specific expression patterns of CcbHLHs in different tissue types. Furthermore, we verified expression patterns of seven CcbHLHs (CcbHLH001, CcbHLH015, CcbHLH017, CcbHLH022, CcbHLH101, CcbHLH118, and CcbHLH134) in various tissue types at different growth stages using qRT-PCR. This study opens a new avenue for subsequent research on anthocyanin biosynthesis regulated by CcbHLH TFs in C. camphora

New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China

Background Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources. Methods Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods. Results Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage. Discussion The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots of haplotype diversity in the Dalou Mountains and Wuling Mountains likely benefited from gene flow from the Wu Mountains and Yungui Plateau. Collectively, these results indicate that mountain regions should be the main units for conserving and collecting genetic resources of L. chinense and other similar species in subtropical China

Electrochemical mechanical micromachining based on confined etchant layer technique

National Science Foundation of China [91023006, 91023047, 91023043, 21061120456, 21021002]; Natural Science Foundation of Fujian Province of China [2012J06004]; Fundamental Research Funds for the Central Universities [2010121022]; Scientific Research Foundation for the Returned Overseas Chinese Scholars (State Education Ministry)The confined etchant layer technique (CELT) has been proved an effective electrochemical microfabrication method since its first publication at Faraday Discussions in 1992. Recently, we have developed CELT as an electrochemical mechanical micromachining (ECMM) method by replacing the cutting tool used in conventional mechanical machining with an electrode, which can perform lathing, planing and polishing. Through the coupling between the electrochemically induced chemical etching processes and mechanical motion, ECMM can also obtain a regular surface in one step. Taking advantage of CELT, machining tolerance and surface roughness can reach micro-or nano-meter scale

Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs

Genetic diversity and geographic distribution patterns of Cinnamomum camphora under climate change in China

Cinnamomum camphora is a representative species of subtropical forests in eastern Asia, and an important raw material for essential oil production with high economic value around the world. However, with human activities, the living environment of wild C. camphora is experiencing serious damage. In this study, based on the SNP markers developed by transcriptome sequencing, the genetic diversity and genetic structure of 186 representative samples from 17 populations were evaluated. Furthermore, the potential distribution was predicted according to 10 environmental variables using MaxEnt modeling. The results showed that the genetic variation of C. camphora was moderate (Ho = 0.428 and He = 0.409), and the degree of differentiation between populations was low (FST = 0.069). The populations of C. camphora were divided into two groups based on genetic structure. The species distribution model showed that C. camphora is widely distributed in the southern region of China. In the future, with the increase in precipitation and temperature, the suitable area for C. camphora will expand northward. We believe that C. camphora will have wider application prospects in the future due to the expansion of suitable habitat areas. The research results in this study provide new perspectives for the management of C. camphora resources

Genotyping-by-Sequencing Study of the Genetic Diversity and Population Structure of the Endangered Plant <i>Tsoongiodendron odorum</i> Chun in China

Tsoongiodendron odorum Chun is a large evergreen tree in the Magnoliaceae family and an ancient relict species represented by small wild populations. It has excellent material quality, high ornamental value, and scientific significance. However, due to the complicated natural reproduction and notable habitat destruction, its wild populations must be urgently conserved. We used genotyping-by-sequencing to examine 17 natural populations of T. odorum in China, the species’ primary habitat, to better understand the genetic diversity of this species and use its germplasm resources. T. odorum had a very low level of genetic diversity; its mean values for Ho, He, Pi, and PIC were 0.175, 0.123, 0.160, and 0.053, respectively. With an average within-population Fst of 0.023 and an inter-population gene flow Nm of 10.918, population genetic variation was primarily found within populations, demonstrating minute genetic divergence between populations. The 17 natural populations of T. odorum were divided into two major categories: the Fujian populations in eastern China and the Jiangxi, Guangdong, Hunan, and Guangxi populations in central and western China. Our research contributes to the understanding of T. odorum’s genetic diversity and organization and offers a theoretical framework for the species’ conservation, breeding, and selection

The complete chloroplast genome sequence of Actinidia styracifolia C. F. Liang

The complete chloroplast (cp) genome sequence of Actinidia styracifolia C. F. Liang was assembled using Illumina pair-end sequencing data in this study. The assembled plastome was 156,845 bp in length, including a large single copy (LSC) region of 88,624 bp and a small single copy (SSC) region of 20,535bp, which were separated by two inverted repeat (IR) regions of 23,843 bp. The plastome contains 113 different genes, consisting of 79 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis based on chloroplast genomes revealed that A. styracifolia has a close genetic relationship with A. eriantha

Genome-Scale Identification, Classification, and Expression Profiling of MYB Transcription Factor Genes in Cinnamomum camphora

The camphor tree (Cinnamomum camphora (L.) Presl.) is the representative species of subtropical evergreen broadleaved forests in eastern Asia and an important raw material for essential oil production worldwide. Although MYBs have been comprehensively characterized and their functions have been partially resolved in many plants, it has not been explored in C. camphora. In this study, 121 CcMYBs were identified on 12 chromosomes in the whole genome of C. camphora and found that CcMYBs were mainly expanded by segmental duplication. They were divided into 28 subgroups based on phylogenetic analysis and gene structural characteristics. In the promoter regions, numerous cis-acting elements were related to biological processes. Analysis of RNA sequencing data from seven tissues showed that CcMYBs exhibited different expression profiles, suggesting that they have various roles in camphor tree development. In addition, combined with the correlation analysis of structural genes in the flavonoid synthesis pathway, we identified CcMYBs from three subgroups that might be related to the flavonoid biosynthesis pathway. This study systematically analyzed CcMYBs in C. camphora, which will set the stage for subsequent research on the functions of CcMYBs during their lifetime and provide valuable insights for the genetic improvement of camphor trees

RAD-Seq Data Point to a Distinct Split in Liriodendron (Magnoliaceae) and Obvious East–West Genetic Divergence in L. chinense

Liriodendron is a Tertiary period relic tree genus with a typical East Asian and North American disjunction distribution pattern. As an angiosperm base group of trees, Liriodendron provides a valuable resource for the study of evolution processes. Here, we reconstruct the phylogeny and population genetic structure of Liriodendron based on the restriction site-associated DNA sequencing (RAD-Seq) of a wide collection of individuals from 16 populations. Our results reveal a clear phylogenetic break between L. chinense and L. tulipifera and obvious genetic divergence between the eastern and western populations of L. chinense, which are consistent with the patterns of geographical distributions. The phylogeographic history and long-term geographical isolation of the genus may be responsible for this pattern. Furthermore, a closer relationship was found between L. tulipifera and the eastern populations of L. chinense, indicating the ancient phylogeny of L. chinense in this area. The results of this study will aid in the development of scientific strategies for the conservation and utilization of the Liriodendron germplasm