Search

In order to obtain the optimal conditions for the protoplast preparation of Pleurotus giganteus, two strains, PG46 and PG79, with different temperature types, were selected as materials to study the effects of five factors (mycelial age, osmotic stabilizer type, lywallzyme concentration, enzymatic hydrolysis duration and enzymatic hydrolysis temperature) based on single factor and orthogonal experimental methods. The results were as follows: (1) In the single factor test, the optimal conditions for the protoplast preparation of P. giganteus were mycelial culture for 5 d, using 2.5% lywallzyme with 0.6 mol·L-1 mannitol, incubated for 4 h at 32°C (PG46) or 27-35°C (PG79). (2) Orthogonal experiment verified and optimized the single factor test results. Combination 2 (mycelial age 5 d, lywallzyme concentration 2.5%, 0.6 mol·L-1 mannitol, incubated for 4 h at 32°C) could be used as the optimal condition for the protoplast preparation of PG46 and PG79 at the same time, and the protoplast yields were 11.22 × 106 CFU·mL-1 and 7.28 × 106 CFU·mL-1, respectively. (3) For F-test, the influence degree of various factor on the protoplast preparation were as follows: mycelial age>lywallzyme concentration>enzymatic hydrolysis temperature>enzymatic hydrolysis duration (PG46), and mycelial age>enzymatic hydrolysis duration>enzymatic hydrolysis temperature>lywallzyme concentration (PG79), respectively. In conclusion, the protoplast preparation conditions of the two P. giganteus strains with different temperature types were basically the same, and the effects of mycelial age on the protoplasts yield of the two strains were the most significant. The results can lay a foundation for further cross-breeding, genetic transformation, whole genome sequencing and promote the molecular genetics development of P. giganteus. [ABSTRACT FROM AUTHOR]

Hibiscus mutabilis is native to China with a long cultivation history, and is an ancient garden tree species and medicinal plant. In this study, we selected three cultivars of H. mutabilis in a hybrid combination(H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen)to investigate evolutionary characteristics between the cultivars of H. mutabilis and its related species, and clarify the phylogenetic relationship between the cultivars of H. mutabilis and its related species, as well as explore the genetic model of chloroplast genome(cpDNA)of H. mutaibilis at the same time. We first sequenced the three cultivars of H. mutaibilis using Illumina NovaSeq. After assembly and annotation, three complete chloroplast genome sequences were obtained. The cpDNAs of the related species H. taiwanensis from our group, and H. syricus and H. rosa-sinensis from the gene bank. Then we carried out comparative analysis on composition and structure of cpDNAs of four species of Hibiscus and three cultivars of H. mutabilis, and completed its phylogenetic tree reconstruction. The results were as follows: (1)Total sizes of cpDNAs of H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen were 160 880, 160 879, 160 920 bp, respectively, and the total gene number was 130, including 85 protein-coding genes, eight ribosomal RNAs, and 37 transfer RNAs. (2) The comparative analyses showed that the cpDNAs of three cultivars of H. mutabilis and the related species H. taiwanensis were highly conserved, and the inverted repeat regions(IR)were all 26 300 bp; H. rosa-sinensis and H. syriacus shrank to at 25 745 and 25 598 bp, respectively.(3)The phylogenetic analysis revealed that the three cultivars were planted into a monophyletic branch, and then together with H. taiwanensis into a high support branch, indicating that H. mutabilis and H. taiwanensis had the closest relationship; Compared with H. syriacus and H. rosa-sinensis, H. mutabilis and H. taiwanensis were more closely related to H. hamabo, H. tiliaceum and H. canabinus.(4)Three cultivars of H. mutabilis could be distinguished by cpDNA sequence, the length of LSC/SSC of H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen were 89 355 bp/18 925 bp, 89 353 bp/18 926 bp, 89 400 bp/18 920 bp, respectively. And candidate molecular markers and DNA barcodes had been developed from repeat sequence and nucleotide diversity analyses, which could be used as a tool for cultivars identification.(5)The cpDNAs of H. mutabilis cv. Danbanbai and H. mutabilis cv. Jinqiusong showed a minimum difference and had the closest phylogenetic relationship. According to the relationship between their female and offspring, the maternal genetic characteristics of the cpDNAs of Hibiscus were proved. This study will help us to understand the evolutionary characteristics and phylogenetic relationship of cpDNAs of three cultivars of H. mutabilis and H. taiwanensis, and provide basic data on cpDNA for accurate identification of the cultivars of H. mutabilis and breeding of excellent cultivars. [ABSTRACT FROM AUTHOR]

canthocalyx alba is a common medicinal plant in Tibetan of China, and there are few reports on its whole chloroplast genome now. In order to reveal basic characteristics of the whole chloroplast genome of A. alba and explore its phylogeographic structure, ten individuals from five wild populations were sequenced by Illumina sequencing platform. After assembly and annotation, ten complete chloroplast genome sequences were obtained. Moreover, genome characteristics and phylogenetic relationships were explored. The results were as follows:(1)The complete chloroplast genomes of A. alba were 155 335-156 266 bp. A total of 113 genes were annotated, including 72 protein-coding genes, 30 tRNA genes and four rRNA genes. The chloroplast genome was highly conserved in species in terms of size, structure, GC content and gene composition.(2)Genomic comparative analysis showed that the fragments with large variation were located in the single copy region, and there was no obvious expansion and contraction at the IR boundaries.(3)Analysis of population genetics revealed rich genetic diversity in the wild populations and significant geographic structure, and there were certain relationships between genetic distances and geographic distances. This study lays the foundation for studies on population genetics and phylogenomics of species in Acanthocalyx. [ABSTRACT FROM AUTHOR]

Carpinus tientaiensis is an endangered plant species with sparse population densities and is endemic to China. The distribution of this species is restricted to the territory of Zhejiang Province and its survival rate is very low. Based on data of chloroplast genome(cpDNA)single nucleotide polymorphism(SNP)in six natural populations(including the mother plants of all populations), we investigated genealogical structure and systematic development, assessed how endangered C. tientaiensis is and put forward relevant conservation strategies. The genomic DNA of C. tientaiensis was extracted using TIANGEN kit method and a library was constructed for high-throughput sequencing with Illumina NovaSeq 6000. To obtain the sequence of chloroplast complete genome, cpDNA maps were constructed using the online program OGDRAW. Nucleotide diversity was analyzed by DnaSP software while PopART was used for haploid network construction and RAxML was adopted for maximum likelihood(ML)tree construction. Finally, MrBayes software was used for construction of Bayes tree. The results were as follows:(1)According to chloroplast complete genome sequence analysis of C. tientaiensis, most of the protein-coding genes and amino acid sequences showed obvious codon preference. Moreover, chloroplast long-term relationship(cpLTR)revealed 32 forward repeats, 25 palindromic repeats and 22 reverse repeats. We detected 87 simple sequence repeats(SSR)in different types, most of which were A/T rich and the number of single nucleotides was the largest.(2)A total of 314 SNPs was identified in the cpDNA of C. tientaiensis. Single-nucleotide substitution indicated that C. tientaiensis was monophyletic and could be categorized into Tiantai County(THS)and Jingning County(JST)populations. The evolution of the haplotypes of the population manifested stellar radiation.(3)The variation of nucleotide diversity was low in all populations(Pi<0.005)and the haplotype diversity of THS and JST populations was also low(Hd 0.5-0.6). This indicated that C. tientaiensis had undergone historically local expansions after experiencing bottlenecks across its evolution history, with lower genetic variation within populations and higher level of diversity among populations. The results of SNP of the cpDNA reveal the genetic diversity and lineage differentiation of C. tientaiensis, and provide theoretical basis for conservation of the genetic resources as well as rescue of this endangered plant species. [ABSTRACT FROM AUTHOR]

Estimating the time scale of species evolution is an important part of life evolution study. It is found that there are significant differences in the evolution rates of different genes and species in recent years, which challenges the molecular clock hypothesis to a great extent. Therefore, new methods are needed to re-estimate the evolutionary event time. The whole genome sequence of angiosperms makes it possible to estimate the evolutionary time from the whole genome perspective. In order to re-estimate the evolution time of angiosperms, an evolution rate correction model based on genomic data is established according to the idea that shared polyploidy events or shared divergence events should have the same Ks peak. The results were as follows:(1)Three common ways to obtain Ks distribution were compared and analyzed, which showed that the best way was to extract the median of Ks values on collinear blocks.(2)The change process of Ks distribution was simulated with time accumulation coefficient(v)of Ks values. When v was assumed to obey the normal distribution, the Ks distribution had a long tail phenomenon.(3)The correction process was described in detail, which was conducive to the understanding and wide spread of this method. From the application of correction method in angiosperms, it was found that the Ks peak before correction was not linear with time, while the Ks peak after correction was directly proportional to time, indicating that it is very necessary to estimate the time of species evolution events after correcting the Ks peak. It was also found that although the evolution rate of angiosperms was significantly different, the evolution rate between different branches was still partially consistent. For example, Magnoliids had the slowest evolutionary rate, followed by Eudicots and Monocots. When the environment changed greatly, most species of different lineages of angiosperms had synchronous radial evolution and adaptive evolution. Finally, a relatively reliable angiosperm evolution time axis was establish, which helps to understand the evolution process and model, especially to understand the phylogenetic relationship and the causes of diversity and provides phylogenetic and evolutionary support for plant research. [ABSTRACT FROM AUTHOR]

Opisthopappus taihangensis and O. longilobus, being perennial cliff herbs and endemic to Taihang Mountains, are important wild germplasm resources of Compositae, and have high economic and ecological values. To determine the appropriate sequencing strategy for the whole genome of O. taihangensis and O. longilobus, in this study, the genome sizes, heterozygosity, GC content, and repeatability were analyzed through the flow cytometry and high-throughput sequencing methods. The results were as follows:(1) Using maize of known genome size as controls, the genome size of O. taihangensis was approximately 2.1 Gb, while that of O. longilobus was approximately 2.4 Gb.(2) For O. taihangensis, the revised genome size was 3.13 Gb, and the repetitive sequences proportion, heterozygosity and GC content in the whole genome were estimated to be 84.35%, 0.99% and 36.56% respectively. Within O. longilobus, the revised genome size, the repetitive sequences proportion, heterozygosity and GC content were 3.18 Gb, 83.83%, 1.17% and 36.62% respectively.(3) The initial depth and content distribution of GC appeared abnormal after initial assembly, which might be related to the relatively high heterozygous rate of the two species. Above all, the whole genomes of O. taihangensis and O. longilobus were both large and complex genomes with high heterozygosity and repetitiveness. Therefore, it suggests that the use of Illumina + PacBio sequencing assembly strategy for the whole genome sequencing analysis of two Opisthopappus species in the future. [ABSTRACT FROM AUTHOR]

The pan-genome can represent all of the genetic diversities in a species or population, which is a limitation for obtaining only one single reference genome. The pan-genomics is becoming a new hot research area and being widely applicated in researches of many species in plants, animals and microorganisms, as the development of the whole genome sequencing and analysis technology. It provides powerful tools for resolving the genetic variation and polymorphism at levels of species or taxa, researches of functional genomics and reconstruction of phylogenetics, obtaining abundant of significant research achievements. However, present researches on pan-genomics still need to improve due to several problems, e.g., extensive cost of whole genome sequencing and data analysis, inconsistent analysis standards, lack of deeper and comprehensive explanation of the obtained data, and difficulty of application of the research achievements. We summarized the research progresses of pan-genomes on exploitation of genetic diversity and functional genomics, including construction of a pan-genome map, identification of genome variations and favorable genes, polymorphism of functional genes, population genetic diversity and systematic evolution, and discussed its potential in application of different research fields. Furthermore, we discussed the limitations existed in the present studies and possible solutions, and presented the prospect in the future on pan-genomics. [ABSTRACT FROM AUTHOR]