Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

Transcriptional regulations of pollen tube reception are associated with the fertility of the ginger species Zingiber zerumbet and Zingiber corallinum

Zingiber zerumbet and Zingiber corallinum are economically valuable species in the genus Zingiber. While Z. corallinum is sexually active, Z. zerumbet adopts clonal propagation, although it has the potential for sexual reproduction. It is unclear so far at which step during the sexual reproduction of Z. zerumbet inhibition occurs, and what are the regulatory mechanisms underlying this inhibition. Here, by comparing with the fertile species Z. corallinum using microscopy-based methods, we show that rare differences were observed in Z. zerumbet up to the point when the pollen tubes invaded the ovules. However, a significantly higher percentage of ovules still contained intact pollen tubes 24 h after pollination, suggesting pollen tube rupture was impaired in this species. Further RNA-seq analysis generated accordant results, showing that the transcription of ANX and FER, as well as genes for the partners in the same complexes (e.g., BUPS and LRE, respectively), and those putative peptide signals (e.g., RALF34), were timely activated in Z. corallinum, which ensured the pollen tubes being able to grow, reorient to ovules, and receipt by embryo sacs. In Z. zerumbet, genes for these complexes were cooperatively suppressed, which would result in the maintenance of PT integrity due to the disruption of RALF34-ANX/BUPS signaling in PT and the failure of PT reception by an active synergid due to the insufficiency of the synergid-harbored FER/LRE complex. Taking the results from the cytological and RNA-seq studies together, a model is proposed to illustrate the possible regulation mechanisms in Z. zerumbet and Z. corallinum, in which the regulations for pollen tube rupture and reception are proposed as the barrier for sexual reproduction in Z. zerumbet.

Pattern of Adaptive Divergence in Zingiber kawagoii Hayata (Zingiberaceae) along a Narrow Latitudinal Range

Ecological and evolutionary processes linking adaptation to environment are related to species’ range shifts. In this study, we employed amplified-fragment-length-polymorphism-based genome scan methods to identify candidate loci among Zingiber kawagoii populations inhabiting varying environments distributed at low to middle elevations (143–1488 m) in a narrow latitudinal range (between 21.90 and 25.30° N). Here, we show evidence of selection driving the divergence of Z. kawagoii. Twenty-six F_ST outliers were detected, which were significantly correlated with various environmental variables. The allele frequencies of nine F_ST outliers were either positively or negatively correlated with the population mean F_ST. Using several independent approaches, we found environmental variables act in a combinatorial fashion, best explaining outlier genetic variation. Nonetheless, we found that adaptive divergence was affected mostly by annual temperature range, and it is significantly positively correlated with latitude and significantly negatively correlated with the population mean F_ST. This study addresses a latitudinal pattern of changes in annual temperature range (which ranged from 13.8 °C in the Lanyu population to 18.5 °C in the Wulai population) and emphasizes the pattern of latitudinal population divergence closely linked to the allele frequencies of adaptive loci, acting in a narrow latitudinal range. Our results also indicate environmentally dependent local adaptation for both leading- and trailing-edge populations.

"Breeding on Mountains" Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants (Ligusticum chuanxiong Hort.)

"Breeding on mountains, cultivation in dam areas" is a unique propagation method for the vegetatively propagated plant Ligusticum chuanxiong, including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on L. chuanxiong and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in L. chuanxiong increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of L. chuanxiong, while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant Gibberella, Phoma, Pericona, Paraphoma, and Neocosmospora. The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.

Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization

Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.

The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family

Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level.

Analysis of Microbial Diversity in Soil under Ginger Cultivation

Ginger is a perennial monocotyledonous herb, which can be used as both a vegetable and a medicinal plant. However, it is susceptible to various plant pathogens. Microbial diversity in soil is related closely to the health and productivity of plant crops including ginger. In the current study, we compared microbial diversity from soil samples under ginger cultivation (disease incidence of >50% [relatively unhealthy sample] versus disease incidence of <10% [relatively healthy sample]). The bacterial and fungal taxa were analyzed by Illumina-based sequencing, with 16S and ITS identification, respectively. Both bacterial and fungal OTUs were significantly more in the healthy soil sample than the unhealthy sample. Moreover, the dominant bacterial and fungal genera were detected to be different in each sample. Rhodanobacter and Kaistobacter were the dominant bacterial genera in the healthy sample, while Rhodoplanes and Bradyrhizobium were the dominant genera in the unhealthy sample. For fungal analysis, Cladosporium, Cryptococcus, and Tetracladium were the dominant genera in the healthy sample, while Lecanicillium, Pochonia, and Rhodotorula were the dominant genera in the unhealthy sample. Collectively, the basic information of microbial diversity in ginger soil is helpful for elucidating the ginger-microbe interactions and potentially selecting suitable plant growth-promoting rhizobacteria and biocontrol agents for ginger production.