Recent Fragmentation May Not Alter Genetic Patterns in Endangered Long-Lived Species: Evidence From Taxus cuspidata

Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers

In angiosperms cytoplasmic DNA is typically passed on maternally through ovules. Genes in the mtDNA may cause male sterility. When male-sterile (female) cytotypes produce more seeds than cosexuals, they pass on more copies of their mtDNA and will co-occur with cosexuals with a neutral cytotype. Cytoplasmic gynodioecy is a well-known phenomenon in angiosperms, both in wild and crop plants. In some conifer families (e.g. Pinaceae) mitochondria are also maternally inherited. However in some other families (e.g. Taxaceae and Cupressaceae) mtDNA is paternally inherited through the pollen. With paternal mtDNA inheritance, male cytotypes that produce more pollen than cosexuals are expected to co-occur with cosexuals. This is uncharted territory. An ESS model shows that the presence of male cytotypes selects for more female allocation in the cosexual, i.e. for sexual specialisation. An allele that switches sex from male to female can then invade. This leads to rapid loss of the neutral cytotype of the cosexual, fixation of the male cytotype and dioecy with 50% males and 50% females. The models suggest that paternal inheritance of mtDNA facilitates the evolution dioecy. Consistent with this hypothesis the Pinaceae are 100% monoecious, while dioecy is common in the Taxaceae family and in the genus Juniperus (Cupressaceae). However, no reliable data are yet available on both mode of inheritance of mtDNA and gender variation of the same species. When cosexuals benefit from reproductive assurance (high selfing rate, low inbreeding depression, low fertilisation) they maintain themselves next to males and females. This predicted pattern with three sex types present in the same population is observed in conifers in nature.

Research on the Medicinal Chemistry and Pharmacology of Taxus × media

Taxus × media, belonging to the genus Taxus of the Taxaceae family, is a unique hybrid plant derived from a natural crossbreeding between Taxus cuspidata and Taxus baccata. This distinctive hybrid variety inherits the superior traits of its parental species, exhibiting significant biological and medicinal values. This paper comprehensively analyzes Taxus × media from multiple dimensions, including its cultivation overview, chemical composition, and multifaceted applications in the medical field. In terms of chemical constituents, this study delves into the bioactive components abundant in Taxus × media and their pharmacological activities, highlighting the importance and value of these components, including paclitaxel, as the lead compounds in traditional medicine and modern drug development. Regarding its medicinal value, the article primarily discusses the potential applications of Taxus × media in combating tumors, antibacterial, anti-inflammatory, and antioxidant activities, and treating diabetes. By synthesizing clinical research and experimental data, the paper elucidates the potential and mechanisms of its primary active components in preventing and treating these diseases. In conclusion, Taxus × media demonstrates its unique value in biological research and tremendous potential in drug development.

Spatial genetic structure and seed quality of a southernmost Abies nephrolepis population

Abies nephrolepis (Trautv. ex Maxim.) Maxim. has its southernmost populations in South Korea and they are expected to decline under climate change. To establish a strategic conservation plan, this study aimed to investigate the spatial genetic structure and seed characteristics of A. nephrolepis. We used nine microsatellite markers on 165 individuals of A. nephrolepis and sampled seeds in a southernmost population at Mt. Hambaeksan, South Korea. We observed a high level of heterozygosity, and a simulation study found that sampling 20 individuals was enough to secure sufficient genetic diversity on average. Spatial autocorrelation analysis revealed that individuals had a positive genetic relationship until 30 m. Bayesian clustering models, STRUCTURE and GENELAND, failed to achieve a consensus in the optimal number of population (K), estimating K = 1 and K = 2, respectively. Principal coordinate analysis supported the absence of genetic substructure within the study population. There was a large variance in seed production among mother trees. On average, seeds of A. nephrolepis from Mt. Hambaeksan had a purity of 70.4% and a germination percentage of 32.2%. We found that seed weight was the most effective indicator of seed quality. Mother trees at higher altitudes had poorer purity which is threatening to A. nephrolepis considering the upslope retreat of subalpine species under climate change. Our results provide insights into the interactions among spatial processes, genetic structure, and seed quality within a population of A. nephrolepis.

¿Where do migratory fish spawn in a neotropical Andean basin regulated by dams?

Spawning sites play a key role in the reproduction of fish allowing populations to endure over time. The Nechí River is an important spawning area for potamodromous fish species where one of the threats is dam construction. In order to determine the importance of the Nechí River as a spawning site in the Magdalena River basin, sampling was conducted during the low-water-to-high-water season transition period between 2018 and 2019 at seven sampling sites. The average density of ichthyoplankton was 42.4 ind.10m-3 (SD = 7.1). Of the individuals in the post-larval stage, seven migratory species were identified, and two additional taxa were identified to genus; Prochilodus magdalenae, Megaleporinus muyscorum, and Pseudoplatystoma magdaleniatum presented the greatest density. At the temporal level, the greatest density of larvae of potamodromous species was observed in the first high-water season of 2019 with a total of 5.7 ind.10m-3(SD = 1.044), of which the most representative at the seasonal level were the Cauca River, Magdalena River, and Nechí River before it flows into the Cauca River. There were significant differences in the frequency of embryos and vitelline larvae of the potamodromous species in the interaction of the sampling sites and high-water seasons, as well as with the density of post-larvae. The average drift distance of the spawning areas is roughly 52.1 km. A positive association was found between the volume of turbined water and the presence of ichthyoplankton in the Porce River site, after discharge from the Porce III Hydroelectric Plant. The Nechí River is an important spawning site and there seems to be an association between the increase in ichthyoplankton densities and the distance to the dam (Porce III) as long as there are floodplains along the course of the river.

Epigenetic architecture of Pseudotaxus chienii: Revealing the synergistic effects of climate and soil variables

Whether conifers can withstand environmental changes especially temperature fluctuations has been controversial. Epigenetic analysis may provide new perspectives for solving the issue. Pseudotaxus chienii is an endangered gymnosperm species endemic to China. In this study, we have examined the genetic and epigenetic variations in its natural populations aiming to disentangle the synergistic effects of climate and soil on its population (epi)genetic differentiation by using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP) techniques. We identified 23 AFLP and 26, 7, and 5 MSAP outliers in P. chienii. Twenty-one of the putative adaptive AFLP loci were found associated with climate and/or soil variables including precipitation, temperature, K, Fe, Zn, and Cu, whereas 21, 7, and 4 MSAP outliers were significantly related to precipitation of wettest month (Bio13), precipitation driest of month (Bio14), percent tree cover (PTC), and soil Fe, Mn, and Cu compositions. Total precipitation and precipitation in the driest seasons were the most influential factors for genetic and epigenetic variation, respectively. In addition, a high full-methylation level and a strong correlation between genetic and epigenetic variation were detected in P. chienii. Climate is found of greater importance than soil in shaping adaptive (epi)genetic differentiation, and the synergistic effects of climate and climate-soil variables were also observed. The identified climate and soil variables should be considered when applying ex situ conservation.

The blowfly Chrysomya latifrons inhabits fragmented rainforests, but shows no population structure

Climate change and deforestation are causing rainforests to become increasingly fragmented, placing them at heightened risk of biodiversity loss. Invertebrates constitute the greatest proportion of this biodiversity, yet we lack basic knowledge of their population structure and ecology. There is a compelling need to develop our understanding of the population dynamics of a wide range of rainforest invertebrates so that we can begin to understand how rainforest fragments are connected, and how they will cope with future habitat fragmentation and climate change. Blowflies are an ideal candidate for such research because they are widespread, abundant, and can be easily collected within rainforests. We genotyped 188 blowflies (Chrysomya latifrons) from 15 isolated rainforests and found high levels of gene flow, a lack of genetic structure between rainforests, and low genetic diversity - suggesting the presence of a single large genetically depauperate population. This highlights that: (1) the blowfly Ch. latifrons inhabits a ~ 1000 km stretch of Australian rainforests, where it plays an important role as a nutrient recycler; (2) strongly dispersing flies can migrate between and connect isolated rainforests, likely carrying pollen, parasites, phoronts, and pathogens along with them; and (3) widely dispersing and abundant insects can nevertheless be genetically depauperate. There is an urgent need to better understand the relationships between habitat fragmentation, genetic diversity, and adaptive potential-especially for poorly dispersing rainforest-restricted insects, as many of these may be particularly fragmented and at highest risk of local extinction.

Possible northern persistence of Siebold's beech, Fagus crenata, at its northernmost distribution limit on an island in Japan Sea: Okushiri Island, Hokkaido

Siebold's beech, Fagus crenata, is widely distributed across the Japanese Archipelago and islands in Japan Sea. Similar to the northern limit of the geographical distribution of F. crenata on the mainland of Hokkaido, the northern limit of the distribution of F. crenata on islands in the Japan Sea is observed on Okushiri Island (ca 42°N). To understand the genetic relationships of F. crenata on Okushiri Island, we examined chloroplast (cp) DNA haplotypes and 11 nuclear microsatellite (SSR) loci among 1,838 individuals from 44 populations from Okushiri Island, mainland Hokkaido, and the northern part of the Tohoku region on Honshu Island. We identified 2 cpDNA haplotypes, which represent not only populations on the Japan Sea coast but also those on the Pacific coast and this suggested the Okushiri Island populations might not be formed by single colonization. Genetic diversity of the Okushiri Island populations of nuclear SSR was not lower than the mainland and the STRUCTURE analysis revealed the Okushiri Island individuals were admixed between Hokkaido and Tohoku clusters. Approximate Bayesian computation inferred that divergence between Tohoku and Hokkaido, and admixture between two populations which generated Okushiri populations occurred before the last glacial maximum (LGM), that is, 7,890 (95% hyper probability density (HPD): 3,420 - 9,910) and 3,870 (95% HPD: 431- 8,540) generations ago, respectively. These inferences were well supported by a geological history which suggested an isolation of Okushiri Island from Hokkaido started prior to the Middle Pleistocene. We discuss the possible persistence of F. crenata during the last glacial maximum on northern islands in the Japan Sea such as Okushiri Island.

Response of distribution patterns of two closely related species in Taxus genus to climate change since last inter-glacial

Climate change affects the species spatio-temporal distribution deeply. However, how climate affects the spatio-temporal distribution pattern of related species on the large scale remains largely unclear. Here, we selected two closely related species in Taxus genus Taxus chinensis and Taxus mairei to explore their distribution pattern. Four environmental variables were employed to simulate the distribution patterns using the optimized Maxent model. The results showed that the highly suitable area of T. chinensis and T. mairei in current period was 1.616 × 10⁵ km² and 3.093 × 10⁵ km², respectively. The distribution area of T. chinensis was smaller than that of T. mairei in different periods. Comparison of different periods shown that the distribution area of the two species was almost in stasis from LIG to the future periods. Temperature and precipitation were the main climate factors that determined the potential distribution of the two species. The centroids of T. chinensis and T. mairei were in Sichuan and Hunan provinces in current period, respectively. In the future, the centroid migration direction of the two species would shift towards northeast. Our results revealed that the average elevation distribution of T. chinensis was higher than that of T. mairei. This study sheds new insights into the habitat preference and limiting environment factors of the two related species and provides a valuable reference for the conservation of these two threatened species.

Identification of genes associated with biosynthesis of bioactive flavonoids and taxoids in Taxus cuspidata Sieb. et Zucc. plantlets exposed to UV-B radiation

UV-B radiation is a typical environmental stressor that can promote phytochemical accumulation in plants. Taxus species are highly appreciated due to the existence of bioactive taxoids (especially paclitaxel) and flavonoids. However, the effect of UV-B radiation on taxoid and flavonoid biosynthesis in Taxus cuspidata Sieb. et Zucc. is largely unknown. In the present work, the accumulation of taxoids and flavonoids in T. cuspidata plantlets was significantly induced by 12 and 24 h of UV-B radiation (3 W/m²), and a large number of significantly differentially expressed genes were obtained via transcriptomic analysis. The significant up-regulation of antioxidant enzyme- and flavonoid biosynthesis-related genes (phenylalanine ammonia lyase 1, chalcone synthase 2, flavonol synthase 1, and flavonoid 3', 5'-hydroxylase 2), suggested that UV-B might cause the oxidative stress thus promoting flavonoid accumulation in T. cuspidata. Moreover, the expression of some genes related to jasmonate metabolism and taxoid biosynthesis (taxadiene synthase, baccatin III-3-amino 3-phenylpropanoyltransferase 1, taxadiene-5α-hydroxylase, and ethylene response factors 15) was significantly activated, which indicated that UV-B might initiate jasmonate signaling pathway that contributed to taxoid enhancement in T. cuspidata. Additionally, the identification of some up-regulated genes involved in lignin biosynthesis pathway indicated that the lignification process in T. cuspidata might be stimulated for defense against UV-B radiation. Overall, our findings provided a better understanding of some potential key genes associated with flavonoid and taxoid biosynthesis in T. cuspidata exposed to UV-B radiation.

Transposable Elements: Distribution, Polymorphism, and Climate Adaptation in Populus

Transposable elements (TEs) are a class of mobile genetic elements that make effects on shaping rapid phenotypic traits of adaptive significance. TE insertions are usually related to transcription changes of nearby genes, and thus may be subjected to purifying selection. Based on the available genome resources of Populus, we found that the composition of Helitron DNA family were highly variable and could directly influence the transcription of nearby gene expression, which are involving in stress-responsive, programmed cell death, and apoptosis pathway. Next, we indicated TEs are highly enriched in Populus trichocarpa compared with three other congeneric poplar species, especially located at untranslated regions (3'UTRs and 5'UTRs) and Helitron transposons, particularly 24-nt siRNA-targeted, are significantly associated with reduced gene expression. Additionally, we scanned a representative resequenced Populus tomentosa population, and identified 9,680 polymorphic TEs loci. More importantly, we identified a Helitron transposon located at the 3'UTR, which could reduce WRKY18 expression level. Our results highlight the importance of TE insertion events, which could regulate gene expression and drive adaptive phenotypic variation in Populus.

The Research Progress of Taxol in Taxus

BACKGROUND

Taxus is a valuable woody species with important medicinal value. The bark of Taxus can produce taxol, a natural antineoplastic drug that is widely used in the treatment of breast, ovarian and lung cancers. However, the low content of taxol in the bark of Taxus can not meet the growing clinical demands, so the current research aims at finding ways to increase taxol production.

OBJECTIVE

In this review, the research progress of taxol including the factors affecting the taxol content, biosynthesis pathway of taxol, production of taxol in vitro and the application of multi-omics approaches in Taxus as well as future research prospects will be discussed.

RESULTS

The taxol content is not only dependent on the species, age and tissues but is also affected by light, moisture levels, temperature, soil fertility and microbes. Most of the enzymes in the taxol biosynthesis pathway have been identified and characterized. Total chemical synthesis, semi-synthesis, plant cell culture and biosynthesis in endophytic fungi have been explored to product taxol. Multi-omics have been used to study Taxus and taxol.

CONCLUSION

Further efforts in the identification of unknown enzymes in the taxol biosynthesis pathway, establishment of the genetic transformation system in Taxus and the regulatory mechanism of taxol biosynthesis and Taxus cell growth will play a significant role in improving the yield of taxol in Taxus cells and plants.

Comparative Genomic Analysis Reveals the Mechanism Driving the Diversification of Plastomic Structure in Taxaceae Species

Inverted repeat (IR) regions in the plastomes from land plants induce homologous recombination, generating isomeric plastomes. While the plastomes of Taxaceae species often lose one of the IR regions, considerable isomeric plastomes were created in Taxaceae species with a hitherto unclarified mechanism. To investigate the detailed mechanism underpinning the IR-independent genesis of plastomic diversity, we sequenced four Taxaceae plastomes, including Taxus cuspidata Siebold & Zuccarini, Taxus fauna Nan Li & R. R. Mill, and two individuals of Taxus wallichiana Zuccarini. Then we compared these structures with those of previously reported Taxaceae plastomes. Our analysis identified four distinct plastome forms that originated from the rearrangements of two IR-flanking inverted fragments. The presence of isomeric plastomes was then verified in T. cuspidata individuals. Both rearrangement analyses and phylogenetic results indicated that Taxaceae were separated into two clades, one including Taxus and Pseudotaxus and another formed by Amentotaxus and Torreya. Our reconstructed scenario suggests that the minimum number of inversion events required for the transformation of the plastome of Cephalotaxus oliveri Masters into the diversified Taxaceae plastomes ranged from three to six. To sum up, our study reveals a distinct pattern and the mechanism driving the structural diversification of Taxaceae plastomes, which will advance our understanding of the maintenance of plastomic diversity and complexity in conifers.

Differential Responses to Climate and Land-Use Changes in Threatened Chinese Taxus Species

Rapid climate and land-use changes have been considered as the foremost threat to global biodiversity. China contains more than 3500 threatened higher plants, whereas the relative influence of climate and land-use changes on these endangered plants have not been explored simultaneously under topographical constraints. Here, using Taxus plants as the case study genus, we simulated the distribution range of threatened species under three scenarios of current and future climate and land-use conditions under topographical constraints. We also measured the associated difference in the responses of Taxus species to climate and land-use changes. Our results demonstrated the substantial influence of climate and land-use changes on the distributions of Taxus species. However, we observed different responses of Taxus species to these environmental changes. The distribution range of T. cuspidate Siebold & Zuccarini and T. mairei Lemee & H. Léveillé would substantially shrink, whereas the habitat range of T. fuana Nan Li & R. R. Mill would sharply expand under RCP 8.5(Representative Concentration Pathway scenarios) scenario. Meanwhile, T. wallichiana Zuccarini and T. chinensis (Pilger) Florin would experience apparent range shifts. Furthermore, topographical factors played non-negligible roles in shaping species distributions, and modifying the influence of climate and land-use changes. Together, these results provide robust evidence that even threatened species will have multiple responses to climate and land-use changes (e.g., shrinking, expanding, shifting). Our findings highlight that taking species ecological traits, habitat characteristics, and topographical constraints into account might provide valuable insights into threatened species conservation in the face of global environmental changes.