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Background Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress ( Thlaspi arvense ) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica . Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.

The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish.

Epigenetic variation may play an important role in how plants cope with novel environments. While significant epigenetic differences among plants from contrasting habitats have often been observed in the field, the stability of these differences remains little understood. Here, we combined field monitoring with a multi-generation common garden approach to study the dynamics of DNA methylation variation in invasive Chinese populations of the clonal alligator weed ( ). Using AFLP and MSAP markers, we found little variation in DNA sequence but substantial epigenetic population differentiation. In the field, these differences remained stable across multiple years, whereas in a common environment they were maintained at first but then progressively eroded. However, some epigenetic differentiation remained even after 10 asexual generations. Our data indicate that epigenetic variation in alligator weed most likely results from a combination of environmental induction and spontaneous epimutation, and that much of it is neither rapidly reversible (phenotypic plasticity) nor long-term stable, but instead displays an intermediate level of stability. Such transient epigenetic stability could be a beneficial mechanism in novel and heterogeneous environments, particularly in a genetically impoverished invader.

Alligator weed ( Alternanthera philoxeroides ) is a highly invasive species that has successfully established in numerous tropical and subtropical regions worldwide. Previous literature suggests that alligator weed was introduced to China in the 1930s as fodder for military horses by Japanese, while its presence in Japan only became apparent in the 1990s. Consequently, the introduction and genetic relationship between alligator weed populations in China and Japan remain uncertain, and the native source population is still unidentified. This study aimed to characterize the genetic diversity and structure of populations within the introduced range of China and Japan, as well as the native range of Argentina, using amplified fragment length polymorphism (AFLP) markers. Nine primer pairs were employed, resulting in a total of 573 distinct amplified bands for the China and Japan populations. However, none of these bands displayed polymorphism, indicating a uniform genetic background across all sampled populations in China and Japan. In contrast, the Argentine populations yielded 251 identifiable amplified bands using four well-performing primer pairs, of which 209 (80.69%) were found to be polymorphic. Genetic relationship and population structure analyses based on AFLP data revealed that the population from Jujuy, Argentina, exhibited the closest genetic affinity to the invasive populations in China and Japan, as indicated by Nei’s genetic identity value of 0.9281. Additionally, using methylation-sensitive amplified polymorphism (MSAP), we identified 258 epigenetic variation sites using five primer pairs in the Chinese and Japanese populations. Principal coordinate analysis (PCoA) based on the MSAP data revealed a geographic epigenetic structure within the alligator weed populations of China and Japan, with DNA methylation variation patterns exhibiting correlation with geographic distribution, thus implying their potential involvement in environmental adaptation. This research enhances our understanding of the invasion mechanisms of alligator weed and provides valuable insights into the roles of epigenetic factors in its successful spread.

Background Alternanthera philoxeroides (alligator weed) is a highly invasive alien plant that has continuously and successfully expanded from the tropical to the temperate regions of China via asexual reproduction. During this process, the continuous decrease in temperature has been a key limiting environmental factor. Results In this study, we provide a comprehensive analysis of the cold tolerance of alligator weed via transcriptomics. The transcriptomic differences between the southernmost population and the northernmost population of China were compared at different time points of cold treatments. GO enrichment and KEGG pathway analyses showed that the alligator weed transcriptional response to cold stress is associated with genes encoding protein kinases, transcription factors, plant-pathogen interactions, plant hormone signal transduction and metabolic processes. Although members of the same gene family were often expressed in both populations, the levels of gene expression between them varied. Further ChIP experiments indicated that histone epigenetic modification changes at the candidate transcription factor gene loci are accompanied by differences in gene expression in response to cold, without variation in the coding sequences of these genes in these two populations. These results suggest that histone changes may contribute to the cold-responsive gene expression divergence between these two populations to provide the most beneficial response to chilling stimuli. Conclusion We demonstrated that the major alterations in gene expression levels belonging to the main cold-resistance response processes may be responsible for the divergence in the cold resistance of these two populations. During this process, histone modifications in cold-responsive genes have the potential to drive the major alterations in cold adaption necessary for the northward expansion of alligator weed.

Background Potato ( Solanum tuberosum ) is one of the most important global food crops. However, potato bacterial wilt, a destructive soil-borne disease caused by Ralstonia solanacearum , poses a huge threat to global potato production and quality, leading to serious economic losses worldwide. The wild potato species Solanum commersonii exhibits resistance to bacterial wilt, but the underlying molecular mechanisms remain largely obscure. Results In this study, we identified differentially expressed miRNAs (microRNAs), phased secondary short-interfering RNAs (phasiRNAs), along with their target transcripts, and elucidated the potential pathways involved in bacterial wilt resistance through high-throughput sequencing analyses of transcriptome, sRNAome, and degradome on normal and R. solanacearum -infected potato roots, which were collected from the susceptible diploid potato clone S. tuberosum group Phureja SP15-65 and the resistant diploid S. commersonii germplasm CM804. The results revealed that 3,434 and 1,045 differentially expressed genes (DEGs) were identified in susceptible SP15-65 and resistant CM804, respectively, with 7,652 DEGs identified between SP15-65 and CM804 upon pathogen inoculation. 23 transcripts specifically expressed in CM804 were identified to be responsive to R. solanacearum infection. Functional enrichment analysis of DEGs revealed that mitogen-activated protein kinase (MAPK) activation, reactive oxygen species (ROS) generation, calcium signaling, hormone signaling, secondary metabolism, and transcriptional reprogramming for defense were potential pathways in potato root response to R. solanacearum infection. Furthermore, 115 unique known and 147 putative novel miRNAs showed differential expression in SP15-65 or CM804 after pathogen infection. Among these differentially expressed miRNAs, some miR482 , miR6024 , and miR390 family members triggered the biosynthesis of phasiRNAs through the cleavage of phasiRNA-generating ( PHAS ) precursor transcripts, as validated by degradome-seq. The resulting phasiRNAs directed the cleavage of their downstream target mRNAs. Six miRNA-mRNA pairs and four pairs of phasiRNA-mRNA displayed negatively correlated expression changes, which may be related to bacterial wilt resistance in potato. Conclusions This study sheds lights on the regulatory roles of small RNAs in potato resistance against bacterial wilt, and will provide a theoretical foundation for the cultivation of disease-resistant potato varieties.

Human cultivation facilitates the naturalization and subsequent invasion of non-native plant species through, for example, protection from predators or reducing environmental stochasticity. With the development of tourism, non-native plant species have been increasingly introduced into rural home gardens for landscape greening and amenity planting. However, few studies have examined non-native flora in rural home gardens, and in particular the importance of tourism in determining changes of garden non-native flora has not been scrutinized. In this study, we investigated non-native plant species in 135 home gardens across five rural tourism villages in tropical China. Attributes related to garden or household characteristics were also collected through interviews and questionnaires. A distance-based redundancy analysis was then performed to reveal the relationships between the non-native species composition and garden attributes. A total of 338 non-native plant species were recorded in the surveyed gardens. Among them, the majority (63%) were ornamentals, whereas 19% were for nutritional uses and 12% were spontaneous weeds. Gardening preference and distance to tourist attractions governed the non-native compositions, with gardens preferring cultural (ornamental) cultivation or gardens close to tourist attractions having more non-native species. These results highlight an increasing role of tourism in promoting non-native cultivation in rural gardens. Recommendations for species risk assessment, trade and supply regulation, and proper garden management are provided to help harness plant invasion along tourism development in rural China and other regions around the world.

Phenotypic plasticity has been proposed as an important adaptive strategy for clonal plants in heterogeneous habitats. Increased phenotypic plasticity can be especially beneficial for invasive clonal plants, allowing them to colonize new environments even when genetic diversity is low. However, the relative importance of genetic diversity and phenotypic plasticity for invasion success remains largely unknown. Here, we performed molecular marker analyses and a common garden experiment to investigate the genetic diversity and phenotypic plasticity of the globally important weed Alternanthera philoxeroides in response to different water availability (terrestrial vs. aquatic habitats). This species relies predominantly on clonal propagation in introduced ranges. We therefore expected genetic diversity to be restricted in the two sampled introduced ranges (the USA and China) when compared to the native range (Argentina), but that phenotypic plasticity may allow the species' full niche range to nonetheless be exploited. We found clones from China had very low genetic diversity in terms of both marker diversity and quantitative variation when compared with those from the USA and Argentina, probably reflecting different introduction histories. In contrast, similar patterns of phenotypic plasticity were found for clones from all three regions. Furthermore, despite the different levels of genetic diversity, bioclimatic modeling suggested that the full potential bioclimatic distribution had been invaded in both China and USA. Phenotypic plasticity, not genetic diversity, was therefore critical in allowing A. philoxeroides to invade diverse habitats across broad geographic areas.

Seed germination and dispersal have an important impact on the establishment and spread of invasive plants. Understanding the extent of intraspecific seed trait variations can enhance our understanding of how invasive plants respond to environmental change after introduction and help predict the dynamic of invasive species under future environmental conditions. However, less attention has been given to the variation in seed traits within species as opposed to among species. We compared seed production, seed morphological traits, dispersal ability, and seedling performance of Chromolaena odorata from 10 introduced populations in Asia and 12 native populations in America in a common garden. The results showed that range (introduced vs. native) and climate affected these traits. Compared with the native population, the introduced populations had higher seed numbers per capitula, lighter seeds, and higher potential dispersal ability seeds (lower terminal velocity) but lower germination rates and seedling lengths. Climatic clines in seed numbers per capitula and pappus length were observed; however, the clines in pappus length differed between the introduced and native populations. Trait covariation patterns were also different between both ranges. In the native populations, there was a trade-off between seed numbers per capitula and seed mass, while this relationship was not found for the introduced populations. These results indicate that C. odorata alters the ecological strategy of seed following invasion, which facilitates its establishment and fast dispersal and contributes to successful invasion in the introduced ranges.

Transgenerational plasticity (TGP) occurs when maternal environments influence the expression of traits in offspring, and in some cases may increase fitness of offspring and have evolutionary significance. However, little is known about the extent of maternal environment influence on gene expression of offspring, and its relationship with trait variations across generations. In this study, we examined TGP in the traits and gene expression of field pennycress ( Thlaspi arvense ) in response to cadmium (Cd) stress. In the first generation, along with the increase of soil Cd concentration, the total biomass, individual height, and number of seeds significantly decreased, whereas time to flowering, superoxide dismutase (SOD) activity, and content of reduced glutathione significantly increased. Among these traits, only SOD activity showed a significant effect of TGP; the offspring of Cd-treated individuals maintained high SOD activity in the absence of Cd stress. According to the results of RNA sequencing and bioinformatic analysis, 10,028 transcripts were identified as Cd-responsive genes. Among them, only 401 were identified as transcriptional memory genes (TMGs) that maintained the same expression pattern under normal conditions in the second generation as in Cd-treated parents in the first generation. These genes mainly participated in Cd tolerance-related processes such as response to oxidative stress, cell wall biogenesis, and the abscisic acid signaling pathways. The results of weighted correlation network analysis showed that modules correlated with SOD activity recruited more TMGs than modules correlated with other traits. The SOD-coding gene CSD2 was found in one of the modules correlated with SOD activity. Furthermore, several TMGs co-expressed with CSD2 were hub genes that were highly connected to other nodes and critical to the network’s topology; therefore, recruitment of TMGs in offspring was potentially related to TGP. These findings indicated that, across generations, transcriptional memory of gene expression played an important role in TGP. Moreover, these results provided new insights into the trait evolution processes mediated by phenotypic plasticity.