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Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type-which included inversions, duplications, deletions, translocations, and mobile element insertions-was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.

Understanding population genetic structure and its possible causal factors is critical for utilizing genetic resources and genetic breeding of economically important plants. Although Torreya grandis is an important conifer producing nuts in China, little is known about its population structure, let alone the causal factors that shaped its genetic variation pattern and population structure. In this work, we intended to characterize the genetic variation pattern and population structure of the nut-yielding conifer T. grandis throughout its whole geographical distribution and further explore the potentially causal factors for the population structure using multiple approaches. A moderate level of genetic diversity and a novel population structure were revealed in T. grandis based on eleven robust EST-SSR loci and three chloroplast fragments. Alien genetic composition derived from the closely related species T. nucifera endemic to Japan was detected in the Kuaiji Mountain area, where the seed quality of T. grandis is considered the best in China. Demography history and niche modeling were inferred and performed, and the contribution of geographic isolation to its population structure was compared with that of environmental isolation. Significant demographic changes occurred, including a dramatic population contraction during the Quaternary, and population divergence was significantly correlated with geographic distance. These results suggested that early breeding activities and demographic changes significantly contributed to the population structure of T. grandis. In turn, the population structure was potentially associated with the excellent variants and adaptation of cultivars of T. grandis. The findings provide important information for utilizing genetic resources and genetic breeding of T. grandis in the future. [ABSTRACT FROM AUTHOR]

Inferring the geographic mode of speciation is essential for explaining the generation and assembly of biodiversity, but has been rarely applied to the temperate flora of China. Fagus longipetiolata and F. lucida are a sister pair of beech species with largely overlapping ranges in subtropical China, however, little is known about the geographic mode of speciation and the formation of their sympatric distributions. In this study, we used IMa2 and fastsimcoal2 to simulate the speciation history of the two sisters. On the basis of 11 nuclear loci screened for 27 populations/species, their divergence time was estimated to 8.37 Mya by IMa2, and weak interspecific gene flow was detected. The simulation by fastsimcoal2 found that F. longipetiolata and F. lucida diverged ~8.53 Mya, then came into contact and hybridized at 0.8 Mya. The extended Bayesian skyline plots indicated that F. lucida began demographic expansion prior to the Pleistocene at 3 Mya, whereas F. longipetiolata increased its effective population size during the Quaternary, between 0.8 and 0.5 Mya. Ecological niche analysis and niche modelling showed that the two beeches had subtle niche differentiation and their projected distributions were largely overlapped across the late Quaternary. These results, coupled with well-studied fossil records in Fagus , demonstrate that these two beech species diverged allopatrically at the high latitudes of the Northern Hemisphere, and came into contact and hybridized with each other after successive migrations into subtropical (i.e. warm temperate) China recently. However, the two beeches may have developed strong intrinsic reproductive barriers due to long-term allopatry, allowing them to coexist in subtropical China. Our results illuminate the assembly history of the temperate woody flora in subtropical China, supporting that many relict temperate lineages in subtropical China may have established their populations recently. [ABSTRACT FROM AUTHOR]

Soil waterlogging and high temperature (HT) are serious abiotic stresses that negatively affect cotton growth and yield. Yet effects of prewaterlogging to HT subsequently in cotton seedlings have not been obtained. To address this, two temperature conditions (30/20°C and 35/25°C) and two soil waterlogging levels (0 and 3 days) were established during the cotton seedling stage. Results showed that indexes of plant performance were decreased markedly under HT. Unexpectedly, plant performance for the treatment of HT combined with 3 days of soil waterlogging (HW) was better than HT treatment (specifically, increase of 7.9%, 9.0%, 10.2%, 5.4% and 4.6% in leaf area, plant height, belowground biomass, aboveground biomass and root‐to‐shoot ratio was detected). Decreases in MDA (malondialdehyde), H2O2 (hydrogen peroxide) contents and O2−$$ {\mathrm{O}}_2^{-} $$ (superoxide radicals) generation rate under HW treatment were observed by 14.1%, 7.7% and 14.1%, respectively, compared with HT. Moreover, ASA (ascorbic acid) content and DHAR (dehydroascorbate reductase) activity were improved by 19.7% and 13.8% for HW treatment relative to HT, however, the opposite situation for activities of APX (ascorbate peroxidase) and GR (glutathione reductase). Besides, activities of SOD (superoxide dismutase), CAT (catalase) and POD (peroxidase) in HW treatment were increased by 16.7%, 8.3% and 18.4%, separately. Thus, we concluded that short‐term soil waterlogging improved cotton cross‐tolerance to the continued high‐HT stress by enhanced SOD, CAT, POD and DHAR activities, increased ASA content in cotton seedlings. These results were expected to provide a theoretical basis for understanding cotton's cross‐tolerance to abiotic stress. [ABSTRACT FROM AUTHOR]

Pinus bhutanica is a critically endangered conifer and occurs only in central Bhutan, northwestern Yunnan and southeastern Xizang in China. In this study, the complete chloroplast genome of Pinus bhutanica was first assembled based on next-generation sequencing. The genome sequence was 116,919 bp in length with an overall GC content of 38.75%. A total of 106 functional genes were detected in the genome, including 72 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The phylogenetic tree reconstructed by 12 chloroplast genomes revealed that P. bhutanica is most closely related to Pinus wangii in subsection Strobus of Pinus. [ABSTRACT FROM AUTHOR]

Gynostemma pentaphyllum (Thunb.) Makino is a perennial creeping herbaceous plant in the family Cucurbitaceae, which has great medicinal value and commercial potential, but urgent conservation efforts are needed due to the gradual decreases and fragmented distribution of its wild populations. Here, we report the high-quality diploid chromosome-level genome of G. pentaphyllum obtained using a combination of next-generation sequencing short reads, Nanopore long reads, and Hi-C sequencing technologies. The genome is anchored to 11 pseudo-chromosomes with a total size of 608.95 Mb and 26 588 predicted genes. Comparative genomic analyses indicate that G. pentaphyllum is estimated to have diverged from Momordica charantia 60.7 million years ago, with no recent whole-genome duplication event. Genomic population analyses based on genotyping-by-sequencing and ecological niche analyses indicated low genetic diversity but a strong population structure within the species, which could classify 32 G. pentaphyllum populations into three geographical groups shaped jointly by geographic and climate factors. Furthermore, comparative transcriptome analyses showed that the genes encoding enzyme involved in gypenoside biosynthesis had higher expression levels in the leaves and tendrils. Overall, the findings obtained in this study provide an effective molecular basis for further studies of demographic genetics, ecological adaption, and systematic evolution in Cucurbitaceae species, as well as contributing to molecular breeding, and the biosynthesis and biotransformation of gypenoside. [ABSTRACT FROM AUTHOR]

Background and Aims Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). Methods DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). Key Results Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. Conclusions These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora. [ABSTRACT FROM AUTHOR]

Background: Mountains have not only provided refuge for species, but also offered dispersal corridors during the Neogene and Quaternary global climate changes. Compared with a plethora of studies on the refuge role of China’s mountain ranges, their dispersal corridor role has received little attention in plant phylogeographic studies. Using phylogeographic data of Eomecon chionantha Hance (Papaveraceae), this study explicitly tested whether the Nanling Mountains, which spans from west to east for more than 1000 km in subtropical China, could have functioned as a dispersal corridor during the late Quaternary in addition to a glacial refugium. Results: Our analyses revealed a range-wide lack of phylogeographic structure in E. chionantha across three kinds of molecular markers [two chloroplast intergenic spacers, nuclear ribosomal internal transcribed spacer (nrITS), and six nuclear microsatellite loci]. Demographic inferences based on chloroplast and nrITS sequences indicated that E. chionantha could have experienced a strong postglacial range expansion between 6000 and 1000 years ago. Species distribution modelling showed that the Nanling Mountains and the eastern Yungui Plateau were the glacial refugia of E. chionantha. Reconstruction of dispersal corridors indicated that the Nanling Mountains also have acted as a corridor of population connectivity for E. chionantha during the late Quaternary. Conclusions: Our results suggest that the Nanling Mountains may acted dual roles as a dispersal corridor in east-west direction and as a glacial refugium in subtropical China during the late Quaternary. The population connectivity mediated by the mountain range and a strong postglacial range expansion are the most likely reasons for the lack of phylogeographic structure in E. chionantha. The hypothesis of dual roles of the mountain range presented here sheds new insights into the phylogeographic patterns of organisms in subtropical China. [ABSTRACT FROM AUTHOR]

Pinus bhutanica is a critically endangered conifer and occurs only in central Bhutan, northwestern Yunnan and southeastern Xizang in China. In this study, the complete chloroplast genome of Pinus bhutanica was first assembled based on next-generation sequencing. The genome sequence was 116,919 bp in length with an overall GC content of 38.75%. A total of 106 functional genes were detected in the genome, including 72 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The phylogenetic tree reconstructed by 12 chloroplast genomes revealed that P. bhutanica is most closely related to Pinus wangii in subsection Strobus of Pinus ., Competing Interests: The authors have no conflicts of interest to declare., (© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)