A chromosome-scale genome assembly of Castanopsis hystrix provides new insights into the evolution and adaptation of Fagaceae species.

Fagaceae species dominate forests and shrublands throughout the Northern Hemisphere, and have been used as models to investigate the processes and mechanisms of adaptation and speciation. Compared with the well-studied genus Quercus, genomic data is limited for the tropical-subtropical genus Castanopsis. Castanopsis hystrix is an ecologically and economically valuable species with a wide distribution in the evergreen broad-leaved forests of tropical-subtropical Asia. Here, we present a high-quality chromosome-scale reference genome of C. hystrix, obtained using a combination of Illumina and PacBio HiFi reads with Hi-C technology. The assembled genome size is 882.6 Mb with a contig N50 of 40.9 Mb and a BUSCO estimate of 99.5%, which are higher than those of recently published Fagaceae species. Genome annotation identified 37,750 protein-coding genes, of which 97.91% were functionally annotated. Repeat sequences constituted 50.95% of the genome and LTRs were the most abundant repetitive elements. Comparative genomic analysis revealed high genome synteny between C. hystrix and other Fagaceae species, despite the long divergence time between them. Considerable gene family expansion and contraction were detected in Castanopsis species. These expanded genes were involved in multiple important biological processes and molecular functions, which may have contributed to the adaptation of the genus to a tropical-subtropical climate. In summary, the genome assembly of C. hystrix provides important genomic resources for Fagaceae genomic research communities, and improves understanding of the adaptation and evolution of forest trees.

Enhancing electro-reduction of nitrite to ammonia by loading Co3O4 on CuO to construct elecrocatalytic dual-sites.

Improving the performance of CuO in electrocatalytic nitrite reduction to ammonia (NIRA) is the priority for designing efficient NIRA electrocatalysts. The electrocatalytic activity of CuO was enhanced by growing Co3O4 nanospheres on it. By comparing Co3O4@CuO with the mechanically mixed CuO and Co3O4 on a rotating ring-disk electrode, we discovered that the enhancement was attributed to a dual-site catalytic pathway.

The Maternal Donor of Chrysanthemum Cultivars Revealed by Comparative Analysis of the Chloroplast Genome.

Chrysanthemum (Chrysanthemum morifolium Ramat) is an important floricultural crop and medicinal herb. Modern chrysanthemum cultivars have complex genetic backgrounds because of multiple cycles of hybridization, polyploidization, and prolonged cultivation. Understanding the genetic background and hybrid origin of modern chrysanthemum cultivars can provide pivotal information for chrysanthemum genetic improvement and breeding. By now, the origin of cultivated chrysanthemums remains unclear. In this study, 36 common chrysanthemum cultivars from across the world and multiple wild relatives were studied to identify the maternal donor of modern chrysanthemum. Chloroplast (cp) genomes of chrysanthemum cultivars were assembled and compared with those of the wild relatives. The structure of cp genomes was highly conserved among cultivars and wild relatives. Phylogenetic analyses based on the assembled cp genomes showed that all chrysanthemum cultivars grouped together and shared 64 substitutions that were distinct from those of their wild relatives. These results indicated that a diverged lineage of the genus Chrysanthemum, which was most likely an extinct or un-sampled species/population, provided a maternal source for modern cultivars. These findings provide important insights into the origin of chrysanthemum cultivars, and a source of valuable genetic markers for chrysanthemum breeding programs.

Bi-Functional Fe3 O4 /Au/CoFe-LDH Sandwich-Structured Electrocatalyst for Asymmetrical Electrolyzer with Low Operation Voltage.

The reduction of the overall electrolysis potential to produce hydrogen is a critical target for fabricating applicable hydrogen evolution cells. Sandwich-structured Fe3 O4 /Au/CoFe-LDH is synthesized via a spontaneous galvanic displacement reaction. A series of structural characterizations indicate the successful synthesis of sandwich-structured Fe3 O4 /Au/CoFe-LDH electrocatalyst. The trace amount of Au laying between Fe3 O4 and CoFe-LDH significantly improves the intrinsic conductivity and catalytic activity of the composite catalyst. In-depth investigations indicate that Fe3 O4 and CoFe-LDH are responsible for the electrocatalytic hydrogen evolution reaction (HER) whereas Au is responsible for the electrocatalytic glucose oxidation (GOR). The electrocatalytic tests indicate Fe3 O4 /Au/CoFe-LDH offers excellent electrocatalytic activity and stability for both HER and GOR, even at high current density (i.e., 1000 mA cm-2 ). Further electrochemistry examinations in a two-compartment cell with a two-electrode configuration show that Fe3 O4 /Au/CoFe-LDH can significantly reduce the overall potential for this asymmetrical cell, with only 0.48 and 0.89 V required to achieve 10 mA cm-2 current density with and without iR-compensation, which is the lowest overall potential requirement ever reported. The design and synthesis of Fe3 O4 /Au/CoFe-LDH pave a new way to electrochemically produce hydrogen and gluconate under extremely low cell voltage, which can readily match with a variety of solar cells.

Complete chloroplast genome sequence of a Dutch cultivar of Chrysanthemum, Chrysanthemum morifolium 'Orizaba' (Asteraceae).

The complete plastid genome of Chrysanthemum morifolium 'Orizaba', a cultivar from Holland, was determined and analyzed in this work. It is a circular chromosome and has a length of 151,060 bp. The LSC and SSC of 82,858 bp and 18,294 bp were separated by two IRs of 24,954 bp. The chloroplast genome of C. morifolium 'Orizaba' contains 125 genes, including 83 protein-coding genes, eight ribosomal RNA genes, and 34 transfer RNA genes. Phylogenetic analysis showed that C. morifolium 'Orizaba' clustered together with other Chrysanthemum varieties in the family Asteraceae. The plastome is useful for the elucidation of phylogenetics and evolution in the Asteraceae and Chrysanthemum varieties.

Complete chloroplast genome sequence of a Chinese traditional cultivar in Chrysanthemum, Chrysanthemum morifolium 'Anhuishiliuye'.

The complete plastid genome of Chrysanthemum morifolium 'Anhuishiliuye', a Chinese traditional cultivar, was determined and analyzed in this work. It had a circular-mapping molecular with the length of 151,059 bp.The LSC and SSC of 82,857 bp and 18,294 bp were separated by two IRs of 24,954 bp. The chloroplast genome of C. morifolium 'Anhuishiliuye' contains 125 genes, including 83 protein-coding genes, 34 ribosomal RNA genes and 8 transfer RNA genes. Phylogenetic analysis showed that C. morifolium 'Anhuishiliuye' clustered together with other Chrysanthemum species. The data provided would be useful for elucidation of phylogenetics and evolution in Chrysanthemum cultivars.

Morning glory species co-occurrence is associated with asymmetrically decreased and cascading reproductive isolation.

Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are (1) the expectation that asymmetric hybridization or gene flow will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within-species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from highly selfing Ipomoea lacunosa into mixed-mating Ipomoea cordatotriloba in regions where they co-occur. Because of the direction of this gene flow, we predicted that reproductive barrier strength would be more strongly affected in I. cordatotriloba than I. lacunosa. We also predicted that changes to reproductive barriers in sympatric I. cordatotriloba populations would affect compatibility with allopatric populations of that species. We tested these predictions by measuring the strength of a reproductive barrier to seed set across the species' ranges. Consistent with our first prediction, we found that sympatric and allopatric I. lacunosa produce the same number of seeds in crosses with I. cordatotriloba, whereas crosses between sympatric I. cordatotriloba and I. lacunosa are more successful than crosses between allopatric I. cordatotriloba and I. lacunosa. This difference in compatibility appears to reflect an asymmetric decrease in the strength of the barrier to seed set in sympatric I. cordatotriloba, which could be caused by I. lacunosa alleles that have introgressed into I. cordatotriloba. We further demonstrated that changes to sympatric I. cordatotriloba have decreased its ability to produce seeds with allopatric populations of the same species, in line with our second prediction. Thus, in a manner analogous to cascade reinforcement, we suggest that introgression associated with hybridization not only influences between-species isolation but can also contribute to isolation within a species.

Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes.

Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.

Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis.

The phylogeographic histories of plants in East Asia are complex and shaped by both past large-scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping-by-sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among-population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.