Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution

As one of the largest families of angiosperms,the Orchidaceae family is diverse.Dendrobium represents the second largest genus of the Orchidaceae.However,an assembled high-quality genome of species in this genus is lacking.Here,we report a chromosome-scale reference genome of Dendrobium chrysotoxum,an important ornamental and medicinal orchid species.The assembled genome size of D.chrysotoxum was 1.37 Gb,with a contig N50 value of 1.54 Mb.Of the sequences,95.75%were anchored to 19 pseudochromosomes.There were 30,044 genes predicted in the D.chrysotoxum genome.Two whole-genome polyploidization events occurred in D.chrysotoxum.In terms of the second event,whole-genome duplication(WGD)was also found to have occurred in other Orchidaceae members,which diverged mainly via gene loss immediately after the WGD event occurred;the first duplication was found to have occurred in most monocots(tau event).We identified sugar transporter(SWEET)gene family expansion,which might be related to the abundant medicinal compounds and fleshy stems of D.chrysotoxum.MADS-box genes were identified in D.chrysotoxum,as well as members of TPS and Hsp90 gene families,which are associated with resistance,which may contribute to the adaptive evolution of orchids.We also investigated the interplay among carotenoid,ABA,and ethylene biosynthesis in D.chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers.The reference D.chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.

Correction: The Cymbidium genome reveals the evolution of unique morphological traits

After online publication of the article 1 the author noticed minor typo in Fig.4c.CeSEP1/2/3/4 should be read as CeSEP1/3/4.Revised figure supplied during the proof correction was inadvertently not reproduced in the final version.In addition,the affiliation numbers of the authors revised in the original article during proof correction,but not reflected in the title page in Supplementary Information.

The Cymbidium genome reveals the evolution of unique morphological traits

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms.The genus Cymbidium in Orchidaceae is well known for its unique vegetation,floral morphology,and flower scent traits.Here,a chromosomescale assembly of the genome of Cymbidium ensifolium(Jianlan)is presented.Comparative genomic analysis showed that C.ensifolium has experienced two whole-genome duplication(WGD)events,the most recent of which was shared by all orchids,while the older event was the t event shared by most monocots.The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation,and flower shape mutations in C.ensifolium were shown to be associated with the abnormal expression of MADS-box genes.The most abundant floral scent components identi fied included methyl jasmonate,acacia alcohol and linalool,and the genes involved in the floral scent component network of C.ensifolium were determined.Furthermore,the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves,while the increased expression of MADS-box genes in leaves led to perianth-like leaves.Our results provide fundamental insights into orchid evolution and diversi fication.

Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm

The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors that shape and maintain genetic diversity.Here,we assembled a high-quality chromosome-level reference of the Chinese common apricot‘Yinxiangbai’,and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries.We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries.We also detected seven migration events among different apricot groups,where 27%of the genome was identified as being introgressed.Remarkably,we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups.Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.

The genome sequence of star fruit(Averrhoa carambola)

Oxalidaceae is one of the most important plant families in horticulture,and its key commercially relevant genus,Averrhoa,has diverse growth habits and fruit types.Here,we describe the assembly of a high-quality chromosomescale genome sequence for Averrhoa carambola(star fruit).Ks distribution analysis showed that A.carambola underwent a whole-genome triplication event,i.e.,the gamma event shared by most eudicots.Comparisons between A.carambola and other angiosperms also permitted the generation of Oxalidaceae gene annotations.We identified unique gene families and analyzed gene family expansion and contraction.This analysis revealed significant changes in MADS-box gene family content,which might be related to the cauliflory of A.carambola.In addition,we identified and analyzed a total of 204 nucleotide-binding site,leucine-rich repeat receptor(NLR)genes and 58 WRKY genes in the genome,which may be related to the defense response.Our results provide insights into the origin,evolution and diversification of star fruit.

The Cymbidium goeringii genome provides insight into organ development and adaptive evolution in orchids

Cymbidium goeringii is one of the important ornamental orchids,but its high-quality genome has not been previously published.Here,we report a chromosome-level genome of C.goeringii and report the gene family expansion,and contraction of the C.goeringii genome and the regulation mechanism of MADS-box genes in floral organ development.We constructed the pathways of carotenoids and anthocyanins that contribute to the different flower colors of C.goeringii and the metabolic pathways of the main components of flower fragrance.Moreover,we found the genes that regulate colourful leaves and analyzed the resistance genes involved in the adaptive evolution of C.goeringii.Our results provide valuable genomic resources for the improvement of orchids and other ornamental plants.

Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism

Orchidaceae(with>28,000 orchid species)are one of the two largest plant families,with economically and ecologically important species,and occupy global and diverse niches with primary distribution in rainforests.Among orchids,70%grow on other plants as epiphytes;epiphytes contribute up to~50%of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes,thereby contributing to the health of these ecosystems.Orchids account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of epiphytism.Extensive phylogenetic studies of Orchidaceae and subgroups have;been crucial for understanding relationships among many orchid lineages,although some uncertainties remain.For example,in the largest subfamily Epidendroideae with nearly all epiphytic orchids,relationships among some tribes and many subtribes are still controversial,hampering evolutionary analyses of epiphytism.Here we obtained 1,450 low-copy nuclear genes from 610 orchid species,including 431 with newly generated transcriptomes,and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and subtribes.We also provide generally wellsupported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies.Molecular clock analyses estimated the Orchidaceae origin at~132 million years ago(Ma)and divergences of most subtribes from 52 to 29 Ma.Character reconstruction supports at least 14 parallel origins of epiphytism;one such origin was placed at the most recent common ancestor of~95%of epiphytic orchids and linked to modern rainforests.Ten occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary,contributing to~80%of the Orchidaceae diversity.This study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and new insights into the evolution of epiphytism in vascular plants.

Methodology for credibility assessment of historical global LUCC datasets

Land use-induced land cover change(LUCC)is an important anthropogenic driving force of global change that has influenced,and is still influencing,many aspects of regional and global environments.Accurate historical global land use/cover datasets are essential for a better understanding of the impacts of LUCC on global change.However,there are not only evident inconsistencies in current historical global land use/cover datasets,but inaccuracies in the data in these global dataset revealed by historical record-based reconstructed regional data throughout the world.A focus in historical LUCC and global change research relates to how the accuracy of historical global land cover datasets can be improved.A methodology for assessing the credibility of existing historical global land cover datasets that addresses temporal as well as spatial changes in the amount and distribution of land cover is therefore needed.Theoretically,the credibility of a global land cover dataset could be assessed by comparing similarities or differences in the data according to actual land cover data(the"true value").However,it is extremely difficult to obtain historical evidence for assessing the credibility of historical global land cover datasets,which cannot be verified through field sampling like contemporary global land cover datasets.We proposed a methodological framework for assessing the credibility of global land cover datasets.Considering the types and characteristics of the available evidence used for assessments,we outlined four methodological approaches:(1)accuracy assessment based on regional quantitative reconstructed land cover data,(2)rationality assessment based on regional historical facts,(3)rationality assessment based on expertise,and(4)likelihood assessment based on the consistency of multiple datasets.These methods were illustrated through five case studies of credibility assessments of historical cropland cover data.This framework can also be applied in assessments of other land cover types,such as forest and grassland.

The Melastoma dodecandrum genome and the evolution of Myrtales

Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum,Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.

The camphor tree genome enhances the understanding of magnoliid evolution

Magnoliids represent the third largest branch of the most diverse and species-rich angiosperms,and their phylogenetic position relative to monocots and eudicots remains uncertain(Dong et al.,2021).Here,we describe the assembly of a high-quality chromosome-level genome sequence for Cinnamomum camphora(camphor),an evergreen tree belonging to Lauraceae.Genomebased phylogenetic analysis indicated possible incomplete lineage sorting(ILS)during the rapid diversification of the early diverging branches of angiosperms,which may have led to the unstable phylogenetic position of magnoliids.