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The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole-genome duplications, which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its three-dimensional chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.

The Aloe species is known for its medicinal and cosmetic properties. Aloin is an active ingredient found in the leaves of medicinal plants of the genus Aloe. Aloin has attracted considerable interest for its antiinflammatory, anticancer, antibacterial, and antioxidant activities. However, since its clinical application is restricted by its unclear mechanism of action, a deeper understanding of its pharmacological activity is required. This review provides an overview of current pharmacological and toxicological studies published in English from February 2000 to August 2021. Herein, we summarized the sources and potential health benefits of aloin from a clinical application perspective to guide for further studies on the sources of aloin, aimed at efficiently increasing aloin production. Importantly, the function and mechanism of action of aloin remain unclarified. In future research, it is necessary to develop new approaches for studying the pharmacological molecular mechanisms underlying the activity of this compound against various diseases.

We have successfully demonstrated quasi-aligned 3C-SiC nanoarrays with tiny cobalt nanotips as new-type hetero-structure based field emitters, which thus offer the superior field emission properties with much lower turn-on field.

Salvia bowleyana is a traditional Chinese medicinal plant that is a source of nutritional supplements rich in salvianolic acid B and a potential experimental system for the exploration of salvianolic acid B biosynthesis in the Labiatae. Here, we report a high-quality chromosome-scale genome assembly of S. bowleyana covering 462.44 Mb, with a scaffold N50 value of 57.96 Mb and 44,044 annotated protein-coding genes. Evolutionary analysis revealed an estimated divergence time between S. bowleyana and its close relative S. miltiorrhiza of ~3.94 million years. We also observed evidence of a whole-genome duplication in the S. bowleyana genome. Transcriptome analysis showed that SbPAL1 (PHENYLALANINE AMMONIA-LYASE1) is highly expressed in roots relative to stem and leaves, paralleling the location of salvianolic acid B accumulation. The laccase gene family in S. bowleyana outnumbered their counterparts in both S. miltiorrhiza and Arabidopsis thaliana, suggesting that the gene family has undergone expansion in S. bowleyana. Several laccase genes were also highly expressed in roots, where their encoded proteins may catalyze the oxidative reaction from rosmarinic acid to salvianolic acid B. These findings provide an invaluable genomic resource for understanding salvianolic acid B biosynthesis and its regulation, and will be useful for exploring the evolution of the Labiatae.

As a popular traditional fermented beverage, kombucha has been extensively studied for its health benefits. However, the science behind the anti-inflammatory effect of kombucha has not been well studied, and there is an urgent need to uncover the secrets of the anti-inflammatory properties of kombucha. Here, we investigate kombucha's protective effects against lipopolysaccharide (LPS)-induced sepsis and on the intestinal microecology in mice. The contents of reducing sugars, polyphenols, catechins, and organic acids in the kombucha group were identified using various methods. The results showed that the concentrations of acetic acid, gluconic acid, polyphenol, and glucuronic acid in the kombucha group were 55.70 ± 2.57 g L-1, 50.20 ± 1.92 g L-1, 2.36 ± 0.31, and 1.39 ± 0.22 g L-1, respectively. The result also demonstrated that kombucha effectively improves the survival rate from 0% to 40%, and increases the thermoregulation in LPS-treated mice, which showed decreased mobility and had lost their appetite for food. Furthermore, kombucha reduced the levels of tumor necrosis factor-α and interleukins (IL)-1β and IL-6, restored the levels of T cells and macrophages in LPS-challenged mice, alleviated the histopathological damage, and inhibited NF-κB signaling in mice with LPS-induced sepsis. We demonstrated that kombucha effectively prevents cellular immune function disorder in mice at the initial stage of sepsis and exerts an immunomodulatory effect. In addition, the effect of kombucha on the gut microbiota was investigated during sepsis. Kombucha supplementation altered the diversity of the gut microbiota and promoted the growth of butyrate-producing bacteria, which exert anti-inflammatory effects. Our results illustrate the potential of kombucha as a novel anti-inflammatory agent against the development of systemic inflammatory responses associated with sepsis.

Although nanostructured materials have recently enabled a dramatic improvement of the current energy-storage units in portable electronics with enhanced functionality, it is still challenging to provide a cost-efficient solution to attain the ultrahigh energy and power densities of supercapacitors (SCs) since nearly arbitrary electrodes are limited to the thinner porous structure with de facto rather low mass loading (∼1 mg cm-2) because of the huge limitations of pronounced impaired ion transport in subnanometer pores in thicker compact electrodes. In this contribution, we report the fabrication of a macro/mesoporous hybrid hierarchical nanocomposite SiC/holey-graphene/holey-MnO2 (SiC/HG/h-MnO2) with tailored porosity by knitting together the quasi-aligned single-crystalline doped 3C-SiC nanowire array and in situ surface-reduced holey graphene framework into a three-dimensional quasi-ordered structure, which enables the mass growth of ultrathin h-MnO2 nanosheets at approximately practical levels of mass loading. The produced synergistically favorable interconnected porous architecture allows for the highly efficient electron transfer and rapid ion transport up to interior surfaces of the network. Remarkably, the all-solid-state flexible asymmetric supercapacitors (ASCs) made with SiC/HG/h-MnO2 and SiC/graphitic carbon (GC) nanoarrays are mechanically robust and show a high areal capacity (0.32 mWh cm-2) and a high rate capability (280 mW cm-2) at ultrahigh mass loading (6.5 mg cm-2), much higher than most of previous superior SCs in aqueous or gelled electrolytes and thus offer an entirely new prototype of textile-based ASCs, which represents a critical step toward practical applications for various portable electronics.

Transglutaminase-catalyzed reactions can be used widely to modify the functional properties of food proteins, biopharmaceuticals and in tissue engineering. Transglutaminase-producing organisms obta...

The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation, and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes, and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.

Sapindus mukorossi is an environmentally friendly plant and renewable energy source whose fruit has been widely used for biomedicine, biodiesel, and biological chemicals due to its richness in saponin and oil contents. Here, we report the first chromosome-scale genome assembly of S. mukorossi (covering ~391 Mb with a scaffold N50 of 24.66 Mb) and characterize its genetic architecture and evolution by resequencing 104 S. mukorossi accessions. Population genetic analyses showed that genetic diversity in the southwestern distribution area was relatively higher than that in the northeastern distribution area. Gene flow events indicated that southwest species may be the donor population for the distribution areas in China. Genome-wide selective sweep analysis showed that a large number of genes are involved in defense responses, growth and development, including SmRPS2, SmRPS4, SmRPS7, SmNAC2, SmNAC23, SmNAC102, SmWRKY6, SmWRKY26, and SmWRKY33. We also identified several candidate genes controlling six agronomic traits by genome-wide association studies, including SmPCBP2, SmbHLH1, SmCSLD1, SmPP2C, SmLRR-RKs, and SmAHP. Our study not only provides a rich genomic resource for further basic research on Sapindaceae woody trees but also identifies several economically significant genes for genomics-enabled improvements in molecular breeding.

There is a high potential for coal spontaneous combustion (CSC) above the roof beams of supports during the mining-stopped period. Early detection of temperature abnormal zones and corresponding measures are necessary to prevent CSC. In this work, a top-coal temperature measurement method was proposed, combining the coal surface temperature detection and the drilling temperature observation. Furthermore, an apparatus was developed that dramatically increases the rate of dry ice sublimation, resulting in the rapid release of cryogenic carbon dioxide gas. The device utilizes water from firefighting pipes in underground coal mines as a heat source for dry ice sublimation without electrical energy and has been applied and validated taking Silaogou Coal Mine in China as a field test site. Specifically, we found that during the stoppage period, the coal above the supports near the air inlet tunnel is more likely to appear hot spots; the carbon dioxide gas generated by the dry ice phase change device can quickly reduce the hot spots temperature, and the coal temperature does not rebound after the gas injection is stopped. Based on the above analysis, this work can effectively prevent the early top-coal spontaneous combustion during the stop mining period.

Chitooligosaccharide is a kind of functional food, which is the degradation product of chitosan (COS) catalyzed by the endo-chitosanase (COSE) enzyme. A COSE with a molecular weight of 34 kDa was purified and characterized from a newly isolated Mitsuaria sp. C4 (C4), and a 38.46% recovery rate and 4.79-fold purification were achieved. The purified C4 COSE exhibited optimum activity at 40°C and pH 7.2 and was significantly inhibited in the presence of Cu2+ and Fe3+. The Km and Vmin of the COSE toward COS were 2.449 g/L and 0.042 g/min/L, respectively. The highest COSE activity reached 8.344 U/ml after optimizing, which represented a 1.34-fold of increase. Additionally, chitooligosaccharide obtained by COSE hydrolysis of COS was verified by using thin-layer chromatography and high-performance liquid chromatography analysis. Whole-genome sequencing demonstrated that the C4 strain contains 211 carbohydrate enzymes, our purified COSE belonging to GHs-46 involved in carbohydrate degradation. Phylogenetic analysis showed that the novel COSE obtained from the C4 strain was clustered into the degree of polymerization = two to three groups, which can perform catalysis in a similar manner to produce (GlcN)2 and (GlcN)3. This work indicates that the C4 strain could be a good resource for enhancing carbohydrate degradation and might represent a useful tool for chitooligosaccharide production in the functional food industry.

A pedunculate barnacle Capitulum mitella (Linnaeus, 1758) is a dominant intertidal cirripede (Lee et al., 2000). C. mitella distribute in the mid- and high-intertidal zone of tropical and subtropical coasts and is common in the East Sea and South Sea of China. C. mitella has a great commercial value in China, the petiole muscle of which has been a source of traditional delicious seafood (Yuan et al., 2016). The local market demand led to high-intensity catching activity, and this behavior caused significant decrease in quantity and habitat destruction in recent years. Artificial aquaculture of fishery resources will help to reduce overexploitation of natural stocks and meet market needs for fishery products. In general, the barnacle life cycle consists of six nauplius instars and a nonfeeding cyprid instar. In the barnacle life history, the cyprid is a transitory phase between the pelagic and sessile lifestyle. The cyprid role is responsible for locating, exploring, and attaching to a suitable substratum; subsequently, a complex metamorphosis and permanent settlement happen (Lagersson and Hoeg, 2002). Cypris attachment and metamorphosis are also known as “cypris settlement” (Clare and Matsumura, 2000; Franco et al., 2016). The cypris settlement is a crucial event for the survival and development of both adults and subsequent generations. Within the last three decades, the basic biology of C. mitella such as reproductive characteristics, sperm ultrastructure, and larval culture conditions was investigated in our lab. C. mitella cyprids have been cultured on a relatively large scale. However, they cannot attach and metamorphose into juveniles in an artificial environment, so they would die eventually and interrupt their life history. In recent years, the cypris morphology of C. mitella has been depicted minutely using SEM (Rao and Lin, 2014). After we had successfully induced metamorphosis of the C. mitella cyprids into juveniles, we described a time line and specific morphological changes during the metamorphosis under microscopy and SEM (Lin and Rao, 2017). The impacts of external (i.e., water temperature and salinity) and internal (i.e., cyprid age) factors on the metamorphosis of C. mitella were researched (Rao and Lin, 2020). These efforts are possible for completing the life history in an artificial environment and aquaculture of C. mitella. Not only is the artificial aquaculture for C. mitella a production activity but also it helps to reduce the stress on overexploited populations. Barnacles are frequently dominant marine foulings and widely distributed around the world that play crucial roles in marine ecology (Marechal and Hellio, 2011). Recently, there are a few transcriptome researches on barnacles, such as a model animal Amphibalanus amphitrite (Chen et al., 2011; Yan et al., 2012; Chandramouli et al., 2015; Sarah et al., 2016), a giant barnacle Megabalanus volcano (Yan et al., 2017) and a stalked barnacle Neolepas marisindica (Ryu et al., 2019). These efforts showed that the transcriptome databases could greatly promote the research on molecular mechanisms of barnacle settlement. Genome sequencing has been performed for an acorn barnacle Amphibalanus amphitrite, but there is still no genome sequencing information for a stalked barnacle. Numerous reports on C. mitella were mainly related to mitochondrial DNA sequencing and quantitative proteomics analyses (Song and Yoon, 2013; Yoon et al., 2013; Yuan et al., 2016; Tian et al., 2020). So far, no genome literature on the C. mitella is available. Whereas a lack of genome information on the barnacles has obstructed further inquiry on the molecular mechanisms with development, attachment, metamorphosis, genetic evolution, and so on, so does on C. mitella. Accordingly, in this study, we aimed to sequence and assemble the genome of C. mitella. The baseline data obtained from this study will be very useful in taxonomical identification, phylogenetic analysis, larval settlement mechanisms, artificial breeding and aquaculture, and species protection for C. mitella.

Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals of humans because of its high fucoxanthin (Fx) content. However, multi-omics analysis of the regulation networks for Fx biosynthesis in I. galbana has not been reported. In this study, we report a high-quality genome sequence of I. galbana LG007, which has a 92.73 Mb genome size, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenomic inferences confirmed the monophyly of Haptophyta, with I. galbana sister to Emiliania huxleyi and Chrysochromulina tobinii. Evolutionary analysis revealed an estimated divergence time between I. galbana and E. huxleyi of ∼ 133 million years ago (Mya). Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, including IgPLMT, IgOAR1, and IgDEGS1. Metabolome analysis showed that the content of carotenoids in I. galbana cultured under green light for 7 days was higher than that of white light, and β-carotene was the main carotenoid, accounting for 79.09% of the total carotenoids. Comprehensive analysis of multi-omics analysis revealed that β-carotene, antheraxanthin, zeaxanthin, and Fx content was increased by green light induction, which was significantly correlated with the expression of IgMYB98, IgZDS, IgPDS, IgLHCX2, IgZEP, IgLCYb, and IgNSY. These findings contribute to understanding Fx biosynthesis and its regulation, providing a valuable reference for food and pharmaceutical applications.

Fucoxanthin and eicosapentaenoic acid (EPA) are high-value compounds that can be found in the marine diatom Phaeodactylum tricornutum. Yet, the growth rate of this microalga is relatively low under photoautotrophic conditions. The purpose of this study was to evaluate the feasibility of using spent yeast, the second-major by-product of the brewing industry, as a useful substrate for P. tricornutum cultivation. Different pretreatments, concentrations of spent yeast, and initial cell densities of P. tricornutum were investigated. After 12 days of cultivation in f/2 medium, P. tricornutum supplemented with 1.33 g L−1 preautoclaved spent yeast yielded 3.28 times more fucoxanthin (5.97 mg L−1) and 3.55 times more EPA (16.82 mg L−1) than P. tricornutum grown without the yeast (fucoxanthin 1.82 mg L−1, EPA 4.64 mg L−1). Nutrient analysis showed that the nitrogen and phosphorus released by the spent yeast were consumed over time. Overall, spent yeast effectively promoted the fucoxanthin and EPA yields of P. tricornutum.

With the rapid development of lightweight, portable, and even wearable electronics, there is an increasing demand for flexible supercapacitors with excellent electrochemical performance. Here, we present the design and preparation of a novel architecture with SnO2 dots uniformly confined on the activated porous carbon nanofibers (CNFs) using copper and its oxides as the hard templates for generating holes. Not only does the single electrode itself with a certain loading mass of SnO2 show larger specific capacitance, better rate capability, and higher conductivity than the bare CNFs and activated CNFs/SnO2 electrodes, but the assembled quasi-solid-state symmetric supercapacitor also exhibits good flexibility as well as superior electrochemical property with satisfactory energy density and favorable cycling stability, which indicates the great potential for practical applications. This work may provide a versatile and low-cost strategy to construct carbon/metal oxide nanostructures with robust binding force at the interface for adhesive-free supercapacitors.

Despite the great progress in genome editing in the model organism Saccharomyces cerevisiae, regulating the carbon flux to ethanol in the ethanol metabolic pathway to achieve high ethanol yield and productivity remains a challenge. Here, we developed an efficient strategy for single-step, high-efficiency, simultaneous multiple gene disruptions in S. cerevisiae based on the CRISPR/Cas9 system. Three genes, the alcohol dehydrogenase (ADH) 2 gene, the glycerol-3-phosphate dehydrogenase (GPD) 1 gene, and the aldehyde dehydrogenase (ALD) 4 gene, were disrupted singly and combinatorially with efficiency ranging from 80 to 100%. We applied our genome engineering tool to explore all possible single, double, and triple gene disruption combinations to search for strains with high ethanol production. This exploratory analysis identified strains with ethanol production at least 1.41-fold greater than that of the wild-type strain. Our study illustrates the applicability of this highly efficient multiplex genome engineering approach for genome editing and the regulation of metabolic flux in S. cerevisiae.

Ethanol tolerance involves complex interactions of several genes in the Saccharomyces cerevisiae genome that encodes proteins that are the subunits of the SAGA (Spt-Ada-Gcn5-acetyltransferase) comp...

Isochrysis galbana is an important producer in the aquatic ecosystem because of its rich fucoxanthin content and fast growth. However, little is known about its evolutionary adaptation to live in a specific, complex and harsh environment. We report a high-quality genome sequence of I. galbana LG007, which has a 92.73 Mb genome size, a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenomic inferences confirmed the monophyly of Haptophyta, showing I. galbana is a sister to E. huxleyi and C. tobinii. Evolutionary analysis revealed an estimated divergence of I. galbana from its close relative E. huxleyi ~133 million years ago, and I. galbana underwent one round of whole-genome duplication. Genes related to environmental adaptation and metabolic regulation in I. galbana were relatively conserved, but the basic transcriptional regulation toolkit for terrestrial plant development has been contracted or was not detected. The domain identification of one novel fucoxanthin biosynthesis gene that encodes diadinoxanthin-fucoxanthin hydroxylase (DFH) was investigated. Comparative genomic analysis revealed that I. galbana acquired several transcription factors specific to the control of pigment accumulation and production of LHCX2 to harvest blue-green light, which facilitates adaptation to the underwater environment. These findings provide new insights into the genomic characteristics of I. galbana and algae evolution for adaptation to blue-green light underwater.

Background The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. Results In this study, a total of more than 74 million Illumina reads for progenitor ‘Sunset’ were mapped onto transgenic papaya ‘SunUp’ reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between ‘Sunset’ and ‘SunUp’. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4 × 10− 4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. A total of 3430 nuclear plastid DNA (NUPT) and 2764 nuclear mitochondrial DNA (NUMT) junction sites have been found in ‘SunUp’, which is proportionally higher than the predicted total NUPT and NUMT junction sites in ‘Sunset’ (3346 and 2745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by ‘SunUp’ and ‘Sunset’. The average identity between ‘SunUp’ specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by ‘SunUp’ and ‘Sunset’. Six ‘SunUp’ organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18 ~ 100%). None of the paired-end spans of mapped ‘Sunset’ reads were elongated by any ‘SunUp’ transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions. Conclusions Comparative whole-genome analyses between ‘SunUp’ and ‘Sunset’ provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.

Schizochytrium sp. is the best natural resource for omega-3 long-chain polyunsaturated fatty acids. We report a high-quality genome sequence of Schizochytrium limacinum SR21, which has a 63 Mb genome size, with a contig N50 of 2.67 Mb and 6,838 protein-coding genes. Phylogenomic and comparative genomic analyses revealed that DHA-producing Schizochytrium and Aurantiochytrium strains were highly similar and possessed similar genes. Analysis of the fatty acid synthase (FAS) for LC-PUFAs production results in the annotation of all genes in map00062 and map01212. A gene cluster and 10 ORFs related to PKS pathway were found in the genome. 1,402 differentially expressed genes (DEGs) of the treated groups (0.5 g/L yeast extract) were identified by comparing with the control groups (1.0 g/L yeast extract) at 36 h. A weighted gene coexpression network analysis revealed that 2 of 7 modules correlated highly with the fatty acid and DHA contents. The DEGs and transcription factors were significantly correlated with fatty acid biosynthesis, including MYB, Zinc Finger and ACOX. The results showed that these hub genes are regulated by genes involved in fatty acid biosynthesis pathways. The results providing an important reference for further research on promoting fatty acid and DHA accumulation in S. limacinum SR21.

Background In this study, renewable tea waste hydrolysate was used as a sole carbon source for carotenoids and lipid production. A novel Rhodosporidium toruloides mutant strain, RM18, was isolated through atmospheric and room-temperature plasma mutagenesis and continuous domestication in tea waste hydrolysate from R. toruloides ACCC20341. Results RM18 produced a larger biomass and more carotenoids and α-linolenic acid compared with the control strain cultured in tea waste hydrolysate. The highest yields of torularhodin (481.92 μg/g DCW) and torulene (501 μg/g DCW) from RM18 cultured in tea waste hydrolysate were 12.86- and 1.5-fold higher, respectively, than that of the control strain. In addition, α-linolenic acid production from RM18 in TWH accounted for 5.5% of total lipids, which was 1.58 times more than that of the control strain. Transcriptomic profiling indicated that enhanced central metabolism and terpene biosynthesis led to improved carotenoids production, whereas aromatic amino acid synthesis and DNA damage checkpoint and sensing were probably relevant to tea waste hydrolysate tolerance. Conclusion Tea waste is suitable for the hydrolysis of microbial cell culture mediums. The R. toruloides mutant RM18 showed considerable carotenoids and lipid production cultured in tea waste hydrolysate, which makes it viable for industrial applications.

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes. The assembled genome size was close to the estimated size, and 659.42 Mb of the assembly was assigned to 29 superscaffolds (scaffold N50 21.22 Mb). A total of 59.20% repetitive sequences were identified, among which long terminal repeats (LTRs) were the most abundant class (28.97% of the genome). Genome evolution analysis suggested that the divergence time of Cladopus chinensis (106 Mya) was earlier than that of Malpighiales (82 Mya) and that this taxon diverged into an independent branch of Podestemales. A recent whole-genome duplication (WGD) event occurred 4.43 million years ago. Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation, photosynthesis and isoflavonoid metabolism genes in Cladopus chinensis are probably related to the genomic characteristics of this growing submerged species. Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses, including WUSCHEL (WUS), ASYMMETRIC LEAVES (ASL), SHOOT MERISTEMLESS (STM), NAC2, NAC8, NAC29, NAC47, NAC73, NAC83 and NAC102. These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae.

Additional file 1: Table S1. Distribution of structural variations on nine pseudomolecules of papaya.

Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish-the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.

Additional file 5: Figure S1. Chromosomal and genome-wide distribution of the frequency of A. SNP/InDels B. SNPs and C. InDels per 1 kb in the Sunset genome compared to the SunUp reference genome.

Additional file 6: Figure S2. Transitions and transversions of homo and hetero SNPs identified in the Sunset genome compared to the SunUp reference genome. A. Frequency of different nucleotide substitution types in homo and hetero SNPs. B. Numbers and percentages of transitions (Ts) and transversions (Tv), and the Ts/Tv ratio in homo/hetero SNPs and total SNPs.