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Glebionis coronaria is a popular vegetable with special aroma and a medical plant in East Asia and Mediterranean, but its biological studies and breeding have been hindered by the lack of reference genome. Here, we present a chromosome-level reference genome of G. coronaria, with assembled genome size of 6.8 Gb, which is the largest among all the published genomes of diploid Asteraceae species. The large genome size of G. coronaria is mainly caused by the recent widespread explosions of long-terminal-repeat retrotransposons. Analyses of macro-synteny and synonymous mutation rate distribution indicate that the G. coronaria genome experienced a whole-genome triplication at 40–45 million years ago, shared with all Asteraceae species. In subtribe Artemisiinae, Glebionis arose before the divergence of Chrysanthemum from Artemisia, and Glebionis species evolved much faster than Chrysanthemum and Artemisia species. In G. coronaria, the synthesis genes of monoterpenoids 8-oxocitronellyl enol and isopiperitenone were expanded, and the higher expressions of these expanded genes in leaves and stems may contribute to its special aroma. The G. coronaria genomic resources will promote the evolution studies of Asteraceae, the metabolism mechanism studies of bioactive compounds, and the breeding improvement of agronomic traits in G. coronaria.

Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first reference genome for the subgenus Albersia, combining PacBio HiFi, Nanopore ultra-long and Hi–C data. The contig N50 size was 906 kb, and 99.58% of contig sequence was anchored to the 17 chromosomes, totalling 520 Mb. We annotated 27,813 protein-coding genes with an average 1.3 kb coding sequence and 5.3 exons. We inferred that A. tricolor underwent a whole-genome duplication (WGD) and that the WGD shared by amaranths occurred in the last common ancestor of subfamily Amaranthoideae. Moreover, we comprehensively identified candidate genes in betalain biosynthesis pathway. Among them, DODAα1 and CYP76ADα1, located in one topologically associated domain (TAD) of an active (A) compartment on chromosome 16, were more highly expressed in red leaves than in green leaves, and DODAα1 might be the rate-limiting enzyme gene in betalains biosynthesis. This study presents new genome resources and enriches our understanding of amaranth evolution, betalains production, facilitating molecular breeding improvements and the understanding of C4 plants evolution.

Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical, and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by Pacific Biosciences HiFi and Hi-C sequencing, with the assembly size of 733.0 Mb, the contig N50 of 43.8 Mb, the scaffold N50 of 45.7 Mb, and the Benchmarking Universal Single-Copy Orthologs complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere to telomere. The transposable element content of Ipomoea cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the Benchmarking Universal Single-Copy Orthologs complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that Ipomoea cairica formed a clade with Ipomoea aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of Ipomoea cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness.

Inulin is an important reserve polysaccharide in Asteraceae plants, and is also widely used as a sweetener, a source of dietary fibre and prebiotic. Nevertheless, a lack of genomic resources for inulin-producing plants has hindered extensive studies on inulin metabolism and regulation. Here, we present chromosome-level reference genomes for four inulin-producing plants: chicory (Cichorium intybus), endive (Cichorium endivia), great burdock (Arctium lappa) and yacon (Smallanthus sonchifolius), with assembled genome sizes of 1.28, 0.89, 1.73 and 2.72 Gb, respectively. We found that the chicory, endive and great burdock genomes were shaped by whole genome triplication (WGT-1), and the yacon genome was shaped by WGT-1 and two subsequent whole genome duplications (WGD-2 and WGD-3). A yacon unique whole genome duplication (WGD-3) occurred 5.6-5.8 million years ago. Our results also showed the genome size difference between chicory and endive is largely due to LTR retrotransposons, and rejected a previous hypothesis that chicory is an ancestor of endive. Furthermore, we identified fructan-active-enzyme and transcription-factor genes, and found there is one copy in chicory, endive and great burdock but two copies in yacon for most of these genes, except for the 1-FEH II gene which is significantly expanded in chicory. Interestingly, inulin synthesis genes 1-SST and 1-FFT are located close to each other, as are the degradation genes 1-FEH I and 1-FEH II. Finally, we predicted protein structures for 1-FFT genes to explore the mechanism determining inulin chain length.

Background Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads. Results We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the “RNA complete” criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes. Conclusions HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host–microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.

Background The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings. Findings We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution. Conclusions The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.

Background Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood. Findings In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination. Conclusions This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.

Apolygus lucorum (Miridae) is an omnivorous pest that occurs worldwide and is notorious for the serious damage it causes to various crops and substantial economic losses. Although some studies have examined the biological characteristics of the mirid bug, no reference genome is available in Miridae, limiting in-depth studies of this pest. Here, we present a chromosome-scale reference genome of A. lucorum, the first sequenced Miridae species. The assembled genome size was 1.02 Gb with a contig N50 of 785 kb. With Hi-C scaffolding, 1,016 Mb contig sequences were clustered, ordered and assembled into 17 large scaffolds with scaffold N50 length 68 Mb, each corresponding to a natural chromosome. Numerous transposable elements occur in this genome and contribute to the large genome size. Expansions of genes associated with omnivorousness and mesophyll feeding such as those related to digestion, chemosensory perception, and detoxification were observed in A. lucorum, suggesting that gene expansion contributed to its strong environmental adaptability and severe harm to crops. We clarified that a salivary enzyme polygalacturonase is unique in mirid bugs and has significantly expanded in A. lucorum, which may contribute to leaf damage from this pest. The reference genome of A. lucorum not only facilitates biological studies of Hemiptera as well as an understanding of the damage mechanism of mesophyll feeding, but also provides a basis on which to develop efficient control technologies for mirid bugs.

Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. However, in molluscs, the second most diverse group, the existence of HGT is still controversial. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation. Based on the phylogenetic topologies, ten HGT genes were identified to have been transferred into the possible molluscan ancestor, possibly before its radiation. Furthermore, most of the donor organisms were predicted to be familiar bacteria in marine environments. These horizontally transferred genes were under a strong negative selection and could be transcribed in octopus functionally. The predicted biochemical functions of these genes include metabolism, neurotransmission, immune defense and tissue integrity. Seven Zn-metalloproteinases were validated as the main type of HGT genes in octopus with divergent motif composition, intron presence and phylogenetic relationship to the endogenous ones. Furthermore, the functions of Zn-metalloproteinase were predicted to be responsible for immune defense and tissue remolding. Three HGT genes were distributed mainly in the nervous system and were predicted to regulate the neurotransmission through glia-neuronal interactions. The results collectively indicated the existence of HGT in molluscs and its potential contribution to the evolution of octopus with regards to functional innovation and adaptability.

Whole-genome duplication (WGD) has been observed across a wide variety of eukaryotic groups, contributing to evolutionary diversity and environmental adaptability. Mollusks are the second largest group of animals, and are among the organisms that have successfully adapted to the nonmarine realm through aquatic-terrestrial (A-T) transition, and no comprehensive research on WGD has been reported in this group. To explore WGD and the A-T transition in Mollusca, we assembled a chromosome-level reference genome for the giant African snailAchatina immaculata, a global invasive species, and compared the genomes of two giant African snails (A. immaculataandAchatina fulica) to the other available mollusk genomes. The chromosome-level macrosynteny, colinearity blocks, Ks peak and Hox gene clusters collectively suggested the occurrence of a WGD event shared byA. immaculataandA. fulica. The estimated timing of this WGD event (∼70 MYA) was close to the speciation age of the Sigmurethra-Orthurethra (within Stylommatophora) lineage and the Cretaceous-Tertiary (K-T) mass extinction, indicating that the WGD reported herein may have been a common event shared by all Sigmurethra-Orthurethra species and could have conferred ecological adaptability and genomic plasticity allowing the survival of the K-T extinction. Based on macrosynteny, we deduced an ancestral karyotype containing 8 conserved clusters for the Gastropoda-Bivalvia lineage. To reveal the mechanism of WGD in shaping adaptability to terrestrial ecosystems, we investigated gene families related to the respiration, aestivation and immune defense of giant African snails. Several mucus-related gene families expanded early in the Stylommatophora lineage, functioning in water retention, immune defense and wound healing. The hemocyanins, PCK and FBP families were doubled and retained after WGD, enhancing the capacity for gas exchange and glucose homeostasis in aestivation. After the WGD, zinc metalloproteinase genes were highly tandemly duplicated to protect tissue against ROS damage. This evidence collectively suggests that although the WGD may not have been the direct driver of the A-T transition, it provided an important legacy for the terrestrial adaptation of the giant African snail.

In this work, two different liquid charging methods are designed to use in different pump-assisted capillary phase change loops. The aim of present work is to investigate the impact of the liquid charging processes on the operational characteristics of the loop. For the two pump-assisted capillary loops, the loop structure and the main parameters of the components keep the same. In addition, methanol is used as the working fluid in both loops. The experimental results demonstrate that the vaporization temperature of the loop 2 has a notable decrease due to the optimized liquid charging process. The corresponding thin film boiling in the evaporator of loop 2 occurs even though a lower heat load is applied. Meanwhile, with a high heat load applied to loop 2, the unique vapor superheating in the vapor chamber is observed. Comparing the heat transfer performance between the loops, the loop 2 presents a superior capability at low heat loads, while loop 1 can transfer a higher heat load for the upper bound of the heater surface temperature. For both of the loops, the evaporator thermal resistance, if not included the heat load of 10 W at a pumping power of 2 W in loop 2, varies between 0.15 K/W and 0.3 K/W.

Background The golden apple snail (Pomacea canaliculata) is a freshwater snail listed among the top 100 worst invasive species worldwide and a noted agricultural and quarantine pest that causes great economic losses. It is characterized by fast growth, strong stress tolerance, a high reproduction rate, and adaptation to a broad range of environments. Results Here, we used long-read sequencing to produce a 440-Mb high-quality, chromosome-level assembly of the P. canaliculata genome. In total, 50 Mb (11.4%) repeat sequences and 21,533 gene models were identified in the genome. The major findings of this study include the recent explosion of DNA/hAT-Charlie transposable elements, the expansion of the P450 gene family, and the constitution of the cellular homeostasis system, which contributes to ecological plasticity in stress adaptation. In addition, the high transcriptional levels of perivitelline genes in the ovary and albumen gland promote the function of nutrient supply and defense ability in eggs. Furthermore, the gut metagenome also contains diverse genes for food digestion and xenobiotic degradation. Conclusions These findings collectively provide novel insights into the molecular mechanisms of the ecological plasticity and high invasiveness.

Figure S21. The influences of CTC and MCE on the hindgut microbial functions. The heatmap of KEGG metabolic pathways in hindgut (12 samples for each group, including 6 samples from AA chickens and 6 samples from LY chickens). The relative abundance of each pathway was colored according to its row z-score ((value – row mean)/row standard deviation). Black and white rectangles at the right side of the heatmap represent the significant decrease (P 0.05) compared to BLANK, respectively. The Kruskal-Wallis test (Storey’s methods for adjustment) was used followed by a post-hoc Wilcoxon rank-sum test. (PDF 256 kb)

Figure S4. The NMDS plot of the chicken, human and pig gut samples based on Bray-Curtis dissimilarities at KO level. (PDF 900 kb)

Figure S10. Microbial gene functional differences between foregut and hindgut though eggNOG annotation (Wilcoxon rank-sum test, Storeyâ s methods for multiple tests adjustment). (PDF 812 kb)

Figure S5. Microbial community compositions of the duodenum, jejunum, ileum, cecum, and colorectum across 495 chicken gut samples. (a) Phylum-level compositions. (b) Genus-level compositions. â Othersâ refers to all the other phyla or genera in the samples (unclassified not included). (PDF 429 kb)

Figure S2. Functional annotation of gut microbial genes based on KEGG orthologous groups (KOs) and eggNOG orthologous groups (OGs). (a) Comparison of the total gene numbers and the functionally annotated gene numbers of the chicken, human and pig catalogs. (b) Comparison of the number of KOs and OGs presented in the chicken, human and pig catalogs. (PDF 165 kb)

Figure S6. The NMDS plot of foregut samples in five Distribution groups (DGY, DHC, DHK, DSL, DST) based on Bray-Curtis dissimilarities at the species level. (PDF 887 kb)

Figure S3. Venn diagram of eggNOG orthologous groups (OGs) presented in and shared by the chicken, human and pig catalogs. (PDF 103 kb)