The fall armyworm (Spodoptera frugiperda) is a lepidopteran insect pest that causes huge economic losses. This notorious insect pest has rapidly spread over the world in the past few years. However, ...the mechanisms of rapid dispersal are not well understood. Here, we report a chromosome‐level assembled genome of the fall armyworm, named the ZJ‐version, using PacBio and Hi‐C technology. The sequenced individual was a female collected from the Zhejiang province of China and had high heterozygosity. The assembled genome size of ZJ‐version was 486 Mb, containing 361 contigs with an N50 of 1.13 Mb. Hi‐C scaffolding further assembled the genome into 31 chromosomes and a portion of W chromosome, representing 97.4% of all contigs and resulted in a chromosome‐level genome with scaffold N50 of 16.3 Mb. The sex chromosomes were identified by genome resequencing of a single male pupa and a single female pupa. About 28% of the genome was annotated as repeat sequences, and 22,623 protein‐coding genes were identified. Comparative genomics revealed the expansion of the detoxification‐associated gene families, chemoreception‐associated gene families, nutrition metabolism and transport system gene families in the fall armyworm. Transcriptomic and phylogenetic analyses focused on these gene families revealed the potential roles of the genes in polyphagia and invasion of fall armyworm. The high‐quality of the fall armyworm genome provides an important genomic resource for further explorations of the mechanisms of polyphagia and insecticide resistance, as well as for pest management of fall armyworm.
SUMMARY
The section Oleifera (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome‐scale genome of the sect. Oleifera ...using diploid wild Camellia lanceoleosa with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. Camellia lanceoleosa underwent a whole‐genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of C. lanceoleosa and Camellia sinensis (approx. 6–7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in C. lanceoleosa were significantly enriched in oil biosynthesis, and the expansion of homomeric acetyl‐coenzyme A carboxylase (ACCase) genes and the seed‐biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde‐3‐phosphate dehydrogenase and stearoyl‐ACP desaturase could be of primary importance for the high oil and oleic acid content found in C. lanceoleosa. Theanine and catechins were present in the leaves of C. lanceoleosa. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM‐dependent N‐methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late‐acting self‐incompatibility of C. lanceoleosa is likely to have favoured a novel mechanism co‐occurring with gametophytic self‐incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. Oleifera.
Significance Statement
Section Oleifera in the genus Camellia attracts considerable attention because the seeds produce edible oils with abundant unsaturated fatty acids. Our study uncovered the genome information of sect. Oleifera with diploid wild Camellia lanceoleosa, elucidated the genomic rearrangement between C. lanceoleosa and Camellia sinensis, and performed analyses of oil biosynthesis, caffeine distribution and self‐incompatibility in C. lanceoleosa.
SUMMARY
Coumarins are natural products with important medicinal values, and include simple coumarins, furanocoumarins and pyranocoumarins. Female ginseng (Angelica sinensis) is a renowned herb with ...abundant coumarins, originated in China and known for the treatment of female ailments for thousands of years. The molecular basis of simple coumarin biosynthesis in A. sinensis and the evolutionary history of the genes involved in furanocoumarin biosynthesis are largely unknown. Here, we generated the first chromosome‐scale genome of A. sinensis. It has a genome size of 2.37 Gb, which was generated by combining PacBio and Hi‐C sequencing technologies. The genome was predicted to contain 43 202 protein‐coding genes dispersed mainly on 11 pseudochromosomes. We not only provided evidence for whole‐genome duplication (WGD) specifically occurring in the Apioideae subfamily, but also demonstrated the vital role of tandem duplication for phenylpropanoid biosynthesis in A. sinensis. Combined analyses of transcriptomic and metabolomic data revealed key genes and candidate transcription factors regulating simple coumarin biosynthesis. Furthermore, phylogenomic synteny network analyses suggested prenyltransferase genes involved in furanocoumarin biosynthesis evolved independently in the Moraceae, Fabaceae, Rutaceae and Apiaceae after ζ and ε WGD. Our work sheds light on coumarin biosynthesis, and provides a benchmark for accelerating genetic research and molecular breeding in A. sinensis.
Significance Statement
The genomic resources of Angelica sinensis in this study will facilitate efficient germplasm exploration, facilitate comparative and functional genomics studies, and the improvement of A. sinensis for medicinal uses, especially for the specific production of bioactive molecules in planta.
The brown planthopper Nilaparvata lugens, white‐backed planthopper Sogatella furcifera, and small brown planthopper Laodelphax striatellus are three major insect pests of rice. They are genetically ...close; however, they differ in several ecological traits such as host range, migration capacity, and in their sex chromosomes. Though the draft genome of these three planthoppers have been previously released, the quality of genome assemblies need to be improved. The absence of chromosome‐level genome resources has hindered in‐depth research of these three species. Here, we performed a de novo genome assembly for N. lugens to increase its genome assembly quality with PacBio and Illumina platforms, increasing the contig N50 to 589.46 Kb. Then, with the new N. lugens genome and previously reported S. furcifera and L. striatellus genome assemblies, we generated chromosome‐level scaffold assemblies of these three planthopper species using HiC scaffolding technique. The scaffold N50s significantly increased to 77.63 Mb, 43.36 Mb and 29.24 Mb for N. lugens, S. furcifera and L. striatellus, respectively. To identify sex chromosomes of these three planthopper species, we carried out genome re‐sequencing of males and females and successfully determined the X and Y chromosomes for N. lugens, and X chromosome for S. furcifera and L. striatellus. The gene content of the sex chromosomes showed high diversity among these three planthoppers suggesting the rapid evolution of sex‐linked genes, and all chromosomes showed high synteny. The chromosome‐level genome assemblies of three planthoppers would provide a valuable resource for a broad range of future research in molecular ecology, and subsequently benefits development of modern pest control strategies.
SUMMARY
Wurfbainia villosa is a well‐known medicinal and edible plant that is widely cultivated in the Lingnan region of China. Its dried fruits (called Fructus Amomi) are broadly used in traditional ...Chinese medicine for curing gastrointestinal diseases and are rich in volatile terpenoids. Here, we report a high‐quality chromosome‐level genome assembly of W. villosa with a total size of approximately 2.80 Gb, 42 588 protein‐coding genes, and a very high percentage of repetitive sequences (87.23%). Genome analysis showed that W. villosa likely experienced a recent whole‐genome duplication event prior to the W. villosa–Zingiber officinale divergence (approximately 11 million years ago), and a recent burst of long terminal repeat insertions afterward. The W. villosa genome enabled the identification of 17 genes involved in the terpenoid skeleton biosynthesis pathway and 66 terpene synthase (TPS) genes. We found that tandem duplication events have an important contribution to the expansion of WvTPSs, which likely drove the production of volatile terpenoids. In addition, functional characterization of 18 WvTPSs, focusing on the TPS‐a and TPS‐b subfamilies, showed that most of these WvTPSs are multi‐product TPS and are predominantly expressed in seeds. The present study provides insights into the genome evolution and the molecular basis of the volatile terpenoids diversity in W. villosa. The genome sequence also represents valuable resources for the functional gene research and molecular breeding of W. villosa.
Significance Statement
The present study reports a high‐quality chromosome‐level reference genome of Wurfbainia villosa with comprehensive genomic, transcriptomic, and metabolic analyses, as well as the identification and functional characterization of 66 terpene synthase (TPS)‐encoding genes, which can provide insights into the molecular genetic basis of the diversity and abundance of volatile terpenoids.
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.
Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, ...the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high‐quality chromosome‐level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein‐coding genes annotated. Two rounds of recent independent whole‐genome duplication (WGD) were revealed. Numerous genes from the recent species‐specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.
The bean bug (Riptortus pedestris) causes great economic losses of soybeans by piercing and sucking pods and seeds. Although R. pedestris has become the focus of numerous studies associated with ...insect–microbe interactions, plant–insect interactions, and pesticide resistance, a lack of genomic resources has limited deeper insights. Here, we report the first R. pedestris genome at the chromosomal level using PacBio, Illumina, and Hi‐C technologies. The assembled genome was 1.080 Gb in size with a contig N50 of 2.882 Mb. More than 96.3% of the total genome bases were successfully anchored to six unique chromosomes. Genome resequencing of male and female individuals and chromosomic staining demonstrated that the sex chromosome system of R. pedestris is XO, and the shortest chromosome is the X chromosome. In total, 19,026 protein‐coding genes were predicted, 18,745 of which were validated as being expressed. Temporospatial expression of R. pedestris genes in six tissues and 37 development stages revealed 4,657 and 7,793 genes mainly expressed in gonads and egg periods, respectively. Evolutionary analysis demonstrated that R. pedestris and Oncopeltus fasciatus formed a sister group and split ∼80 million years ago (Mya). Additionally, a 5.04 Mb complete genome of symbiotic Serratia marcescens Rip1 was assembled, and the virulence factors that account for successful colonization in the host midgut were identified. The high‐quality R. pedestris genome provides a valuable resource for further research, as well as for the pest management of bug pests.
Largemouth bass (LMB; Micropterus salmoides) has been an economically important fish in North America, Europe, and China. This study obtained a chromosome‐level genome assembly of LMB using PacBio ...and Hi‐C sequencing. The final assembled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chromosomal fusion event. LMB is phylogenetically closely related to European seabass and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass species. Eight gene families comprising 294 genes associated with ionic regulation were identified through positive selection, transcriptome and genome comparisons. These genes involved in iron facilitated diffusion (such as claudin, aquaporins, sodium channel protein and so on) and others related to ion active transport (such as sodium/potassium‐transporting ATPase and sodium/calcium exchanger). The claudin gene family, which is critical for regulating cell tight junctions and osmotic homeostasis, showed a significant expansion in LMB with 27 family members and 68 copies for salinity adaptation. In summary, we reported the first high‐quality LMB genome, and provided insights into the molecular mechanisms of LMB adaptation to fresh and brackish water. The chromosome‐level LMB genome will also be a valuable genomic resource for in‐depth biological and evolutionary studies, germplasm conservation and genetic breeding of LMB.
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