Multi‐Omics Analysis of the Response of Angelica sinensis to Alfalfa Mosaic Virus Infection

Alfalfa (Medicago sativa L.) is one of the most widely cultivated forage crops in the world. China is the second largest producer of alfalfa in terms of the planting area worldwide, with Gansu, Henan, Inner Mongolia, and Shaanxi provinces being the production hubs. Alfalfa viruses have been reported on a small-scale survey in some of these areas, but they have not been well characterized. In the present study, seven viruses were detected in 12 fields of 10 cities/counties of the four abovementioned provinces by high-throughput sequencing and assembly of small RNA. Their incidence, distribution, and genetic diversity were analyzed by enzyme-linked immunosorbent assay, polymerase chain reaction (PCR)/reverse transcription-PCR and clone sequencing. The results showed that alfalfa mosaic virus (AMV), pea streak virus (PeSV), lucerne transient streak virus (LTSV), alfalfa dwarf virus (ADV), Medicago sativa alphapartitivirus 1 (MsAPV1), MsAPV2, and alfalfa leaf curl virus (ALCV) were the main viruses infecting alfalfa in four examined provinces. AMV and MsAPV1 had the highest incidences in all 4 provinces. SDT analysis of the 7 viruses isolated in China revealed a highly conserved among AMV, LTSV, ADV, MsAPV1, MsAPV2, and ALCV, but the sequence was a high variation between China isolates to abroad isolates in PeSV, ADV, and ALCV. To our knowledge, this is the first report of ADV in Inner Mongolia and Gansu, ALCV in Inner Mongolia, MsAPV1 and MsAPV2 in all 4 provinces, and PeSV and LTSV in China. These findings provide a basis for future research on the genetic evolution of alfalfa viruses in China and on strategies to prevent diseases in alfalfa caused by these viruses.

The growing number of protein sequences in databases has lead to, among other issues, an increase in redundancy, since many of the new sequences are similar to others already in the databases. While a comprehensive view of the protein space is essential, redundancy hampers large scale searches (such as BLAST) or studies (comparative genomics, functional genomics). One of the solutions to eliminate redundancy in the protein space is through clustering methods, which group redundant proteins into single entities (clusters).In this work we present BOLOS, a web tool that combines a clustered protein space with molecular function GO term annotations, directed for functional genomics. It allows searches over the cluster space with a raw sequence, a Swiss-Prot protein or a molecular function GO term, and provides three GO-based parameters which allow the assessment of cluster quality and biological validity. The user can also chose one of the twelve different significance level cluster spaces available. For each cluster, BOLOS provides the essential information (name and accession number) about proteins and GO terms it contains, as well as relevant statistics, while linking to external databases to allow the users to access further information. BOLOS is available at: http://xldb.di.fc.ul.pt/biotools/bolos/

The present study provides comparative transcriptome analysis, besides identifying functional secondary metabolite genes of Plumbago zeylanica with pharmacological potential for future functional genomics, and metabolomic engineering of secondary metabolites from this plant towards diversified biomedical applications. Plumbago zeylanica is a widely used medicinal plant of the traditional Indian system of medicine with wide pharmacological potential to treat several disorders. The present study aimed to carry out comparative transcriptome analysis in leaf and root tissue of P. zeylanica using Illumina paired end sequencing to identify tissue-specific functional genes involved in the biosynthesis of secondary metabolites, contributing to its therapeutic efficacy. De novo sequencing assembly resulted in the identification of 62,321 "Unigenes" transcripts with an average size of 1325bp. Functional annotation using BLAST2GO resulted in the identification of 50,301 annotated transcripts (80.71%) and GO assigned to 18,814 transcripts. KEGG pathway annotation of the "Unigenes" revealed that 2465 transcripts could be assigned to 242 KEGG pathway maps wherein the number of transcripts involved in secondary metabolism was distinct in root and leaf transcriptome. Among the secondary metabolite biosynthesis pathways, the cluster of "Unigenes" encoding enzymes of 'Phenylpropanoid biosynthesis pathway' represents the largest group (84 transcripts) followed by 'Terpenoid Backbone biosynthesis' (48 transcripts). The transcript levels of the candidate unigenes encoding key enzymes of phenylpropanoid (PAL, TAL) and flavanoid biosynthesis (CHS, ANS, FLS) pathways were up-regulated in root, while the expression levels of candidate "Unigenes" transcript for monoterpenoid (DXS, ISPF), diterpenoid biosynthesis (SPS, SDS) and indole alkaloid pathways (STR) were significantly higher in leaf of P. zeylanica. Interestingly, validation of differential gene expression profile by qRT-PCR also confirmed that candidate "Unigenes" enzymes of phenylpropanoid and flavonoid biosynthesis were highly expressed in the root, while the key regulatory enzymes of terpenoid and indole alkaloid compounds were up-regulated in the leaf, suggesting that (differences in) the levels of these functional genes could be attributed to the (differential) pharmacological activity (between root and leaf) in tissues of P. zeylanica.

Extraction and purification of ferulic acid from flax shives, wheat and corn bran by alkaline hydrolysis and pressurised solvents

OsGSTU34, a Bz2-like anthocyanin-related glutathione transferase transporter, is essential for rice (Oryza sativa L.) organs coloration

Introduction: Improving stratification of breast cancer (BC) patients based on molecular signatures for treatment responses and clinical outcomes is a critical unmet need. Currently, endocrine therapy is first-line for hormone receptor positive (HR+) BC. Chemotherapy is added to patients with high-risk luminal BC. In practice, levels of Ki-67 are used to distinguish luminal tumors as low-risk luminal A (LA) and high-risk luminal B (LB) for adjuvant therapy decisions. Herein, proteomic tumor assessment from ER-positive HER2-negative (ER+/HER2-) BC patients was utilized to define molecular subtyping, estimate congruency between proteomic subtyping and traditionally used Ki67 marker, and define a new set of potential predictive and prognostic therapeutic biomarkers for ER+/HER2- BC patients. Method/Result: Clinical immunohistochemistry (IHC) subtyping of core biopsies was used to select a cohort of 86 BC patients with ER+/HER2- primary tumors from flash-frozen surgical samples. The positive/negative status of ER/PR/HER2 was defined using updated ASCO 2020 guidelines. Ki-67 status was determined using the 2011 St. Gallen’s International Expert Consensus recommendations. The cohort includes 28 LA (Ki67 < 14%) cases and 58 LB1 (Ki67 >= 14%) cases. Integrated consensus clustering algorithms with the most varying proteins in our cohort were applied to identify proteomic subtypes. Two distinct separations were observed from the analysis, resulting in one cluster enriched with LA (40 cases) and the other enriched with LB1 (46 cases) called by Fisher’s exact test. These clusters matched 100% with the clusters generated using 900+ proteins common to the 1500+ proteins used in the CPTAC-BC proteomics-based subtyping analysis (Mertins et al. Nature 2016). The differential analyses demonstrated that there is no significant difference between Ki67-defined subtypes and proteomics-defined subtypes (LA-enriched vs. LA cases, LB1-enriched vs. LB1 cases),indicating they are consistent in the molecular profile. Differential analysis was performed to compare LB1-enriched versus LA-enriched cases, resulting in 672 significantly differentially expressed proteins defined at false discovery rate (FDR) < 0.05 and |log2(fold change)|>1. 353 of the 672 proteins were correlated with mRNA at Pearson correlation > 0.39 as reported in the CPTAC-BC study or cBioPortal for Cancer Genome, and their coding genes were used for progression free interval (PFI) analysis based on TCGA RNA-seq data in the TCGA ER+/HER2- cases (662 cases, c.f. Huo et al. JAMA Oncology 2017). 90 of the 353 coding genes significantly associated with PFI were detected at p-value<0.05. Unsupervised hierarchical clustering method and principal component analysis (PCA) of the 90 genes were applied to our cohort to investigate the clustering performance and 94.2% of the cases were clustered correctly using support vector machine (SVM) method after PCA analysis. Biological process and molecular function GO term over-representation analyses of the 90 coding genes were performed separately. Some significant and biologically meaningful GO terms were identified at FDR<0.05. Conclusions: We identified a set of biomarkers that can be potentially employed as proteomic or gene signatures to stratify ER+/HER2- BC into low risk and high-risk groups. Disclaimers The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions, or policies of Uniformed Services University of the Health Sciences, The Henry M Jackson Foundation for the Advancement of Military Medicine Inc., the Department of Defense or the Departments of the Army, Navy or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Guisong Wang, Punit Shah, Rick Searfoss, J. Leigh Fantacone Campbell, Jeffrey A. Hooke, Brenda Deyarmin, Rebecca N. Zingmark, Stella Somiari, Jianfang Liu, Leonid Kvecher, Lori A. Sturtz, Praveen-Kumar Raj-Kumar, Elder Granger, Linda Vahdat, Mary L. Cutler, Rangaprasad Sarangarajan, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Niven R. Narain, Craig D. Shriver. Identification of proteomics-based biomarkers for ER+/HER2- breast cancer stratification: Implications on clinical outcome [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-34.

Tea production and quality are largely determined by the many genetic and biochemical characteristics that occur in tea plant cultivars. Worldwide, tea is consumed for its pleasing and refreshing effects due to its caffeine content. The present study performed transcriptomics analyses of two tea species (Camellia sinensis var. Shuchazao (SCZ) and Camellia ptilophylla (CAF)) and identified diversity in the gene expression levels and major regulatory transcription factors (TFs) for the characterization of purine alkaloids and phenylpropanoid biosynthesis pathways. The RNA-seq analysis of two species (SCZ and CAF) revealed the differences in caffeine and catechins synthesis. In the purine alkaloid biosynthesis pathway, the S-adenosyl methionine (SAM) and adenosine monophosphate (AMP) pathway genes were significantly related to xanthosine synthesis in contrasting purine alkaloids among (Camellia sinensis var. Shuchazao (SCZ) and Camellia ptilophylla (CAF)). The significant expression of SAMS-5, PPAT-2, IMPDH-2, TCS-2, TCS-3, XMT-1, XMT-13, and XDH-4 in the xanthosine degradation pathway in CAF is attributed to higher theobromine content as compared to SCZ. Moreover, the transcription factors (TFs) AP2/ERF (20%), WRKY (12%), NAC (11%), and MYB (8%) were significantly correlated. The upregulated expression of caffeine synthesis genes in SCZ was correlated with MYB and AP2/ERF transcription factors. This study provides the basis for differences in the genetic mechanism in purine alkaloids, phenylpropanoid, and flavonoid biosynthesis pathways, which would be helpful in the development and selection of tea plant species with high or low caffeine concentrations. This study also provides a road map for future genetic improvement in tea species and cultivars.

Ferulic acid (FA) is a phenolic substance widespread in plants and exhibiting a wide range of potential therapeutic effects, such as antimicrobial and anti-inflammatory, and useful in the treatment of diabetes, lung and cardiovascular diseases. Methanol extracts from the fresh leaves of 40 species from the Lamiaceae family growing in the outdoor collections of the Botanical Garden of the Komarov Botanical Institute of the Russian Academy of Sciences (BIN RAS, Saint-Petersburg) and the experimental station “Otradnoye” BIN RAS (Leningrad region) have been investigated. Ferulic acid was detected in 18 species under investigation, related to the subfamilies Lamioideae Harley (Betonica grandiflora Willd., Galeobdolon luteum Huds., Lamium album L., Sideritis taurica Steph. ex Willd., Stachys byzantine K. Koch) and Nepetoideae Kostel. (Clinopodium vulgare L., Hyssopus officinalis L., Lavandula angustifolia Mill., Meechania urticifolia (Miq.) Makino, Melissa officinalis L., Mentha piperita L., Monarda didyma L., Nepeta bucharica Lipsky, N. grandiflora M. Bieb., Origanum vulgare L., Prunella laciniata (L.) L., Salvia desertum L., Salvia officinalis L., Thymus serpillum L.). Ferulic acid was not detected in the representatives of Ajugoideae Kostel. and Scutellarioideae Caruel subfamilies. For 7 species, FA was detected for the first time. The content of FA in the representatives of Lamiaceae subfamily varied within a broad range from 0.01±0.00 mg/g (Meechania urticifolia) to 6.68±1.30 mg/g (Melissa officinalis L.). The high ferulic acid content was established in the Nepetoideae subfamilty in the species Melissa officinalis (6.68±1.30 mg/g) and Origanum vulgare L. (6.07±1.90 mg/g).

Phenolic acids are secondary metabolic organic compounds produced by plants and often are mentioned as allelochemicals. This study was conducted to determine the genetic basis controlling the ferulic acid content of rice straw in a recombinant inbred (RI) population derived from a cross between a japonica variety, Asominori, with a higher content of ferulic acid, and an indica variety, IR24, with a lower content, using 289 RFLP markers. Continuous distributions and transgressive segregations of ferulic acid content were observed in the RI population, which showed that ferulic acid content in rice straw was quantitatively inherited. Single marker analysis and composite interval mapping identified three quantitative trait loci (QTLs) for ferulic acid content with LOD values of 2.03 (chromosome 3), 3.16 (chromosome 6), and 3.06 (chromosome 7); all three had increased additive effects (13.5, 18.3, and 18.1 microg g(-1)) from the Asominori parent and accounted for 5.5, 16.9, and 12.8% of total phenotypic variation, respectively. This is the first report on the identification of QTLs associated with ferulic acid and their chromosomal localization on the molecular map of rice. The tightly linked molecular markers that flank the QTLs might be useful in breeding and selection of varieties with higher phenolic acid content.

Alfalfa (Medicago sativa L.) is one of the most important leguminous forage crops globally and has grown in importance in China with ∼4.72 million hectares in 2015. A previous study reported the occurrence of several common viruses (e.g., alfalfa mosaic virus [AMV], white clover mosaic virus, bean yellow mosaic virus, and cowpea mosaic virus) in alfalfa fields in China, in Anning District and Gaolan County of Lanzhou, and Jingtai County of Baiyin City, Gansu Province (Zhou et al. 2016). In April 2017 a survey was conducted to identify viruses infecting alfalfa in a temperate region: Yuanyang County, Henan Province (N35°01′, E113°43′). From one field, 117 alfalfa leaf samples with symptoms of macular mosaic (n = 26), mottle mosaic (21), etiolation (1), shrinkage (27), mosaic shrinkage (25), and dwarfism (17) were collected. Total RNA was extracted from a composite sample comprising six leaves exhibiting each above-mentioned symptom using an EASYspin Plant Micro RNA Rapid Extraction Kit (Aidlab Biotechnologies, Beijing, China) following the manufacturer’s guidelines. The RNA was then subjected to high-throughput sequencing of small RNA to detect any viruses using the Illumina Hiseq4000 platform at Biomarker Technologies (Beijing, China). Over 20 million clean reads between 18 and 35 nt were obtained. Using Velvet 1.0 software (Zerbino and Birney 2008), 6,942 contigs from 33 to 416 nt were assembled. Although the majority of the contigs were mapped to the host genome, 58, 13, and 10 contigs were mapped to AMV (Alfamovirus, Bromoviridae, reference sequences [RSs] AMV-RNA1 NC_001495, AMV-RNA2 NC_002024, and AMV-RNA3 NC_002025), alfalfa dwarf virus (ADV, Rhabdovirus, Rhabdoviridae, RS KP205452), and alfalfa leaf curl virus (ALCV, Capulavirus, Geminiviridae, RS KX574859), respectively. The 10 projected ALCV contigs totaled 1,113 nt, accounting for 40.47% of the complete ALCV RS of 2,750 nt. The nucleotide sequence identity between these contigs and the ALCV RS ranged from 96 to 100%. Total DNA was then extracted from the composite sample using a New Plant Genomic DNA Rapid Extraction Kit (Aidlab Biotechnologies) following the manufacturer’s guidelines. The presence of ALCV in the pooled sample was confirmed by PCR using an ALCV-specific primer pair, ALCV-1F 5′-TGGAATATTGTGCTGCTTGG-3′ and ALCV-1R 5′-ATTTTGGGACTTGTGCTCCA-3′ (Roumagnac et al. 2015), and subsequent cloning and Sanger sequencing. The 785-nt-long amplicon, deposited in GenBank as MK422439, exhibited a sequence identity of 96% to the ALCV RS. To further confirm the result, the full genome of ALCV in the pooled sample was amplified by fusion PCR using improved primer pair ALCV-F 5′-CCCTGGCCTGCTAAAGTGGCCCAATTCAACATGG-3′ and ALCV-R 5′-CCAGGGGGCCTTATTCCTCTGGGACCG-3′ adapted from Bernardo et al. (2016), cloned, and sequenced. The complete 2,750-bp sequence was deposited in GenBank as MK422438. BLASTn analysis indicated the sequence shared 90 and 98% identity with previously reported ALCV isolates from France (KT214370) (Roumagnac et al. 2015) and Argentina (MG792039) (Bejerman et al. 2018), respectively, thus confirming the ALCV identity of the virus. To reveal whether ALCV was associated with the symptoms, all samples were subjected to PCR with the primer pair ALCV-1F/ALCV-1R. ALCV was detected in 38 of 117 samples: in 8 of 26 samples with macular mosaic, 5 of 21 with mottle mosaic, 11 of 27 with shrinkage, 8 of 25 with mosaic shrinkage, and 6 of 17 with dwarfism, but not in the single plant showing etiolation. Interestingly, AMV was detected in the pooled sample as well as all 117 individual samples by RT-PCR, whereas ADV failed to be detected by RT-PCR in any of the samples. These results demonstrated that ALCV was present in alfalfa in China, and it often coinfected alfalfa plants with AMV. This is the first report of ALCV infecting alfalfa in China. The distribution of ALCV within alfalfa-growing regions, the identity of potential virus reservoirs, and the economic impact have yet to be determined. The results help expand understanding of this virus and help in selection of virus-free propagation material for resistant breeding of alfalfa and production of high-quality forage.

Halyomorpha halys (Stål) (Heteroptera: Pentatomidae), the brown marmorated stink bug, is an invasive agricultural and nuisance pest rapidly expanding its incidence in North America. This voracious pest poses a significant threat to rural and urban agriculture, especially to specialty crops such as apples, grapes and ornamentals, as well as staple crops including soybean and corn. The object of this study was to generate transcript sequence resources for H. halys. RNA-seq libraries derived from distinct developmental stages and sexes were sequenced and assembled into 248,569 putatively unique transcripts (PUTs). PUTs were segmented into three disjoint tiers of varying reliability, with 4,794 classified as gold tier (highest quality), 16,878 as silver, and 14,357 as bronze. The gold-tier PUTs associated with 2,580 distinct non-redundant protein sequences from the NCBI NR database—1,785 of these (69%) mapped to annotated UniProtKB database proteins, from which 1,273 unique Pfam families and 459 unique Molecular Function GO terms were encountered. Of the silver tier's 6,527 PUTs associated with unique proteins, 4,193 mapped to UniProtKB (64%), from which 1,941 and 640 unique Pfam and Molecular Function GO terms were extracted. H. halys PUTs related to important life processes like immunity, endocrinology, reproduction, development, behavior, neurotransmission, neurotoxicity, olfaction, and small RNA pathways were validated through quantitative Real-Time PCR (qRT-PCR) for differential expression during distinct life stages (eggs, 2nd instar nymphs, 4th instar nymphs, female adults, male adults). PUTs similar to hypothetical proteins identified in symbiont microbes, including Pantoea and Nosema species, were more abundantly expressed in adults versus nymphs. These comprehensive H. halys transcriptomic resources can be utilized to aid development of novel control methodologies to disrupt life processes; to conduct reverse genetic screens to determine host gene function; and to design environmentally unobtrusive means to control host populations or target specific H. halys life stages, such as molecular biopesticides.

Gummy stem blight (GSB) is a pervasive disease that causes considerable economic losses in cucurbit crops and poses a significant threat to pumpkin production. However, the molecular interaction mechanisms between pumpkin and the pathogen remain largely unexplored. In our previous research, we isolated and identified Stagonosporopsis cucurbitacearum (Sc) as the primary causative agent of pumpkin stem blight in Northeast China. Through whole-genome analysis, we identified several pathogenic genes associated with Sc infection in pumpkins. In this study, we performed a comprehensive comparative transcriptomic and metabolomic analysis of unvaccinated and Sc-inoculated pumpkins. We observed distinct differences in gene expression profiles, with these genes being significantly enriched in pathways related to plant-pathogen interactions, phytohormone signal transduction, and metabolic processes, including phenylpropanoid biosynthesis. Joint analysis revealed that the phenylpropanoid biosynthesis pathway was activated in Sc-infected pumpkins. Notably, two metabolites involved in the phenylpropanoid and flavonoid biosynthesis pathways, p-coumaric acid and quercetin, exhibited significant upregulation, suggesting their potential roles in conferring resistance to GSB. These findings enhance our understanding of the molecular mechanisms underlying the defense response against GSB infection in pumpkins and may provide valuable insights for developing strategies to control GSB disease.

4,8-dihydroxy-l-tetralone (4,8-DHT) is an allelochemical isolated from the outer bark of Carya cathayensis that acts as a plant growth inhibitor. In order to explore the mechanism of 4,8-DHT inhibiting weed activity, we treated three species of Digitaria sanguinalis, Arabidopsis thaliana, and Poa annua with different concentrations of 4,8-DHT and performed phenotype observation and transcriptome sequencing. The results showed that with an increase in 4,8-DHT concentration, the degree of plant damage gradually deepened. Under the same concentration of 4,8-DHT, the damage degree of leaves and roots of Digitaria sanguinalis was the greatest, followed by Arabidopsis thaliana, while Poa annua had the least damage, and the leaves turned slightly yellow. Transcriptome data showed that 24536, 9913, and 1662 differentially expressed genes (DEGs) were identified in Digitaria sanguinalis, Arabidopsis thaliana, and Poa annua, respectively. These DEGs were significantly enriched in photosynthesis, carbon fixation, glutathione metabolism, phenylpropanoid biosynthesis, and oxidative phosphorylation pathways. In addition, DEGs were also enriched in plant hormone signal transduction and the MAPK signal pathway in Arabidopsis thaliana. Further analysis showed that after 4,8-DHT treatment, the transcript levels of photosynthesis PSI- and PSII-related genes, LHCA/B-related genes, Rubisco, and PEPC were significantly decreased in Digitaria sanguinalis and Arabidopsis thaliana. At the same time, the transcription levels of genes related to glutathione metabolism and the phenylpropanoid biosynthesis pathway in Digitaria sanguinalis were also significantly decreased. However, the expression of these genes was upregulated in Arabidopsis thaliana and Poa annua. These indicated that 4,8-DHT affected the growth of the three plants through different physiological pathways, and then played a role in inhibiting plant growth. Simultaneously, the extent to which plants were affected depended on the tested plants and the content of 4,8-DHT. The identification of weed genes that respond to 4,8-DHT has helped us to further understand the inhibition of plant growth by allelochemicals and has provided a scientific basis for the development of allelochemicals as herbicides.

Phenylpropanoid biosynthesis and plant-pathogen interaction pathways in saffron and cell wall degrading enzymes in Fusarium oxysporum R1 are key players involved in the interaction. Fusarium oxysporum causes corm rot in saffron (Crocus sativus L.), which is one of the most devastating fungal diseases impacting saffron yield globally. Though the corm rot agent and its symptoms are known widely, little is known about the defense mechanism of saffron in response to Fusarium oxysporum infection at molecular level. Therefore, the current study reports saffron-Fusarium oxysporum R1 (Fox R1) interaction at the molecular level using dual a transcriptomics approach. The results indicated the activation of various defense related pathways such as the mitogen activated protein kinase pathway (MAPK), plant-hormone signaling pathways, plant-pathogen interaction pathway, phenylpropanoid biosynthesis pathway and PR protein synthesis in the host during the interaction. The activation of pathways is involved in the hypersensitive response, production of various secondary metabolites, strengthening of the host cell wall, systemic acquired resistance etc. Concurrently, in the pathogen, 60 genes reported to be linked to pathogenicity and virulence has been identified during the invasion. The expression of genes encoding plant cell wall degrading enzymes, various transcription factors and effector proteins indicated the strong pathogenicity of Fusarium oxysporum R1. Based on the results obtained, the putative molecular mechanism of the saffron-Fox R1 interaction was identified. As saffron is a male sterile plant, and can only be improved by genetic manipulation, this work will serve as a foundation for identifying genes that can be used to create saffron varieties, resistant to Fusarium oxysporum infection.

Cucurbita pepo is one of the earliest cultivated crops. It is native to Central and South America and is now widely cultivated all over the world for its rich nutrition, short growth period, and high yield, which make it suitable for intercropping. Hull-less C. pepo L. (HLCP) is a rare variant in nature that is easier to consume. Its seed has a seed kernel but lacks a seed coat. The molecular mechanism underlying the lack of seed coat development in the HLCP variety is not clear yet. The BGISEQ-500 sequencing platform was used to sequence 18 cDNA libraries of seed coats from hulled C. pepo (CP) and HLCP at three developmental stages (8, 18, and 28 days) post-pollination. We found that lignin accumulation in the seed coat of the HLCP variety was much lower than that of the CP variety. A total of 2,099 DEGs were identified in the CP variety, which were enriched mainly in the phenylpropanoid biosynthesis pathway, amino sugar, and nucleotide sugar metabolism pathways. A total of 1,831 DEGs were identified in the HLCP variety and found to be enriched mainly in the phenylpropanoid biosynthesis and metabolism pathways of starch and sucrose. Among the DEGs, hub proteins (FusA), protein kinases (IRAK4), and several transcription factors related to seed coat development (MYB, bHLH, NAC, AP2/EREBP, WRKY) were upregulated in the CP variety. The relative expression levels of 12 randomly selected DEGs were determined using quantitative real-time PCR analysis and found to be consistent with those obtained using RNA-Seq, with a correlation coefficient of 0.9474. We found that IRAK4 protein kinases, AP2/EREBP, MYB, bHLH, and NAC transcription factors may play important roles in seed coat development, leading to the formation of HLCP.