Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.frag...Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.fragrans to assist in studies of the evolution,genetic diversity,and molecular mechanism of aroma development.A total of over 118 Gb of polished reads was produced from HiSeq(45.1 Gb)and PacBio Sequel(73.35 Gb),giving 100×depth coverage for long reads.The combination of Illumina-short reads,PacBio-long reads,and Hi-C data produced the final chromosome quality genome of O.fragrans with a genome size of 727 Mb and a heterozygosity of 1.45%.The genome was annotated using de novo and homology comparison and further refined with transcriptome data.The genome of O.fragrans was predicted to have 45,542 genes,of which 95.68%were functionally annotated.Genome annotation found 49.35%as the repetitive sequences,with long terminal repeats(LTR)being the richest(28.94%).Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago,which contributed to the current content of 45,242 genes.Metabolic analysis revealed that linalool,a monoterpene is the main aroma compound.Based on the genome and transcriptome,we further demonstrated the direct connection between terpene synthases(TPSs)and the rich aromatic molecules in O.fragrans.We identified three new flower-specific TPS genes,of which the expression coincided with the production of linalool.Our results suggest that the high number of TPS genes and the flower tissue-and stage-specific TPS genes expressions might drive the strong unique aroma production of O.fragrans.展开更多
Alternative polyadenylation(APA)is a pervasive mechanism that is emerging as a formidable player in post-transcriptional regulation.The transcriptional landscape can be altered via APA in response to various stimulati...Alternative polyadenylation(APA)is a pervasive mechanism that is emerging as a formidable player in post-transcriptional regulation.The transcriptional landscape can be altered via APA in response to various stimulating factors.Using the Pac Bio single-molecule long-read sequencing method,we present for the first time the 3′UTR landscape and reveal a global increase of APA events in prostate cancer(PCa)LNCa P cells in response to androgen dihydrotestosterone(DHT),a critical regulator of PCa progression.With evidence from differential gene expression analyses of Illumina RNA-sequencing data,we demonstrated that genes with DHT-induced changes in both expression and APA were enriched in lipid metabolism.These genes predominantly supported de novo fatty acid synthesis,such as FASN and ACSL3.Furthermore,we showed that an isoform switch to the proximal poly(A)site of these genes depended on the androgen receptor,and the expression of cancer-associated genes was upregulated by the escape of mi RNA-regulated repression machinery.To address the role of key gene shortening in PCa,we prepared 22RV1-FS cells missing the distal poly(A)signal of FASN in the AR+PCa cell line 22RV1 using CRISPR/Cas9 technology.As expected,the edited 22RV1-FS cells overexpressed FASN m RNA and protein and were inclined to cell proliferation in vitro and tumorigenesis in vivo.Interestingly,we found that FASN transcripts with a shortened 3′UTR were significantly increased in advanced PCa and castration-resistant prostate cancer compared with benign prostate hyperplasia,suggesting a possible association between usage of the proximal poly(A)site and disease progression.Therefore,our study highlights the importance of the APA mechanism in response to DHT stimulation in PCa cells and provides a novel regulatory mechanism through which DHT-induced APA causes altered expression of de novo lipogenesis genes,with a possible association with the progression of PCa.展开更多
Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chr...Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were generated.After filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage depth.The de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 Mb.The vast majority(99.2%)of the G.elegans assembled sequence was anchored onto 8 pseudo-chromosomes.The genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the assembly.Genome annotation revealed that 43.16%of the G.elegans genome is composed of repetitive elements and 23.9%is composed of long terminal repeat elements.We predicted 26,768 protein-coding genes,of which 84.56%were functionally annotated.The genomic sequences of G.elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.展开更多
基金This work was supported by research grants provided by the National Natural Science Foundation(31870695 and 31601785)the Project of Key Research and Development Plan(Modern Agriculture)in Jiangsu(BE2017375)+1 种基金the Selection and Breeding of Excellent Tree Species and Effective Cultivation Techniques(CX(16)1005)the Project of Osmanthus National Germplasm Bank,and the Top-notch Academic Programs Project of Jiangsu Higher Education Institutions.
文摘Sweet osmanthus(Osmanthus fragrans)is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma.We constructed a chromosome-level reference genome of O.fragrans to assist in studies of the evolution,genetic diversity,and molecular mechanism of aroma development.A total of over 118 Gb of polished reads was produced from HiSeq(45.1 Gb)and PacBio Sequel(73.35 Gb),giving 100×depth coverage for long reads.The combination of Illumina-short reads,PacBio-long reads,and Hi-C data produced the final chromosome quality genome of O.fragrans with a genome size of 727 Mb and a heterozygosity of 1.45%.The genome was annotated using de novo and homology comparison and further refined with transcriptome data.The genome of O.fragrans was predicted to have 45,542 genes,of which 95.68%were functionally annotated.Genome annotation found 49.35%as the repetitive sequences,with long terminal repeats(LTR)being the richest(28.94%).Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago,which contributed to the current content of 45,242 genes.Metabolic analysis revealed that linalool,a monoterpene is the main aroma compound.Based on the genome and transcriptome,we further demonstrated the direct connection between terpene synthases(TPSs)and the rich aromatic molecules in O.fragrans.We identified three new flower-specific TPS genes,of which the expression coincided with the production of linalool.Our results suggest that the high number of TPS genes and the flower tissue-and stage-specific TPS genes expressions might drive the strong unique aroma production of O.fragrans.
基金supported by the National Key Research and Development Program of China(2018YFD1000300)National Crop Germplasm Resources Protection of Ministry of Agriculture of China(NB2018-2130135-07).
文摘Since the publication of this article,the authors have noticed that the NCBI accession number is missing from article.
基金supported by the Key Research and Development Program of Yunnan(202203AC100010)the National Natural Science Foundation of China(32371463,32160236)Spring City Plan:The High-level Talent Promotion and Training Project of Kunming(2022SCP001)。
文摘Alternative polyadenylation(APA)is a pervasive mechanism that is emerging as a formidable player in post-transcriptional regulation.The transcriptional landscape can be altered via APA in response to various stimulating factors.Using the Pac Bio single-molecule long-read sequencing method,we present for the first time the 3′UTR landscape and reveal a global increase of APA events in prostate cancer(PCa)LNCa P cells in response to androgen dihydrotestosterone(DHT),a critical regulator of PCa progression.With evidence from differential gene expression analyses of Illumina RNA-sequencing data,we demonstrated that genes with DHT-induced changes in both expression and APA were enriched in lipid metabolism.These genes predominantly supported de novo fatty acid synthesis,such as FASN and ACSL3.Furthermore,we showed that an isoform switch to the proximal poly(A)site of these genes depended on the androgen receptor,and the expression of cancer-associated genes was upregulated by the escape of mi RNA-regulated repression machinery.To address the role of key gene shortening in PCa,we prepared 22RV1-FS cells missing the distal poly(A)signal of FASN in the AR+PCa cell line 22RV1 using CRISPR/Cas9 technology.As expected,the edited 22RV1-FS cells overexpressed FASN m RNA and protein and were inclined to cell proliferation in vitro and tumorigenesis in vivo.Interestingly,we found that FASN transcripts with a shortened 3′UTR were significantly increased in advanced PCa and castration-resistant prostate cancer compared with benign prostate hyperplasia,suggesting a possible association between usage of the proximal poly(A)site and disease progression.Therefore,our study highlights the importance of the APA mechanism in response to DHT stimulation in PCa cells and provides a novel regulatory mechanism through which DHT-induced APA causes altered expression of de novo lipogenesis genes,with a possible association with the progression of PCa.
基金financially supported by Hunan Provincial Natural Science Foundation of China(grant 2017JJ1017)National Key R&D Program of China(grant 2017YFD0501403)+1 种基金National Natural Science Foundation of China(grant 31400275)Hunan Provincial Natural Science Foundation of China(2018JJ2172).
文摘Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were generated.After filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage depth.The de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 Mb.The vast majority(99.2%)of the G.elegans assembled sequence was anchored onto 8 pseudo-chromosomes.The genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the assembly.Genome annotation revealed that 43.16%of the G.elegans genome is composed of repetitive elements and 23.9%is composed of long terminal repeat elements.We predicted 26,768 protein-coding genes,of which 84.56%were functionally annotated.The genomic sequences of G.elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.
