Genomics最新文献

{"title":"Whole-genome sequencing of two captive black soldier fly populations: Implications for commercial production","authors":"Zexi Cai ,&nbsp;Laura Skrubbeltrang Hansen ,&nbsp;Stine Frey Laursen ,&nbsp;Hanne Marie Nielsen ,&nbsp;Simon Bahrndorff ,&nbsp;Jeffery K. Tomberlin ,&nbsp;Torsten Nygaard Kristensen ,&nbsp;Jesper Givskov Sørensen ,&nbsp;Goutam Sahana","doi":"10.1016/j.ygeno.2024.110891","DOIUrl":"10.1016/j.ygeno.2024.110891","url":null,"abstract":"<div><p>Black soldier fly (BSF; <em>Hermetia illucens</em>) is a promising insect species for food and feed production as its larvae can convert different organic waste to high-value protein. Selective breeding is one way to optimize production, but the potential of breeding is only starting to be explored and not yet utilized for BSF. To assist in monitoring a captive population and implementing a breeding program, genomics tools are imperative. We conducted whole genome sequencing of two captive populations separated by geographical distance - Denmark (DK) and Texas, USA (TX). Various population genetics analyses revealed a moderate genetic differentiation between two populations. Moreover, we observed higher inbreeding in the DK population, and the detection of a subpopulation within DK population aligned well with the recent foundation of the DK population from two captive populations. Additionally, we generated gene ontology annotation and variants annotation for wider potential applications. Our findings establish a robust marker set for research in population genetics, facilitating the monitoring of inbreeding and laying the groundwork for practical breeding programs for BSF.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110891"},"PeriodicalIF":3.4,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001125/pdfft?md5=95c13dd07dc4a0f5c048a3436b3dca14&pid=1-s2.0-S0888754324001125-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141442427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential gene expression and gut microbiota composition in low-altitude and high-altitude goats","authors":"Zhenzhen Zhang ,&nbsp;Xin Zhang ,&nbsp;Tingting Zhang ,&nbsp;Jingjing Li ,&nbsp;Cuomu Renqing ,&nbsp;Zhaxi Baijiu ,&nbsp;Sangzhu Baima ,&nbsp;Wangjie Zhaxi ,&nbsp;Yuzhen Nima ,&nbsp;Wangsheng Zhao ,&nbsp;Tianzeng Song","doi":"10.1016/j.ygeno.2024.110890","DOIUrl":"10.1016/j.ygeno.2024.110890","url":null,"abstract":"<div><p>Previous studies have presented evidence suggesting that altitude exerts detrimental effects on reproductive processes, yet the underlying mechanism remains elusive. Our study employed two distinct goat breeds inhabiting low and high altitudes, and conducted a comparative analysis of mRNA profiles in testis tissues and the composition of gut microbiota. The results revealed a reduced testis size in high-altitude goats. RNA-seq analysis identified the presence of 214 differentially expressed genes (DEGs) in the testis. These DEGs resulted in a weakened immunosuppressive effect, ultimately impairing spermatogenesis in high-altitude goats. Additionally, 16S rDNA amplicon sequencing recognized statistically significant variations in the abundance of the genera <em>Treponema</em>, <em>unidentified_Oscillospiraceae</em>, <em>Desulfovibrio</em>, <em>Butyricicoccus</em>, <em>Dorea</em>, <em>Parabacteroides</em> between the two groups. The collective evidence demonstrated the gut and testis played a synergistic role in causing decreased fertility at high altitudes. Our research provides a theoretical basis for future investigations into the reproductive fitness of male goats.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110890"},"PeriodicalIF":3.4,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001113/pdfft?md5=ab74fc1e5cddecd42bf3124ac17d4442&pid=1-s2.0-S0888754324001113-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141442426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep integration of metabolome and transcriptome characterizes alkaloid metabolism in Houttuynia cordata","authors":"Xue Jiang ,&nbsp;Qian Wang ,&nbsp;Jingtian Yang ,&nbsp;Baoguo Du ,&nbsp;Zhaodi Yuan ,&nbsp;Hongyi Liu ,&nbsp;Jiayi Yuan ,&nbsp;Yang Zhang ,&nbsp;Liao Chen ,&nbsp;Lei Liu","doi":"10.1016/j.ygeno.2024.110881","DOIUrl":"10.1016/j.ygeno.2024.110881","url":null,"abstract":"<div><p>Alkaloids are the main medicinal components in <em>Houttuynia cordata</em>. In this study, two accessions 6# and 7# of <em>H. cordata</em> underwent thorough metabolomic analyses to identify and quantify alkaloid phytometabolites. It turned out that the alkaloid types were largely similar between 6# and 7#, and the identified 81 alkaloids could be divided into nine structural classes. However, the content of alkaloids in the two accessions was quite different. According to transcriptome data, a total of 114 differentially expressed genes related to alkaloid metabolism were screened. The alkaloid synthesis pathway of the two varieties was mainly different in the isoquinoline alkaloid biosynthesis and indole alkaloid biosynthesis; four genes <em>A22110063c_transcript_59323</em>, <em>A22110063c_transcript_60118</em>, <em>A22110063c_transcript_51672</em> and <em>A22110063c_transcript_48784</em> were highly expressed in 7#, which could be key candidate genes of alkaloid metabolism and warrant further analysis. These results provide a reference for the medicinal application of <em>H. cordata</em> and breeding alkaloid rich varieties.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110881"},"PeriodicalIF":3.4,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001022/pdfft?md5=2c0c4cfd0f21ee18fc9de41ea9cca06c&pid=1-s2.0-S0888754324001022-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141436719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of prognostic biomarkers for cholangiocarcinoma by combined analysis of molecular characteristics of clinical MVI subtypes and molecular subtypes","authors":"Ming-Yue Li ,&nbsp;Ya-Hui Liu ,&nbsp;Feng Wei ,&nbsp;Ping Zhang ,&nbsp;Xiao-Dong Sun ,&nbsp;Meng Wang ,&nbsp;Xiao-Hong Du ,&nbsp;Jun-Feng Ye ,&nbsp;Wei Qiu ,&nbsp;Xiao-Ju Shi ,&nbsp;Bai Ji ,&nbsp;Ying-Chao Wang ,&nbsp;Chao Jiang ,&nbsp;Wen-Gang Chai ,&nbsp;Bo Huang ,&nbsp;Xing-Kai Liu ,&nbsp;Qing-Min Chen ,&nbsp;Yu Fu ,&nbsp;Xin-Tong Hu ,&nbsp;Li-Guo Chen ,&nbsp;Guo-Yue Lv","doi":"10.1016/j.ygeno.2024.110889","DOIUrl":"10.1016/j.ygeno.2024.110889","url":null,"abstract":"<div><p>Cholangiocarcinoma (CCA) is widely noted for its high degree of malignancy, rapid progression, and limited therapeutic options. This study was carried out on transcriptome data of 417 CCA samples from different anatomical locations. The effects of lipid metabolism related genes and immune related genes as CCA classifiers were compared. Key genes were derived from MVI subtypes and better molecular subtypes. Pathways such as epithelial mesenchymal transition (EMT) and cell cycle were significantly activated in MVI-positive group. CCA patients were classified into three (four) subtypes based on lipid metabolism (immune) related genes, with better prognosis observed in lipid metabolism-C1, immune-C2, and immune-C4. IPTW analysis found that the prognosis of lipid metabolism-C1 was significantly better than that of lipid metabolism-C2 + C3 before and after correction. KRT16 was finally selected as the key gene. And knockdown of KRT16 inhibited proliferation, migration and invasion of CCA cells.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110889"},"PeriodicalIF":3.4,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001101/pdfft?md5=0d22e1e7daf8eb22ab3a8d218c0688f9&pid=1-s2.0-S0888754324001101-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141431732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Key genes and metabolites that regulate wool fibre diameter identified by combined transcriptome and metabolome analysis","authors":"Lin Yue ,&nbsp;Zengkui Lu ,&nbsp;Tingting Guo ,&nbsp;Jianbin Liu ,&nbsp;Bohui Yang ,&nbsp;Chao Yuan","doi":"10.1016/j.ygeno.2024.110886","DOIUrl":"10.1016/j.ygeno.2024.110886","url":null,"abstract":"<div><h3>Background</h3><p>Fibre diameter is an important economic trait of wool fibre. As the fibre diameter decreases, the economic value of wool increases. Therefore, understanding the mechanism of wool fibre diameter regulation is important in improving the value of wool.</p></div><div><h3>Results</h3><p>In this study, we used non-targeted metabolome and reference transcriptome data to detect differences in metabolites and genes in groups of Alpine Merino sheep with different wool fibre diameter gradients, and integrated metabolome and transcriptome data to identify key genes and metabolites that regulate wool fibre diameter. We found 464 differentially abundant metabolites (DAMs) and 901 differentially expressed genes (DEGs) in four comparisons of groups with different wool fibre diameters. Approximately 25% of the differentially abundant metabolites were lipid and lipid-like molecules. These molecules were predicted to be associated with skin development and keratin filament by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Key genes, including <em>COL5A2</em>, <em>COL5A3</em>, <em>CREB3L4</em>, <em>COL1A1</em>, and <em>SFRP4</em>, were identified by gene set enrichment analysis.</p></div><div><h3>Conclusions</h3><p>Key genes regulating wool fibre diameter were identified, the effects of lipid molecules on wool performance were investigated, and potential synergies between genes and metabolites were postulated, providing a theoretical framework for fine wool sheep breeding.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110886"},"PeriodicalIF":4.4,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001071/pdfft?md5=8fe9cf7927ff09beab88c3383371f85c&pid=1-s2.0-S0888754324001071-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome and metabolome analysis of the developmental changes in Cynanchum thesioides anther","authors":"Xiaoyao Chang ,&nbsp;Xiaoyan Zhang ,&nbsp;Xiumei Huang ,&nbsp;Zhongren Yang ,&nbsp;Fenglan Zhang","doi":"10.1016/j.ygeno.2024.110884","DOIUrl":"10.1016/j.ygeno.2024.110884","url":null,"abstract":"<div><p><em>Cynanchum thesioides</em>, a xerophytic species utilized both as a medicinal herb and a food source, plays a significant role in arid and desert ecosystem management. Its inflorescence is an umbellate cyme, each carrying nearly a thousand flowers; however, its fruiting rate remains remarkably low. The normal development of the anther is a necessary prerequisite for plants to produce seeds. However, our understanding of the anther development process in <em>Cynanchum thesioides</em> remains limited. To better understand the pollen development process in <em>Cynanchum thesioides</em>, the stages of pollen development were determined through paraffin sectioning, and observations were made on the distribution characteristics of polysaccharides and lipid droplets in the pollen development of <em>Cynanchum thesioides</em> using Periodic Acid-Schiff stain (PAS) and 0.5% Sudan Black B tissue staining. Concurrently, the gene expression patterns and metabolite profiles were delineated across various developmental stages of <em>Cynanchum thesioides</em> anthers (T1: microspore stage, T2: tetrad stage, T3: mononuclear stage, and T4: maturation stage). The findings revealed that <em>Cynanchum thesioides</em> pollen is in an aggregate form. Polysaccharides gradually accumulate during maturation and lipid droplets form a surrounding membrane, thereby preventing pollen dispersion. Furthermore, transcriptomic and metabolomic analyses across distinct developmental phases uncovered a plethora of differentially expressed genes and metabolites associated with the flavonoid biosynthesis pathway. Flavonoid levels exhibited dynamic changes concurrent with anther development, aligning with the gene regulatory patterns of the corresponding biosynthetic pathways. The study identified 63 differentially accumulated flavonoid compounds and 21 differentially expressed genes associated with flavonoid biosynthesis. Weighted gene co-expression network analysis revealed six MYB and ten bHLH transcription factors as key candidates involved in flavonoid biosynthesis, with <em>Ct</em>bHLH (Cluster-6587.1050) and <em>Ct</em>MYB (Cluster-6587.31743) specifically regulating structural genes within the pathway. These findings underscore the pivotal role of flavonoid biosynthesis in anther development of <em>Cynanchum thesioides</em>. In conclusion, this research offers a comprehensive insight into the anther development process in <em>Cynanchum thesioides</em>.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110884"},"PeriodicalIF":4.4,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001058/pdfft?md5=f2a3fe88ced43380953765a9b7a08f63&pid=1-s2.0-S0888754324001058-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141327340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of spinal cord injury associated exosomes delivered tRF-41 on the progression of spinal cord injury progression","authors":"Hongfei Cai,&nbsp;Yan Zhang,&nbsp;Fanyu Meng,&nbsp;Yang Li","doi":"10.1016/j.ygeno.2024.110885","DOIUrl":"10.1016/j.ygeno.2024.110885","url":null,"abstract":"<div><h3>Background</h3><p>Spinal cord injury (SCI) is a devastating neurological and pathological condition. Exosomal tsRNAs have reported to be promising biomarkers for cancer diagnosis and therapy. This study aimed to investigate the roles of SCI-associated exosomes, and related tsRNA mechanisms in SCI.</p></div><div><h3>Methods</h3><p>The serum of healthy controls and SCI patients at the acute stage were collected for exosomes isolation, and the two different exosomes were used to treat human astrocytes (HA). The cell viability, apoptosis, and cycle were determined, and the expression of the related proteins were detected by western blot. Then, the two different exosomes were sent for tsRNA sequencing, and four significant known differentially expressed tsRNAs (DE-tsRNAs) were selected for RT-qPCR validation. Finally, tRT-41 was chosen to further explore its roles and related mechanisms in SCI.</p></div><div><h3>Results</h3><p>After sequencing, 21 DE-tsRNAs were identified, which were significantly enriched in pathways of Apelin, AMPK, Hippo, MAPK, Ras, calcium, PI3K-Akt, and Rap1. RT-qPCR showed that tRF-41 had higher levels in the SCI-associated exosomes. Compared with the control HA, healthy exosomes did not significantly affect the growth of HA cells, but SCI-associated exosomes inhibited viability of HA cells, while promoted their apoptosis and increased the HA cells in G2/M phase; but tRF-41 inhibitor reversed the actions of SCI-associated exosomes. Additionally, SCI-associated exosomes, similar with tRF-41 mimics, down-regulated IGF-1, NGF, Wnt3a, and β-catenin, while up-regulated IL-1β and IL-6; but tRF-41 inhibitor had the opposite actions, and reversed the effects induced by SCI-associated exosomes.</p></div><div><h3>Conclusions</h3><p>SCI-associated exosomes delivered tRF-41 may inhibit the growth of HA through regulating Wnt/ β-catenin pathway and inflammation response, thereby facilitating the progression of SCI.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 4","pages":"Article 110885"},"PeriodicalIF":4.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400106X/pdfft?md5=406db73f55e3927714f593d1e8dacb37&pid=1-s2.0-S088875432400106X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A systematic comparison of natural product potential, with an emphasis on RiPPs, by Mining of Bacteria of three large ecosystems","authors":"Yunhai Yi ,&nbsp;Lifeng Liang ,&nbsp;Anne de Jong ,&nbsp;Oscar P. Kuipers","doi":"10.1016/j.ygeno.2024.110880","DOIUrl":"10.1016/j.ygeno.2024.110880","url":null,"abstract":"<div><p>The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 4","pages":"Article 110880"},"PeriodicalIF":4.4,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001010/pdf?md5=5014b7315893fc3280940055e17b776b&pid=1-s2.0-S0888754324001010-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative metabolomics and transcriptomics analyses provide insights into branching changes induced by heterografting in Pinus massoniana seedlings","authors":"Feng Xiao ,&nbsp;Yayan Zhu ,&nbsp;Yao Yang ,&nbsp;Xiurong Wang ,&nbsp;Xueyan Jian ,&nbsp;Yang Zhao","doi":"10.1016/j.ygeno.2024.110882","DOIUrl":"10.1016/j.ygeno.2024.110882","url":null,"abstract":"<div><p>The investigation of dwarfing rootstocks for the establishment of high-generation seed orchards is a prospective avenue of research. In this investigation, <em>Pinus massoniana</em>, <em>Pinus yunnanensis</em> var. <em>pygmaea</em> (<em>P. pygmaea</em>), and <em>P. elliottii</em> seedlings were used as rootstocks for grafting with <em>P. massoniana</em> scions. Grafting <em>P. massoniana</em> onto <em>P. pygmaea</em> rootstock resulted in observable phenotypic alterations in lateral branches, apical buds, and needle length. Certain characteristic metabolites of rootstocks, such as fatty acyls, pregnenolones, steroids, and steroid derivatives, were found to be highly expressed in scions after grafting. RNA-seq analysis revealed <em>MYB-related</em>, <em>SBP</em>, and <em>bHLH</em> demonstrating a significant positive correlation, while <em>C2H2</em> and <em>Orphans</em> exhibited negative correlations with the differential intensity of metabolites related to lipids and lipid-like molecules. This study offers valuable insights for the establishment of rootstock breeding programs.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110882"},"PeriodicalIF":4.4,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001034/pdfft?md5=b710119b88ddae2f7361de19428972b3&pid=1-s2.0-S0888754324001034-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome and metabolome analyses reveal chlorogenic acid accumulation in pigmented potatoes at different altitudes","authors":"Qiu-Ju Dong,&nbsp;Xiao-Yu Xu,&nbsp;Cai-Xia Fan,&nbsp;Ji-Ping Xiao","doi":"10.1016/j.ygeno.2024.110883","DOIUrl":"10.1016/j.ygeno.2024.110883","url":null,"abstract":"<div><p>Pigmented potato tubers are abundant in chlorogenic acids (CGAs), a metabolite with pharmacological activity. This article comprehensively analyzed the transcriptome and metabolome of pigmented potato Huaxingyangyu and Jianchuanhong at four altitudes of 1800 m, 2300 m, 2800 m, and 3300 m. A total of 20 CGAs and intermediate CGA compounds were identified, including 3-o-caffeoylquinic acid, 4-o-caffeoylquinic acid, and 5-o-caffeoylquinic acid. CGA contents in Huaxinyangyu and Jianchuanhong reached its maximum at an altitude of 2800 m and slightly decreased at 3300 m. 48 candidate genes related to the biosynthesis pathway of CGAs were screened through transcriptome analysis. Weighted gene co-expression network analysis (WGCNA) identified that the structural genes of phenylalanine deaminase <em>(PAL),</em> coumarate-3 hydroxylase <em>(C3H),</em> cinnamic acid 4-hydroxylase <em>(C4H)</em> and the transcription factors of MYB and bHLH co-regulate CGA biosynthesis. The results of this study provide valuable information to reveal the changes in CGA components in pigmented potato at different altitudes.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110883"},"PeriodicalIF":3.4,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001046/pdfft?md5=7e616c69140258b9a44765b5295f125a&pid=1-s2.0-S0888754324001046-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}