Functional & Integrative Genomics最新文献

The Integrator complex: an emerging complex structure involved in the regulation of gene expression by targeting RNA polymerase II 整合器复合体：通过靶向 RNA 聚合酶 II 参与基因表达调控的新兴复合结构

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-19 DOI: 10.1007/s10142-024-01479-9

Tingyue Li, Fulei Zeng, Yang Li, Hu Li, Jiayuan Wu

引用次数: 0

Genotyping by sequencing; a strategy for identification and mapping of induced mutation in newly developed wheat mutant lines 通过测序进行基因分型；新开发的小麦突变品系中诱导突变的鉴定和绘图策略

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-16 DOI: 10.1007/s10142-024-01424-w

Sana Zulfiqar, Mehboob-ur- Rahman, Sayyad Ali Raza Bukhari, Bradley Till, Ruixue Gu, Dongcheng Liu, Susanne Dreisigacker

{"title":"Genotyping by sequencing; a strategy for identification and mapping of induced mutation in newly developed wheat mutant lines","authors":"Sana Zulfiqar, Mehboob-ur- Rahman, Sayyad Ali Raza Bukhari, Bradley Till, Ruixue Gu, Dongcheng Liu, Susanne Dreisigacker","doi":"10.1007/s10142-024-01424-w","DOIUrl":"10.1007/s10142-024-01424-w","url":null,"abstract":"<div>Exposing genetic material with physical mutagens can create novel genetic resources capable of combating different stresses. High throughput GBS-DArTseq™ assay was deployed to estimate genetic diversity of 33 newly developed stable wheat mutants as compared to the wild type. The identified 1,57,608 PAVs markers were randomly distributed across wheat chromosomes and sub-genomes with the highest number detected on Chr-7D (2877) and Chr-7B (2711). The B sub-genome contained the most PAVs followed by D and A-sub genome. Among mutant lines, Pb-M-2061 and Pb-M-59 had the highest PAV count, while Pb-M-605 and Pb-M-196 had the lowest. A total of 7,910 PAVs were consistently present over all replicates, with 3,252 specifically present in mutants and absent in wild type. The maximum PAVs (1480) were found in Pb-M-1027 and Pb-M-1323 (656). Functional characterization revealed that out of 3,252, 1,238 were found in wheat transcriptome database that contained 152 characterized and 1,196 uncharacterized genes. COGs and GO-terms analysis linked many PAVs with pathways involving signaling, metabolism and defense. Maximum number of gene-containing PAVs were identified in Pb-M-1027, Pb-M-2302 and Pb-M-1323 which were involved in tolerance to diseases and abiotic stresses, improved photosynthetic efficiency, larger grain size, increased grain yield and harvest index pathways. This study provides valuable insights into the genetic diversity and potential agronomic benefits of PAVs in wheat mutant lines. These findings can help molecular geneticist and breeders for exploiting the induced genetic diversity for unravelling the genetic circuits as well as exploiting in wheat breeding for developing resilient cultivars.</div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcriptome analysis of the allotetraploids of the Dilatata group of Paspalum (Poaceae): effects of diploidization on the expression of defensin and Snakin/GASA genes 树aspalum（Poaceae）Dilatata组异源四倍体的转录组分析：二倍体化对防御素和Snakin/GASA基因表达的影响

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-16 DOI: 10.1007/s10142-024-01466-0

Susana Rodríguez-Decuadro, Stefani Ramos, María José Rodríguez-Ustra, André Marques, Pablo Smircich, Magdalena Vaio

{"title":"Transcriptome analysis of the allotetraploids of the Dilatata group of Paspalum (Poaceae): effects of diploidization on the expression of defensin and Snakin/GASA genes","authors":"Susana Rodríguez-Decuadro, Stefani Ramos, María José Rodríguez-Ustra, André Marques, Pablo Smircich, Magdalena Vaio","doi":"10.1007/s10142-024-01466-0","DOIUrl":"10.1007/s10142-024-01466-0","url":null,"abstract":"<div>Plant Snakin/GASA and defensin peptides are cysteine-rich molecules with a wide range of biological functions. They are included within the large family of plant antimicrobial peptides (AMPs), characterized by their structural stability, broad spectrum of activity, and diverse mechanisms of action. The Dilatata group of Paspalum includes five allotetraploids that share an equivalent genomic formula IIJJ. From RNA-seq data of seedling tissues, we performed an in silico characterization of the defensin and Snakin/GASA genes in these species and diploids with a II and JJ genome formula and studied the evolutionary consequences of polyploidy on the expression of the two AMPs families. A total of 107 defensins (distributed in eight groups) and 145 Snakin/GASA (grouped in three subfamilies) genes were identified. Deletions, duplications and/or gene silencing seem to have mediated the evolution of these genes in the allotetraploid species. In defensin genes, the IIJJ allopolyploids retained the I subgenome defensin copies in some of the identified groups supporting the closeness of their nuclear genome with the I subgenome species. In both AMPs families, orthologous genes in tetraploids exhibit higher similarity to each other than with diploids. This data supports the theory of a single origin for the allotetraploids. Several copies of both defensin and Snakin/GASA genes were detected in the five polyploids which could have arisen due to duplication events occurring independently during the diploidization processes in the allotetraploid taxa.</div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of lncRNAs regulating seed traits in Brassica juncea and development of a comprehensive seed omics database 鉴定调控芸苔属植物种子性状的 lncRNAs 并开发综合性种子 omics 数据库

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-15 DOI: 10.1007/s10142-024-01470-4

Pinky Yadav, Prachi Priyam, Garima Yadav, Abhinandan Yadav, Rubi Jain, Satyam Sunderam, Manoj Kumar Sharma, Inderjeet Kaur, Namrata Dhaka

{"title":"Identification of lncRNAs regulating seed traits in Brassica juncea and development of a comprehensive seed omics database","authors":"Pinky Yadav, Prachi Priyam, Garima Yadav, Abhinandan Yadav, Rubi Jain, Satyam Sunderam, Manoj Kumar Sharma, Inderjeet Kaur, Namrata Dhaka","doi":"10.1007/s10142-024-01470-4","DOIUrl":"10.1007/s10142-024-01470-4","url":null,"abstract":"<div>Brassica juncea is a crucial oilseed crop, and its seeds possess high economic value as they are a source of edible oil. In order to understand the role of long non coding RNAs (lncRNAs) in the regulation of seed development, we carried out computational analysis using transcriptome data of developing seeds of two contrasting genotypes of B. juncea, Pusajaikisan (PJK) and Early Heera 2 (EH2). The seeds were sampled at three stages, 15, 30, and 45 days after pollination. We identified 1,539 lncRNAs, of which 809 were differentially expressed. We also carried out extensive characterization and functional analysis of seed lncRNAome. The expression patterns were analysed using k-means clustering, and the targets were analysed using pathway, transcription factor, and GO enrichment, as well as ortholog information. We shortlisted a total of 25 robust lncRNA candidates for seed size, oil content, and seed coat color. We also identified 4 lncRNAs as putative precursors of miRNAs regulating seed development. Moreover, a total of 28 miRNA-lncRNA-mRNA regulatory networks regulating seed traits were identified. We also developed a comprehensive database, (BrassIca juncea database or “BIJ” (https://bij.cuh.ac.in/), which provides seed omics as well as other functional genomics and genetics data in an easily accessible form. These candidate lncRNAs are suitable for including in crop improvement programs through molecular breeding, as well as for future validations through genome editing. Together, the knowledge of these candidate lncRNAs and availability of BIJ database shall leverage the crop improvement efforts in B. juncea.</div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142434812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification, charectrization and genetic transformation of lignin and pectin polysaccharides through CRISPR/Cas9 in Nicotiana tobacum 通过 CRISPR/Cas9 在烟草中鉴定、分离和遗传转化木质素和果胶多糖

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-14 DOI: 10.1007/s10142-024-01472-2

Rana Imtiaz Ahmed, Angyan Ren, Dalal Sulaiman Alshaya, Sajid Fiaz, Yingzhen Kong, Shoaib Liaqat, Naushad Ali, Muhammad Abu Bakar Saddique, Kotb A. Attia, Mahmood Ul Hassan Taga

{"title":"Identification, charectrization and genetic transformation of lignin and pectin polysaccharides through CRISPR/Cas9 in Nicotiana tobacum","authors":"Rana Imtiaz Ahmed, Angyan Ren, Dalal Sulaiman Alshaya, Sajid Fiaz, Yingzhen Kong, Shoaib Liaqat, Naushad Ali, Muhammad Abu Bakar Saddique, Kotb A. Attia, Mahmood Ul Hassan Taga","doi":"10.1007/s10142-024-01472-2","DOIUrl":"10.1007/s10142-024-01472-2","url":null,"abstract":"<div>CRISPR/Cas9 system has been successfully implemented in animals and plants is a second-generation genome editing tool. We are able to optimize a Cas9 system to edited Ntab06050 and Ntab0857410 genes in HD and K326 tobacco cultivars respectively. The gene Ntab06050 is related to lignin synthesis while the gene Ntab0857410 belongs to pectin synthesis by utilizing Agrobacterium-mediated leaf disc method. We have constructed total eight different constructs for the lignin related gene family CCoAMT, out of which three constructs have been selected from Ntab0184090, two constructs from Ntab0392460 while one construct from each Ntab0540120, Ntab0857410 and Ntab0135940 gene. To study the Cas9 system in pectin related genes, total five constructs have been utilized under Cas9 system and multiple target sites were selected by identifying PAM sequences. Out of which three constructs were targeted from NtabGAE1and NtabGAE6 homologous while two were targeted from NtabGAUT4 homologous. Where as, UDP-D-glucuronate 4-epimerase gene family is a Golgi localized, might have a role in the interconvertion of UDP-D-GlcA and UDP-D-GalA in pectin synthesis. We have succeeded in the mutation of pectin related NtabGAUT4 and lignin related NtabCCoAMT genes with 6.2% and 9.4% mutation frequency.</div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reference-based genome assembly and comparative genomics of Calamus Brandisii Becc. for unveiling sex-specific genes for early gender detection 基于参考文献的菖蒲基因组组装和比较基因组学，揭示用于早期性别检测的性别特异性基因

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-10 DOI: 10.1007/s10142-024-01468-y

Muneera Parveen Abdul Bari, Suma Arun Dev, Sarath Paremmal, Sreekumar V. B, Modhumita Ghosh Dasgupta

{"title":"Reference-based genome assembly and comparative genomics of Calamus Brandisii Becc. for unveiling sex-specific genes for early gender detection","authors":"Muneera Parveen Abdul Bari, Suma Arun Dev, Sarath Paremmal, Sreekumar V. B, Modhumita Ghosh Dasgupta","doi":"10.1007/s10142-024-01468-y","DOIUrl":"10.1007/s10142-024-01468-y","url":null,"abstract":"<div>Calamus brandisii Becc. is an endangered rattan species indigenous to the Western Ghats of India and used in the furniture and handicraft industries. However, its dioecious nature and longer flowering time pose challenges for conservation efforts. Developing markers for early gender detection in seedlings is crucial for maintaining viable populations for in-situ and ex-situ conservation. Currently, no sex chromosomes or gender-specific genes have been reported in the species. We report the first comprehensive comparative genomics study between the male and female genomes of C. brandisii to identify polymorphisms and potential genes for gender determination. Reference-based assembly was conducted and the male and female genomes were predicted to contain 43,810 and 50,493 protein-coding genes respectively. The haploid genome size was ∼691 Mb and ∼884 Mb for male and female genomes respectively. Comparative analysis revealed significant genetic variation between the two genomes including 619,776 SNPs, 73,659 InDels, 212,123 Structural variants (SVs) and 305 copy number variations (CNVs). A total of 5 male-specific and 11 female-specific genes linked to the sex determining region was predicted. The genomic variants identified between the two genomes could be used in development of markers for early gender identification in C. brandisii for restoration programs. The gender-specific genes identified in this study also provide new insights into the mechanisms of sex determination and differentiation in rattans.</div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142411214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The mechanism of MMP14-positive tumor-associated fibroblast subsets in inhibiting PD-1 immunotherapy for esophageal cancer through exosomal tsRNA-10522 MMP14阳性肿瘤相关成纤维细胞亚群通过外泌体tsRNA-10522抑制食管癌PD-1免疫疗法的机制

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-08 DOI: 10.1007/s10142-024-01447-3

Juzheng Wang, Chunlong Zheng, Jiayu Lu, Xinyao Xu, Guangyu Xiang, Jiahe Li, Jipeng Zhang, Xiaorong Mu, Qiang Lu

引用次数: 0

Nuclear integration of MYB36 and APX-1 genes impart heat tolerance in wheat MYB36 和 APX-1 基因的核整合赋予小麦耐热性。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-07 DOI: 10.1007/s10142-024-01456-2

Hina Firdous, Arfan Ali, Muhammad Mubashar Zafar, Faiz Ahmad Joyia, Muhammad Hamza, Abdul Razzaq, Muhammad Uzair, Sezai Ercisli, Waqas Shafqat Chattha, Mahmoud F. Seleiman, Naeem Khan, Xuefei Jiang

{"title":"Nuclear integration of MYB36 and APX-1 genes impart heat tolerance in wheat","authors":"Hina Firdous, Arfan Ali, Muhammad Mubashar Zafar, Faiz Ahmad Joyia, Muhammad Hamza, Abdul Razzaq, Muhammad Uzair, Sezai Ercisli, Waqas Shafqat Chattha, Mahmoud F. Seleiman, Naeem Khan, Xuefei Jiang","doi":"10.1007/s10142-024-01456-2","DOIUrl":"10.1007/s10142-024-01456-2","url":null,"abstract":"<div>Elevated temperatures during grain filling stage, exceeding the optimal range by 3–4 °C, not only results in a substantial yield reduction in wheat by 10–50% but activates disease and insect infestation. In this research, we introduced heat-tolerant MYB36 and APX-1 gene cassettes into wheat, employing an efficient Agrobacterium mediated transformation protocol, demonstrating higher transformation efficiency. The study encompassed the assembly of MYB36 and APX-1 gene cassettes, and confirmation of gene products in Agrobacterium, followed by the transformation of the MYB36 and APX-1 genes into wheat explants. We were able to select transgenic plant with various combinations. The transgenic plants with APX-1 gene alone produced medium sized grain and spike whereas with both APX-1 and MYB36 genes expressed individually under SPS and rd29a promoter respectively showed good tolerance to heat at 32oC at grain filling/milking stage and produced relatively bold grains. While non-transgenic plants grains were wrinkled with thin spike showing susceptibility to heat. This research contributes to the broader scientific understanding of plant stress responses and the combined effectiveness of MYB36 and APX-1 genes in crop improvement without disturbing normal nutritional values. The gene integration can serve as a valuable tool in breeding programs aimed at developing heat-tolerant wheat varieties. These findings also advance our comprehension of the functions of heat-induced genes and lay the foundation for selecting optimal candidates for in-depth functional studies of heat-responsive MYB36 and APX-1 genes in wheat.</div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ALDH2 alleviates inflammation and facilitates osteogenic differentiation of periodontal ligament stem cells in periodontitis by blocking ferroptosis via activating Nrf2 ALDH2 通过激活 Nrf2 阻断铁卟啉沉积，缓解炎症并促进牙周炎中牙周韧带干细胞的成骨分化。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-07 DOI: 10.1007/s10142-024-01465-1

Jia Chen, Chen Hu, Xun Lu, Xiaoqin Yang, Meng Zhu, Xiaozhou Ma, Yiqiang Yang

{"title":"ALDH2 alleviates inflammation and facilitates osteogenic differentiation of periodontal ligament stem cells in periodontitis by blocking ferroptosis via activating Nrf2","authors":"Jia Chen, Chen Hu, Xun Lu, Xiaoqin Yang, Meng Zhu, Xiaozhou Ma, Yiqiang Yang","doi":"10.1007/s10142-024-01465-1","DOIUrl":"10.1007/s10142-024-01465-1","url":null,"abstract":"<div>This paper elucidated the effects and mechanisms of aldehyde dehydrogenase 2 (ALDH2) on periodontitis. Rat model of periodontitis and periodontal ligament stem cell (PDLSC) model of periodontitis were constructed. PDLSC were transfected by ALDH2 overexpression vectors, and then treated by ML385 (Nrf2 inhibitor), ferrostatin-1 (ferroptosis inhibitor) and FIN56 (ferroptosis inducer), respectively. ALDH2, nuclear factor erythroid 2-related factor 2 (Nrf2) and glutathione peroxidase 4 (GPX4) proteins was evaluated by immunohistochemistry and Western blot. Ferroptosis-related factors, including Fe2+ and glutathione (GSH), were assessed by commercial kits. Pro-inflammatory factors (interleukin-6 [IL-6] and tumor necrosis factor-α [TNF-α]) and osteogenic differentiation-related proteins (osteocalcin [OCN] and runt-related transcription factor 2 [RUNX2]) were scrutinized by commercial kits and Western blot. In both periodontal tissues of periodontitis rats and PDLSC model of periodontitis, down-regulated ALDH2, Nrf2, GPX4 and GSH, but elevated Fe2+ level was discovered. ALDH2 overexpression in PDLSC resulted in an increase in Nrf2 expression. In PDLSC model of periodontitis, ALDH2 increased GPX4 and GSH levels, decreased Fe2+, IL-6 and TNF-α levels, and elevated OCN and RUNX2 expression. However, these effects of ALDH2 were counteracted by ML385. Additionally, the suppression of ALDH2 on IL-6 and TNF-α levels and promotion of it on OCN and RUNX2 expression in PDLSC model of periodontitis was further intensified by ferrostatin-1, but reversed by FIN56. ALDH2 may alleviate inflammation and facilitate osteogenic differentiation of PDLSC in periodontitis by hindering ferroptosis via activating Nrf2, suggesting it to be a promising candidate for treating periodontitis.</div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

KRAS mutations detection methodology: from RFLP to CRISPR/Cas based methods KRAS 突变检测方法：从 RFLP 到基于 CRISPR/Cas 的方法。

IF 3.9 4区生物学

Functional & Integrative Genomics Pub Date : 2024-10-05 DOI: 10.1007/s10142-024-01421-z

Firouzeh Morshedzadeh, Mohammad Reza Abbaszadegan, Maryam Peymani, Sina Mozaffari-Jovin

引用次数: 0