scholarly journals Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots

2013 ◽  
Vol 64 (14) ◽  
pp. 4271-4287 ◽  
Author(s):  
Liang Xu ◽  
Yan Wang ◽  
Lulu Zhai ◽  
Yuanyuan Xu ◽  
Liangju Wang ◽  
...  
Keyword(s):  
Raphanus Sativus ◽  
Target Genes ◽  
Genome Wide ◽  
Raphanus Sativus L ◽  
Identification And Characterization

scholarly journals Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 536 ◽  
Author(s):  
Xiaobo Zhao ◽  
Liming Gan ◽  
Caixia Yan ◽  
Chunjuan Li ◽  
Quanxi Sun ◽  
...  
Keyword(s):  
Large Scale ◽  
Target Genes ◽  
Sequencing Data ◽  
Regulatory Processes ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Identification And Characterization ◽  
Lower Expression ◽  
Weighted Correlation

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.

scholarly journals Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus)

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0204137 ◽  
Author(s):  
Tianhua Hu ◽  
Qingzhen Wei ◽  
Wuhong Wang ◽  
Haijiao Hu ◽  
Weihai Mao ◽  
...  
Keyword(s):  
Gene Family ◽  
Raphanus Sativus ◽  
Genome Wide ◽  
Identification And Characterization

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

scholarly journals Genome-Wide Identification and Characterization of MicroRNAs and Target Genes in Lonicera japonica

PLoS ONE ◽  
2016 ◽  
Vol 11 (10) ◽  
pp. e0164140 ◽  
Author(s):  
Heng Xia ◽  
Libin Zhang ◽  
Gang Wu ◽  
Chunhua Fu ◽  
Yan Long ◽  
...  
Keyword(s):  
Target Genes ◽  
Lonicera Japonica ◽  
Genome Wide ◽  
Identification And Characterization

Genome-wide characterization of the WRKY gene family in radish (Raphanus sativus L.) reveals its critical functions under different abiotic stresses

2017 ◽  
Vol 36 (11) ◽  
pp. 1757-1773 ◽  
Author(s):  
Bernard Kinuthia Karanja ◽  
Lianxue Fan ◽  
Liang Xu ◽  
Yan Wang ◽  
Xianwen Zhu ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Raphanus Sativus ◽  
Wrky Gene ◽  
Genome Wide ◽  
Raphanus Sativus L
Sign in / Sign up

Export Citation Format

Share Document