scholarly journals Global identification of genes associated with xylan biosynthesis in cotton fiber

2020 ◽  
Author(s):  
Feng Chen ◽  
Yanjun Guo ◽  
Li Chen ◽  
Xinli Gan ◽  
Min Liu ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Secondary Wall ◽  
Experimental Validation ◽  
Profile Analysis ◽  
Expression Profile Analysis ◽  
Global Identification ◽  
Arabidopsis Mutant ◽  
Xylan Biosynthesis ◽  
Functional Orthologs ◽  
Cell Wall Architecture

Abstract Background: Mature cotton fiber secondary wall comprises largely of cellulose (>90%) and small amounts of xylan and lignin. Little is known about the cotton fiber xylan biosynthesis by far. Results: To comprehensively survey biosynthetic enzymes involved in xylan biosynthesis in cotton fiber, the combination of the phylogenetic analysis with expression profile analysis and co-expression analyses allowed us to identify five IRX9, five IRX10, one IRX14, six IRX15, two FRA8, one PARVUS, eight GUX, four GXM, two RWA, two AXY9, 13 TBL genes. In addition, we also identified two GT61 members, two GT47 members, and two DUF579 family members whose homologs in Arabidopsis were not functionally characterized. These 55 genes were regarded as the most probable genes to be involved in fiber xylan biosynthesis. Further experimental validation of one IRX10 like and two FRA8 related genes by complementation analysis indicated that these three genes are able to partially recover the irregular xylem phenotype conferred by the xylan deficiency in the respective Arabidopsis mutant. We presume that these genes are functional orthologs of respective genes that are implicated in GX biosynthesis. Conclusion: The list of 55 cotton genes presented here provides a solid basis to uncover the biosynthesis of xylan in cotton fiber, leading to optimization of the cell wall architecture for fiber improvement.

scholarly journals Global identification of genes associated with xylan biosynthesis in cotton fiber

2020 ◽  
Author(s):  
Feng Chen ◽  
Yanjun Guo ◽  
Li Chen ◽  
Xinli Gan ◽  
Min Liu ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Experimental Validation ◽  
Genetic Resource ◽  
Profile Analysis ◽  
Future Studies ◽  
Expression Profile Analysis ◽  
Global Identification ◽  
Arabidopsis Mutant ◽  
Xylan Biosynthesis ◽  
Functional Orthologs

Abstract Background: Mature cotton fiber secondary wall comprises largely of cellulose (>90%) and small amounts of xylan and lignin. Little is known about the cotton fiber xylan biosynthesis by far. Results: To comprehensively survey biosynthetic enzymes involved in xylan biosynthesis in cotton fiber, the combination of the phylogenetic analysis with expression profile analysis and co-expression analyses allowed us to identify five IRX9, five IRX10, one IRX14, six IRX15, two FRA8, one PARVUS, eight GUX, four GXM, two RWA, two AXY9, 13 TBL genes. In addition, we also identified two GT61 members, two GT47 members, and two DUF579 family members whose homologs in Arabidopsis were not functionally characterized. These 55 genes were regarded as the most probable genes to be involved in fiber xylan biosynthesis. Further experimental validation of one IRX10 like and two FRA8 related genes by complementation analysis indicated that these three genes are able to partially recover the irregular xylem phenotype conferred by the xylan deficiency in the respective Arabidopsis mutant. We presume that these genes are functional orthologs of respective genes that are implicated in GX biosynthesis. Conclusion: The list of 55 cotton genes presented here provides not only a solid basis to uncover the biosynthesis of xylan in cotton fiber, but also a genetic resource potentially useful for future studies aiming at fiber improvement via biotechnological approaches.

scholarly journals Identification and Characterization of Secondary Wall-Associated NAC Genes and Their Involvement in Hormonal Responses in Tobacco (Nicotiana tabacum)

2021 ◽  
Vol 12 ◽  
Author(s):  
Na Xu ◽  
Lin Meng ◽  
Lin Song ◽  
Xiaoxu Li ◽  
Shasha Du ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Stress Responses ◽  
Secondary Wall ◽  
Profile Analysis ◽  
Nicotiana Sylvestris ◽  
Wall Thickening ◽  
Nac Domain ◽  
Qrt Pcr ◽  
Transactivation Assay ◽  
Expression Profile Analysis

Secondary wall-associated NAC (SWN) genes are a subgroup of NAC (NAM, ATAF, and CUC) transcription factors (TF) that play a key role in regulating secondary cell wall biosynthesis in plants. However, this gene family has not been systematically characterized, and their potential roles in response to hormones are unknown in Nicotiana tabacum. In this study, a total of 40 SWN genes, of which 12 from Nicotiana tomentosiformis, 13 from Nicotiana sylvestris, and 15 from Nicotiana tabacum, were successfully identified. The 15 SWNs from Nicotiana tabacum were further classified into three groups, namely, vascular-related NAC domain genes (NtVNDs), NAC secondary wall thickening promoting factor genes (NtNSTs), and secondary wall-associated NAC domain genes (NtSNDs). The protein characteristic, gene structure, and chromosomal location of 15 NtSWNs (also named Nt1 to Nt15) were also analyzed. The NtVND and NtNST group genes had five conserved subdomains in their N-terminal regions and a motif (LP[Q/x] L[E/x] S[P/A]) in their diverged C- terminal regions. Some hormones, dark and low-temperature related cis-acting elements, were significantly enriched in the promoters of NtSWN genes. A comprehensive expression profile analysis revealed that Nt4 and Nt12 might play a role in vein development. Others might be important for stem development. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) revealed that in the NtNST group, genes such as Nt7, Nt8, and Nt13 were more sensitive than the genes in NtVND and NtSND groups under abiotic stress conditions. A transactivation assay further suggested that Nt7, Nt8, and Nt13 showed a significant transactivation activity. Overall, SWN genes were finally identified and characterized in diploid and tetraploid tobacco, revealing new insights into their evolution, variation, and homology relationships. Transcriptome, cis-acting element, qRT-PCR, and transactivation assay analysis indicated the roles in hormonal and stress responses, which provided further resources in molecular mechanism and genetic improvement.

scholarly journals Global identification of genes associated with xylan biosynthesis in cotton fiber

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Feng CHEN ◽  
Yanjun GUO ◽  
Li CHEN ◽  
Xinli GAN ◽  
Min LIU ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Global Identification ◽  
Xylan Biosynthesis

Cloning and expression profile analysis C1q-binding protein (PmC1qBP) in Penaeus monodon

2013 ◽  
Vol 18 (4) ◽  
pp. 774-781 ◽  
Author(s):  
Xianjun LIU ◽  
Lishi YANG ◽  
Jianhua HUANG ◽  
Falin ZHOU ◽  
Qibin YANG ◽  
...  
Keyword(s):  
Expression Profile ◽  
Profile Analysis ◽  
Binding Protein ◽  
Penaeus Monodon ◽  
Cloning And Expression ◽  
Expression Profile Analysis

scholarly journals Expression profile analysis reveals hub genes that are associated with immune system dysregulation in primary myelofibrosis

Hematology ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 478-490
Author(s):  
Haotian Ma ◽  
Jincen Liu ◽  
Zilong Li ◽  
Huaye Xiong ◽  
Yulei Zhang ◽  
...  
Keyword(s):  
Immune System ◽  
Expression Profile ◽  
Profile Analysis ◽  
Primary Myelofibrosis ◽  
Hub Genes ◽  
Expression Profile Analysis

scholarly journals Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shujuan Tian ◽  
Jiao Jiang ◽  
Guo-qi Xu ◽  
Tan Wang ◽  
Qiyan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Fruit Development ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Citrullus Lanatus ◽  
Binding Motif ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Expression Profile Analysis

Abstract Background Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear. Results In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones. Conclusions Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

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