- Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. - In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development.. - Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development.. - Conclusion: The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. - Cotton fiber is one of the most important renewable resources of the textile industry worldwide. - Cotton fiber develops from a single cell, and the nature of cell elong- ation provides an excellent model for testing gene expressions that relate to fiber development [1]. - During the initiation period of cotton fiber development, only about 25% of cells on the ovule epidermis develop into a spinnable. - cotton fiber [1]. - The cotton fiber developmental process is divided into 4 overlapping developmental stages: fiber initiation, fiber cell elongation, secondary cell wall formation and fiber cell maturation [1]. - Initiation, elong- ation and secondary cell wall of cotton fiber have a great impact on the quantity, length and fineness of fiber, which are the main factors determining the lint yield quality [3]. - The elongation stage of cotton fiber begins immediately after initiation stage and continues for around 3 weeks before the fiber cell switches to intensive deposition of secondary cell wall [4, 5]. - Cotton fiber elongation depends on the genotype and prevailing environmental conditions [5]. - Cotton fiber mutants are valuable materials for studying the molecular genetics and physiological processes of cell fiber development [7–11]. - Recently, several fiber mutants have been revealed and used as model plants to study cotton fiber development, one of which is the monogenic and dominant mutant also known as the Ligon-lintless-1 [12]. - Gene expression analysis in the ovule of Ligon-lintless-1 mutant as compared to the wild-type, only few genes showed differential expression during the initiation stage of cotton fiber development [16, 17].. - To understand the phenomenon of early cessation of fiber elongation in Ligon-lintless-1 mutant as compared to the wild-type, it is paramount to look into the molecular mechanisms or elements that are required to regulate cotton fiber development.. - controlling flowering period [23], gene silencing mechanism, abiotic stress tolerance, important developmental pathways [24 – 27] and cotton fiber development [28]. - The molecular mechanisms or elements underlying the LncRNAs related to cotton fiber development during initiation and early elongation stages are not well-known, thus using Ligon-lintless-1 mutant and its wild-type to identify and analyze differentially expressed long noncod- ing RNAs, which will provide a new dimension of under- standing the cotton fiber development process. - In this study, the sequencing of long non-coding RNA libraries constructed from cotton fiber development stages of Ligon-lintless-1 and wild-type was done. - The functional prediction of long noncoding RNAs (LncRNAs) and their expressions as involved in cotton fiber development were examined. - We investigated putative functional LncRNA candidates by differential expres- sion analysis and co-expression network construction during cotton fiber development between Ligon-lintless-1 mutant and its wild-type.. - Cotton fiber initiation and rapid elongation stages are crucial stages with greater impact on fiber quantity and fiber length. - It is essential to understand the various mo- lecular pathways involved in the development of cotton fiber. - c The number of expressed LncRNA and protein-coding transcripts in each cotton fiber stage. - Differentially expressed LncRNAs at different stages of cotton fiber development. - We examined the expression levels of LncRNAs related to cotton fiber development at 0 and 8 DPA using. - To address whether the expression pattern of the LncRNAs is linked to a specific stage of cotton fiber development, we analyzed the differential expression levels of LncRNAs of each transcript between Ligon-lintless-1 mutant and near isogonic wild-type. - The LncRNAs expression profiles in cotton fiber develop- ment were carried out by Cuffdiff which provided statis- tical procedures of determining the differential expression in a digital transcript of LncRNAs expression data using a model based on the negative binomial distribution [37]. - Common differentially expressed LncRNAs in cotton fiber development. - Cotton fiber initiation and elongation are key stages to determine the number and length of the fiber cell devel- opment. - Lint of cotton fiber is supposed to appear on the day of anthesis (0 DPA) and continuously elongate until three weeks after the day post anthesis [9]. - To predict putative functional LncRNAs related to cotton fiber development during initiation and elongation stages, the expression of 22 common LncRNAs were found at 0 and 8 DPA (Fig. - The result showed that 19 LncRNAs were up-regulated in Ligon-lintless-1 mu- tant as compared to the wild-type during initiation stage of cotton fiber (0 DPA) while only 3 LncRNAs (LNC_. - 017608, LNC_012210 and LNC_007516) were down-reg- ulated in cotton fiber development at 0 DPA (Table 1).. - The ex- pression of these LncRNAs might in part trigger the early cessation of cotton fiber development in the Ligon- lintless-1 mutant. - These LncRNAs have significantly higher transcription levels in normal cotton fiber than in mutant cotton fiber at 8 DPA (q-value <. - Phos- phorylation is a process mediated by protein kinases to activate critical cellular pathways such as metabolism, cell division and cell differentiation during initiation stage in cotton fiber development [43]. - process during cotton fiber development [44]. - They may possibly play an important role during initiation and elongation stages of cotton fiber development. - Based on the GO and KEGG analysis, we identified some potentially key target genes which were enriched in fatty acid biosynthesis, fatty acid metabolism, fatty acid elongation and transport process were down-regulated in Ligon-lintless-1 as compared to the wild-type during the elongation stage of cotton fiber development. - These possible target genes provide new insight into the role of LncRNAs in cotton fiber develop- mental stages. - In addition, plant hormone metabolism could also have effect on cotton fiber development at elongation stage, for example, a large number of LncRNAs were found to be involved in the metabolism of auxin, ethylene, abscisic acid (ABA) and gibberellin [45]. - Table 1 Common differentially expressed LncRNAs in Ligon- lintless-1 mutant as compared to wild-type during cotton fiber development. - In this study, we identified 14 miRNAs which were differentially expressed during cotton fiber development in Ligon-lintless-1 as compared to wild-. - Among these miRNAs, ghr-miR2950 (targeting to fatty acid hydrolase), ghr-miR7506, ghr-miR7504a (tar- geting to cleave carbohydrate-Active enzymes family), ghr-miR7484a (targeted to cleave Ring/U-box domain containing protein) and ghr-miR7502, ghr-miR7499, ghr-miR7492a, ghr-miR399e (targeted to cleave AP2/B3- like transcriptional factor), ghr-miR156c (targeted to cleave squamosal promoter-binding protein), ghr- miR169b and ghr-miR7496a were down-regulated in Ligon-lintless-1 whereas ghr-miR7510a (targeted to cleave peroxidase super family protein) and ghr-miR7506, ghr- miR7498 and ghr-miR7497 were up-regulated in Ligon- lintless-1 during cotton fiber development, indicating that cotton mutation strongly disturbed their expressions. - Recently, the growing evidence suggests that cytoskeleton is involved in regulating cotton fiber development [42]. - The low expression pattern of Actin depolymerizing factor gene affects cotton fiber development [52]. - Tubulin is a vital cytoskeleton protein with significance in cotton fiber elongation [54].. - Expression verification of candidate LncRNAs involved in cotton fiber development. - RT-qPCR analysis showed that all of the up-regulated LncRNAs were highly expressed in Ligon- lintless-1 mutant but not in wild-type, this validates the negative role of LncRNAs in cotton fiber development during elongation stage (Fig. - Addition- ally, the results of this study revealed that the majority of differentially expressed LncRNAs were precisely expressed at the specific stage of development, indicating the functional divergence of LncRNAs in cotton fiber development. - Gene Ontology and KEGG pathway analyses based on differentially expressed LncRNAs on target genes identi- fied fatty acid biosynthesis as an inhibitory process related to cotton fiber development (Figs. - Fatty acid biosynthesis and fatty acid elongation were down-regulated in the Ligon-lintless-1 mutant at 8 DPA contrary to the previous finding in which fatty acid biosynthesis and fatty acid elongation were found to be up-regulated during cotton fiber elongation [66, 57].. - The enzymes that catalyze fatty acid metabolism in Ligon-lintless-1 mutant might indirectly or directly be involved in cotton fiber elong- ation. - Gene Ontology and KEGG pathway analyses based on differentially expressed LncRNAs on target genes identi- fied fatty acid biosynthesis as an inhibitory process re- lated to cotton fiber development (Figs. - In addition, a greater percentage of the differentially expressed LncRNAs in Ligon-lintless-1 were specifically targeted by miRNA, which is an indication of their pos- sible roles in the development process of cotton fiber.. - Privous several studies reported the influence of miR- NAs in cotton fiber development [31, 50]. - Down-regulated LncRNAs (a) and up-regulated LncRNAs (b) were highly expressed in Ligon-lintless-1 mutant and wild-type during cotton fiber development based on RNA-seq data.. - Previously, it was indicated that, ghr-miR7484 had a role in regulating cotton fiber development through targeting MYB in cot- ton [50]. - This implied that ghr-miR7484a might be in- volved in regulation of cotton fiber development during elongation stage. - RING/U-box super family proteins were involved in the transitional developmental stages of cotton fiber [62]. - Peroxidase was found to directly correlates to the accumulation of reactive oxygen species which related to cotton fiber elongation [63]. - The high expression levels of ghr- miR7510b and ghr-miR7492a in Ligon-lintless-1 at 0 DPA were to trigger the initiation of cotton fiber while their lower expression levels during elongation stages at 8 DPA initiated the cessation of cotton fiber elongation.. - This result provides a strong indica- tion that genes related to cell wall metabolism could be playing key roles in cotton fiber development. - In cotton, pectin methylesterase could play an important role in cell fiber wall structure of cotton fiber through pectin deposition [69]. - Lipids are involved in the regulation of cotton fiber elongation stage through facili- tating the transportation of phosphatidylinositol [70].. - 001237, LNC_017085 and ghr-miR2950 being integral molecular elements that are likely involved in the various pathways of cotton fiber development.. - The findings of this study provide novel insights into the better understanding of LncRNAs regulatory role in the molecular pathways regulating cotton fiber development.. - hirsutum , Ligon-lintless-1 mutant (Li2Li2) and its wild-type (li2li2) were derived from self-pollinated Ligon-lintless-1plants of at least more 6 generations in our lab [72]. - Cotton bolls were collected at 0 (ovules) and 8 DPA (Fiber) during cotton fiber develop- ment. - Biological triplicates for each sample were col- lected during cotton fiber development at 0 and 8 DPA from Ligon-lintless-1 and wild-type. - All transcrip- tomes from four cotton fiber development samples were pooled and merged to perform a comprehensive transcrip- tome using Cuffmerge. - Biological triplicates of RNA samples extracted from cotton fiber development at 0 and 8 DPA were combined together for preparation of Ligon-lintless-1 and wild-type micro- RNA libraries, separately. - To examine the LncRNA expression patterns, cotton tissues from Ligon-lintles-1 and its wild-type were har- vested at different stages of cotton fiber development such as and 15 DPA. - RT-qPCR analysis was applied to test LncRNAs expression levels during developmental stages of cotton fiber. - Differentially expressed LncRNAs in Ligon- lintless-1 and wild-type during cotton fiber development were expressed at 0 and 8 DPA. - Differentially expressed LncRNAs during cotton fiber development at 0 DPA in Ligon-lintless-1 and wild-type (XLSX 10464 kb). - Differentially expressed miRNAs in Ligon- lintless-1 mutant as compared to wild-type were expressed during cotton fiber development at 0 and 8 DPA. - Li-1: Ligon-lintless-1. - Development of the cotton Fiber. - Analysis of gene expression in cotton fiber initials.. - Changes in biochemical composition of the cell wall of the cotton fiber during development. - The R3-MYB gene GhCPC negatively regulates cotton Fiber elongation. - Enrichment of a set of microRNAs during the cotton fiber development. - Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant.. - Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. - Transcriptome analysis reveals critical genes and key pathways for early cotton fiber elongation in Ligon lintless-1 mutant.. - Small RNA sequencing and degradome analysis of developing fibers of short fiber revealed a role for miRNAs and their targets in cotton fiber elongation. - Comparative proteomic analysis of cotton Fiber development and protein extraction method comparison in late stage fibers. - Role of abscisic acid in cotton fiber development. - MicroRNA expression profiles during cotton ( Gossypium hirsutum L) fiber early development. - Transcriptome Analysis of Short Fiber Mutant Ligon lintless-1 ( Li 1 ) Reveals Critical Genes and Key Pathways in Cotton Fiber Elongation and Leaf Development. - Comparative evolutionary and developmental dynamics of the cotton ( Gossypium hirsutum ) Fiber transcriptome. - Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation. - Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. - Saturated very-long-chain fatty acids promote cotton Fiber and Arabidopsis cell. - Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development. - GhLTPG1, a cotton GPI- anchored lipid transfer protein, regulates the transport of phosphatidylinositol monophosphates and cotton fiber elongation. - Delineating the glycoproteome of elongating cotton fiber cells. - Comparative transcriptome analysis of TUCPs in Gossypium hirsutum Ligon-lintless-1 mutant and their proposed functions in cotton fiber development
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