scholarly journals Transposable elements play an important role during cotton genome evolution and fiber cell development

2015 ◽  
Vol 59 (2) ◽  
pp. 112-121 ◽  
Author(s):  
Kun Wang ◽  
Gai Huang ◽  
Yuxian Zhu
2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lingling DOU ◽  
Limin LV ◽  
Yangyang KANG ◽  
Ruijie TIAN ◽  
Deqing HUANG ◽  
...  

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.


2021 ◽  
pp. gr.275658.121
Author(s):  
Yuyun Zhang ◽  
Zijuan Li ◽  
Yu'e Zhang ◽  
Kande Lin ◽  
Yuan Peng ◽  
...  

More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.


2021 ◽  
Author(s):  
Matias Rodriguez ◽  
Wojciech Makałowski

AbstractTransposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.


2015 ◽  
Vol 95 (6) ◽  
pp. 1215-1220 ◽  
Author(s):  
Guang-Hui Du ◽  
Fei-Hu Liu ◽  
Gordon Rowland

Du, G.-H., Liu, F.-H. and Rowland, G. 2015. Fiber cell development and fiber yield of flax (Linum usitatissimum L.) affected by the seasonal temperature pattern. Can. J. Plant Sci. 95: 1215–1220. Three fiber flax cultivars ‘Ariane’, ‘Argos’ and ‘Viking’ were cultured in growth chambers under three seasonal temperature patterns (STPs) [parabolic (P), anti-parabolic (AP) and quasi-horizontal (QH) configurations]. The effect of STP was studied on fiber cell development and on fiber yield. The results indicated that, compared with the quasi-horizontal seasonal temperature pattern (QH-STP), the size of fiber cell cavity (SFCC) and fiber content (FC) decreased under parabolic seasonal temperature pattern (P-STP). However, the size of fiber cell (SFC) and SFCC decreased, but the number of fiber cells per bundle (NFCB) increased under anti-parabolic seasonal temperature pattern (AP-STP). Moreover, there was a significant positive correlation between fiber weight (FW) and width of fiber bundle (WFB), also between FC and NFCB. Considering the response of fiber flax cultivars to the different STPs, ‘Ariane’ had smaller SFC and SFCC, thinner thickness of fiber cell wall (TFCW) under AP-STP, and smaller SFCC and thicker TFCW under P-STP than under QH-STP, while ‘Argos’ had smaller SFC and SFCC, and higher NFCB under AP-STP, and smaller SFC under P-STP than under QH-STP. However, STPs had little effect on the fiber cell development of ‘Viking’. All three cultivars had high FC under AP-STP than under P-STP. These observations indicate that the fiber cell development and fiber yield of flax were related to the STP and suggest that AP-STP are the most favorable temperature conditions for fiber flax growth.


Mobile DNA ◽  
2010 ◽  
Vol 1 (1) ◽  
pp. 6 ◽  
Author(s):  
Alexander Belyayev ◽  
Ruslan Kalendar ◽  
Leonid Brodsky ◽  
Eviatar Nevo ◽  
Alan H Schulman ◽  
...  

1973 ◽  
Vol 295 (1) ◽  
pp. 166-173 ◽  
Author(s):  
Gerard J. Van Kamp ◽  
Louis H.M. Schats ◽  
Herman J. Hoenders
Keyword(s):  

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Octavio M. Palacios-Gimenez ◽  
Julia Koelman ◽  
Marc Palmada-Flores ◽  
Tessa M. Bradford ◽  
Karl K. Jones ◽  
...  

Abstract Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. Results We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. Conclusion This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.


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