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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
..., not only into the genomic dynamics in maize but also into the general contribution of LTR-RTs to biodiversity in plants. The selective determinants of TE content are likely diverse, occurring at the TE family level based on insertional preference (e.g., genic vs. nongenic regions) (Stitzer et al. 2021...
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Research: Large haplotypes highlight a complex age structure within the maize pan-genome
- Jianing Liu and
- R. Kelly Dawe
Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122
...-by-all manner and retaining the unique portions contributed by each, we estimated the total (genic and intergenic) pan- size to be ∼7.9 Gb (Supplemental Fig. S6A), which is ∼3.7 times larger than the average assembled size of any single (Hufford et al. 2021). Only ∼4.9% of the total pan- (0.38 Gb) is conserved...
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Research: The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
- Michael Regulski,
- Zhenyuan Lu,
- Jude Kendall,
- Mark T.A. Donoghue,
- Jon Reinders,
- Victor Llaca,
- Stephane Deschamps,
- Andrew Smith,
- Dan Levy,
- W. Richard McCombie,
- Scott Tingey,
- Antoni Rafalski,
- James Hicks,
- Doreen Ware,
- and Robert A. Martienssen
Genome Res. October 2013 23: 1651-1662; Published in Advance June 5, 2013, doi:10.1101/gr.153510.112
..., but not necessarily processed into small RNA (Topp et al. 2004). Gene body methylation may deter transposon insertions Gene body methylation has been widely observed in eukaryotes, but its function is still unclear. Focusing on the genic regions and surrounding promoters, we constructed a ‘‘metagene’’ methylation...
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Research: Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
- Elodie Gazave,
- Fleur Darré,
- Carlos Morcillo-Suarez,
- Natalia Petit-Marty,
- Angel Carreño,
- Urko M. Marigorta,
- Oliver A. Ryder,
- Antoine Blancher,
- Mariano Rocchi,
- Elena Bosch,
- Carl Baker,
- Tomàs Marquès-Bonet,
- Evan E. Eichler,
- and Arcadi Navarro
Genome Res. October 2011 21: 1626-1639; Published in Advance August 8, 2011, doi:10.1101/gr.117242.110
...in these two species, particularly in the orangutan. Comparing the levels of structural polymorphism in genic and nongenic CNVRs among and within species, orangutan and gorilla show a decrease of common variants in genic CNVs, which may be interpreted as genic CNVs being under stronger purifying selection...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...and are dominated by long introns (Francis and Wörheide 2017). Thus, merely targeting gene PAVs in a mammalian pan analysis may obtain limited coding SV information (Sherman and Salzberg 2020). Incorporating both genic and nongenic coding SVs, such as SVs resulting from recently or currently active TE coding...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
..., the absence of H3K9me2 at the genic loci, and the presence of H3K27me3 at both genic and nongenic regions (Methods) (Supplemental Fig. S10A). Differential enrichment analyses revealed 7686 loci possessing significantly higher H3K27me3 occupancy in kd compared with WT, validating the immunostaining...
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