scholarly journals The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

2021 ◽  
Author(s):  
Jack S. Gisby ◽  
Marco Catoni
Keyword(s):  
Genome Evolution ◽  
Dna Sequences ◽  
Plant Genome ◽  
Genome Plasticity ◽  
High Similarity ◽  
Chromosomal Dna ◽  
Dna Transposons ◽  
Automated Annotation ◽  
Plant Genome Evolution

Pack-TYPE transposable elements (TEs) are a group of non-autonomous DNA transposons found in plants. These elements can efficiently capture and shuffle coding DNA across the host genome, accelerating the evolution of genes. Despite their relevance for plant genome plasticity, the detection and study of Pack-TYPE TEs are challenging due to the high similarity these elements have with genes. Here, we produced an automated annotation procedure designed to study Pack-TYPE elements and used it to successfully annotate and analyse more than 4000 new Pack-TYPE TEs in the rice and maize genomes. Our analysis indicates that Pack-TYPE TEs are an abundant and heterogeneous group of elements. We found that these elements are associated with all main superfamilies of Class II DNA transposons in plants and likely share a similar mechanism to capture new chromosomal DNA sequences. Furthermore, we report examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack-TYPE TEs in plant genome evolution.

scholarly journals RNA directed DNA methylation and seed plant genome evolution

2020 ◽  
Vol 39 (8) ◽  
pp. 983-996
Author(s):  
R. Wambui Mbichi ◽  
Qing-Feng Wang ◽  
Tao Wan
Keyword(s):  
Dna Methylation ◽  
Genome Evolution ◽  
Plant Genome ◽  
Seed Plant ◽  
Plant Genome Evolution

scholarly journals Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution

Nature Plants ◽  
2019 ◽  
Vol 5 (1) ◽  
pp. 63-73 ◽  
Author(s):  
Shu-Miaw Chaw ◽  
Yu-Ching Liu ◽  
Yu-Wei Wu ◽  
Han-Yu Wang ◽  
Chan-Yi Ivy Lin ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Plant Genome ◽  
Flowering Plant ◽  
Plant Genome Evolution ◽  
Camphor Tree

Epigenetics and plant genome evolution

2014 ◽  
Vol 18 ◽  
pp. 1-8 ◽  
Author(s):  
Concepcion M Diez ◽  
Kyria Roessler ◽  
Brandon S Gaut
Keyword(s):  
Genome Evolution ◽  
Plant Genome ◽  
Plant Genome Evolution

Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 887-892 ◽  
Author(s):  
Anne-Marie van Dodeweerd ◽  
Caroline R Hall ◽  
Elisabeth G Bent ◽  
Samantha J Johnson ◽  
Michael W Bevan ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Genome Structure ◽  
Plant Genome ◽  
Fine Scale ◽  
Plant Genomics ◽  
Homologous Genes ◽  
Conserved Genes ◽  
Plant Genome Evolution

Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.

scholarly journals Polyploidization as a Retraction Force in Plant Genome Evolution: Sequence Rearrangements in Triticale

PLoS ONE ◽  
2008 ◽  
Vol 3 (1) ◽  
pp. e1402 ◽  
Author(s):  
Miguel Bento ◽  
H. Sofia Pereira ◽  
Margarida Rocheta ◽  
Perry Gustafson ◽  
Wanda Viegas ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Plant Genome ◽  
Plant Genome Evolution ◽  
Retraction Force ◽  
Evolution Sequence
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