Transposons, Genomic Shock, and Genome Evolution

Fedoroff, Nina V.; Bennetzen, Jeffrey L.

doi:10.1002/9781118500156.ch10

Cited by 21 publications

(17 citation statements)

References 171 publications

(167 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The amplification pattern of PgCACTA and Pg167TR suggests a tetraploid lineage-specific evolutionary pathway associated with the recent Pg-a WGD. These data imply that during the Pg-a WGD, PgCACTA amplification could have been triggered in response to genomic shock as in other plants (Fedoroff and Bennetzen, 2013;Kalendar et al, 2000). Concomitant to this amplification was the amplification of Pg167TR, which led to the distinct chromosomal loci in tetraploid ginseng.…”

Section: Discussionmentioning

confidence: 80%

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

Kim

Jayakodi

Lee

et al. 2018

Plant Biotechnology Journal

153

123

View full text Add to dashboard Cite

Summary Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane‐type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome‐scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics‐assisted breeding or metabolic engineering.

show abstract

Section: Discussionmentioning

confidence: 80%

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

Kim

Jayakodi

Lee

et al. 2018

Plant Biotechnology Journal

153

123

View full text Add to dashboard Cite

show abstract

“…The merging of two genomes often results in genomic shock (Fedoroff 2012;Fedoroff and Bennetzen 2013;Renny-Byfield et al 2013). This genomic shock initiates genome reprogramming by altering the epigenetic makeup that sometimes results in subgenome dominance, which is observed in some plants (Paterson et al 2012;RennyByfield et al 2012) including of the LF subgenome of B. rapa, compared to its MF1 and MF2 subgenomes .…”

Section: Dynamics Of Major Repeats In Brassica and Evolutionary Implimentioning

confidence: 99%

“…DNA and histone modifications, which have a central feedback control mechanism involving siRNAs, are at the core of genome dynamics regulation to ensure genome homeostasis (Peng and Karpen 2008;Haag and Pikaard 2011;Fedoroff 2012;Fedoroff and Bennetzen 2013). Events such as abiotic stress responses (Petit et al 2010), polyploidization, or small-scale duplications (De Smet et al 2013;Renny-Byfield et al 2013) that disrupt this homeostasis can initiate TE and TR removal or accumulation.…”

Section: Epigenetic Control Of Res and Crop Improvementmentioning

confidence: 99%

Repeat Evolution in Brassica rapa (AA), B. oleracea (CC), and B. napus (AACC) Genomes

Waminal

Perumal

Lee

et al. 2016

Plant Breed. Biotech.

View full text Add to dashboard Cite

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT The genus Brassica is an important resource for major agricultural products such as oils, vegetable and fodder. The Brassiceae tribe-specific whole-genome triplication that occurred ~15.9 million years ago influenced the speciation and morphological diversification that has been exploited in agriculture, making Brassica an excellent model system for studying polyploidization-mediated evolution. Genome sequencing and comparative genome analysis have revealed conserved structures and uncovered the genome evolution of Brassica species. While chromosome shuffling and asymmetric subgenome gene retention are widely reported in Brassica species, limited information is available about the dynamics of repetitive elements (REs), which are central to epigenetic mechanisms and thus play a pivotal role in plant genome adaptation and evolution. The assembled reference genome sequences of B. rapa (AA) and B. oleracea (CC), and their derived allotetraploid, B. napus (AACC), cover 58%, 86%, and 75% of their respective estimated genome sizes. The remaining non-assembled genome portions vary between these three genome sequences, and the major components remain hidden in each genome. Here, we review the dynamics of the major Brassica repeats that have played roles in speciation of the AA, CC, and AACC genomes. We show that 10 major Brassica repeats appear to occupy more than 50% of each respective unassembled genome sequence, yet represent less than 1% of assembled reference genome sequences. We have estimated their genome proportions using whole-genome Illumina reads and cytogenetic analyses in an attempt to understand the role of these repeats in genome evolution.

show abstract

“…However, TEs generally exist in eukaryotic genomes in a reversibly inactive, genetically undetectable form we now call "epigenetically silenced," whose discovery can also be traced to McClintock's elegant genetic studies (5,6). As the underlying biochemical mechanisms emerged from obscurity and epigenetics became popular toward the end of the 20th century, it was proposed that epigenetic silencing evolved to control the proliferation of TEs and their perceived destructive potential (5,6).…”

mentioning

confidence: 99%