Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function

Mehrotra, Shweta; Goyal, Vinod

doi:10.1016/j.gpb.2014.07.003

Cited by 228 publications

(195 citation statements)

References 93 publications

(103 reference statements)

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“…To determine the relative frequency of metabolic gene clusters per genome, we used the number of protein-encoding genes as a proxy for genome size because plant genomes vary tremendously in physical size due to repetitive sequences (Mehrotra and Goyal, 2014). We obtained the total number of protein-encoding genes from the databases where we obtained the genomes (Goodstein et al, 2012;Kersey et al, 2014) and plotted the number of predicted clusters as a function of the number of protein-encoding genes (Supplemental Fig.…”

Section: Handling Sequencing Gaps In Metabolic Gene Cluster Predictionmentioning

confidence: 99%

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

Schläpfer

Zhang²,

Wang³

et al. 2017

Plant Physiol.

316

284

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Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.

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Section: Handling Sequencing Gaps In Metabolic Gene Cluster Predictionmentioning

confidence: 99%

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

Schläpfer

Zhang²,

Wang³

et al. 2017

Plant Physiol.

316

284

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“…Mehrotra and Goyal [2014] provided a review of monomer sizes of different plant satellite DNA families. Also, information concerning composition and characteristics can be found in PlantSat, a database that provides a list of satellite DNA sequences for many plant species (http://w3lamc.…”

Section: Satellite Dna a Family Of Sequences That Get On Well With Ementioning

confidence: 99%

“…umbr.cas.cz/PlantSat/) [Macas et al, 2002]. According to Mehrotra and Goyal [2014], plant satellite DNA sequences commonly have monomer unit lengths of 135-195 or 315-375 bp, but repeat length may range between 58 bp of the pAm1 satellite DNA of Avena and 5.9 kb of the 2D8 repeats of Solanum bulbocastanum . According to this classical view of satellite DNA, even shorter monomer length has been found as, for example, the 38 bp of VicTR-B satellite DNA of Vicia .…”

Section: Satellite Dna a Family Of Sequences That Get On Well With Ementioning

confidence: 99%

Satellite DNA in Plants: More than Just Rubbish

Garrido-Ramos

2015

Cytogenet Genome Res

145

149

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For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

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“…Despite these challenges, REs hold much information related to epigenetic control mechanisms, chromosome and genome dynamics, gene regulation, and genome evolution (Nowak 1994;Mihai et al 2002;Biémont and Vieira 2006;Chadwick 2009;Biemont 2010;Claros et al 2012;Schatz et al 2012;Melters et al 2013;Mehrotra and Goyal 2014;Renny-Byfield and Wendel 2014). Hence, they deserve genome-wide analysis.…”

Section: Introductionmentioning

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.

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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.

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Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function

Cited by 228 publications

References 93 publications

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

Satellite DNA in Plants: More than Just Rubbish

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

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