Evolutionary dynamics of transposable elements following a shared polyploidization event in the tribe Andropogoneae

AbstractBoth polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a recent shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed existing variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although the genomes of all species studied had abundant LTR-retrotransposons, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these copia elements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.

Download Full-text

Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401596 ◽

2020 ◽

Vol 10 (12) ◽

pp. 4387-4398

Author(s):

Dhanushya Ramachandran ◽

Michael R. McKain ◽

Elizabeth A. Kellogg ◽

Jennifer S. Hawkins

Keyword(s):

Insertional Mutagenesis ◽

Evolutionary Dynamics ◽

Diploid Species ◽

Duplicate Gene ◽

Plant Genome ◽

Abiotic Stress Response ◽

Repeat Content ◽

Gene Copies ◽

Polyploidization Event ◽

Plant Genome Evolution

Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.

Download Full-text

High-throughput vectors for efficient gene silencing in plants

Functional Plant Biology ◽

10.1071/fp02033 ◽

2002 ◽

Vol 29 (10) ◽

pp. 1217 ◽

Cited By ~ 99

Author(s):

Chris A. Helliwell ◽

S. Varsha Wesley ◽

Anna J. Wielopolska ◽

Peter M. Waterhouse

Keyword(s):

Gene Silencing ◽

Insertional Mutagenesis ◽

Single Step ◽

Plant Genome ◽

Specific Gene ◽

Single Polymerase Chain Reaction ◽

Efficient Gene ◽

Gene Redundancy ◽

Endogenous Genes ◽

Rapid Generation

A major challenge in the post-genome era of plant biology is to determine the functions of all genes in the plant genome. A straightforward approach to this problem is to reduce or knockout expression of a gene with the hope of seeing a phenotype that is suggestive of its function. Insertional mutagenesis is a useful tool for this type of study but is limited by gene redundancy, lethal knockouts, non-tagged mutants, and the inability to target the inserted element to a specific gene. The efficacy of gene silencing in plants using inverted-repeat transgene constructs that encode a hairpin RNA (hpRNA) has been demonstrated by a number of groups, and has several advantages over insertional mutagenesis. In this paper we describe two improved pHellsgate vectors that facilitate rapid generation of hpRNA-encoding constructs. pHellsgate 4 allows the production of an hpRNA construct in a single step from a single polymerase chain reaction product, while pHellsgate 8 requires a two-step process via an intermediate vector. We show that these vectors are effective at silencing three endogenous genes in Arabidopsis, FLOWERING LOCUS C, PHYTOENE DESATURASE and ETHYLENE INSENSITIVE 2. We also show that a construct of sequences from two genes silences both genes.

Download Full-text

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

10.1101/786145 ◽

2019 ◽

Cited By ~ 4

Author(s):

Lillian K. Padgitt-Cobb ◽

Sarah B. Kingan ◽

Jackson Wells ◽

Justin Elser ◽

Brent Kronmiller ◽

...

Keyword(s):

Large Scale ◽

Humulus Lupulus ◽

Plant Genome ◽

Repeat Content ◽

Haplotype Variation ◽

Genomic Landscape ◽

Cannabidiolic Acid ◽

Long Read ◽

History Of ◽

Insight Into

AbstractHop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

Download Full-text

The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana

Molecular Biology and Evolution ◽

10.1093/molbev/msaa306 ◽

2020 ◽

Author(s):

Wen-Biao Jiao ◽

Vipul Patel ◽

Jonas Klasen ◽

Fang Liu ◽

Petra Pecinkova ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Natural Populations ◽

Population History ◽

Duplicated Genes ◽

Genetic Incompatibility ◽

Additional Gene ◽

Genomic Changes ◽

Gene Copies ◽

Geographic Origins ◽

The Individual

Abstract Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.

Download Full-text

RNA directed DNA methylation and seed plant genome evolution

Plant Cell Reports ◽

10.1007/s00299-020-02558-4 ◽

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

Download Full-text

Plant Genome Evolution: Meat Lovers Expanded Gene Families for Carnivory and Dropped the Rest

Current Biology ◽

10.1016/j.cub.2020.04.005 ◽

2020 ◽

Vol 30 (12) ◽

pp. R700-R702

Author(s):

Sophie de Vries ◽

Jan de Vries

Keyword(s):

Genome Evolution ◽

Gene Families ◽

Plant Genome ◽

Plant Genome Evolution

Download Full-text

Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data

10.1101/2020.06.19.162107 ◽

2020 ◽

Author(s):

Michael DeGiorgio ◽

Raquel Assis

Keyword(s):

Gene Expression ◽

Gene Duplication ◽

Statistical Learning ◽

Gene Evolution ◽

Functional Divergence ◽

Duplicate Gene ◽

Duplicate Genes ◽

Evolutionary Mechanisms ◽

Retention Mechanisms ◽

Gene Copies

AbstractLearning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. To date, only one method—CDROM—has been developed with this goal in mind. In particular, CDROM employs gene expression distances as proxies for functional divergence, and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the underlying parameters of duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built upon a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents the best available method for classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby also highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.

Download Full-text

Homeolog expression quantification methods for allopolyploids

Briefings in Bioinformatics ◽

10.1093/bib/bby121 ◽

2018 ◽

Vol 21 (2) ◽

pp. 395-407 ◽

Cited By ~ 6

Author(s):

Tony C Y Kuo ◽

Masaomi Hatakeyama ◽

Toshiaki Tameshige ◽

Kentaro K Shimizu ◽

Jun Sese

Keyword(s):

Sequence Similarity ◽

Diploid Species ◽

Ground Truth ◽

Error Rates ◽

Rna Seq ◽

Gene Copies ◽

The Difference ◽

Downstream Analysis ◽

High Level ◽

Expression Quantification

Abstract Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (<1% using EAGLE-RC, <2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method in wheat. In general, disagreement in low-expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.

Download Full-text