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Plant jumping genes: celebrating the legacy of Barbara McClintock
Barbara McClintock was an American geneticist at the Cold Spring Harbor Laboratory, who dedicated her career to the study of hereditary traits in maize. Armed with rudimentary imaging tools and a sharp eye for genetics, McClintock understood that the spotted colouration of maize kernels was due to a complex four gene system, including “jumping genes” capable of changing their position within the chromosome. Largely misunderstood at the time, this phenomenon, nowadays known as transposition, was later identified in other organisms, challenging the general perception of genome organization across kingdoms. For this discovery, Barbara McClintock was finally awarded the Nobel Prize in Physiology or Medicine in 1983, becoming only the third female unshared winner. Transposable elements are nowadays known to comprise the largest single fraction of the genome of most eukaryotes, up to 85% in maize, playing key roles in gene expression regulation and speciation.
To celebrate the 40th anniversary of Barbara McClintock´s Nobel Prize, we have put together a Collection of recent articles on plant “jumping genes” published across Springer Nature journals, highlighting her contribution to current Plant Biology.
Commemorating the 40th anniversary of Barbara McClintock’s Nobel Prize in Physiology or Medicine for her discovery of transposable elements, Cédric Feschotte reflects on McClintock’s life and legacy and how her work has shaped and defined the field of genetics.
Forty years ago, Barbara McClintock — an exceptional plant scientist — was awarded the Nobel Prize for Physiology or Medicine; only the third woman to win a Nobel prize without collaborators.
Assigning assembled chromosomes to subgenome in allopolypoid genome analysis is challenging. Here, the authors report a statistical formwork for identifying evolutionarily coherent subgneomes relying on transposable elements to group chromosomes into sets with shared ancestry and apply it in cyprinids, false flax and strawberry.
Inter- and intra-species comparison of Arabidopsis centromere variation identifies rapid cycles of transposon invasion and purging through satellite homogenization that drive centromere evolution.
How subgenome-divergent and -convergent transcription is mediated and harmonized in hexaploid common wheat genome remains unclear. Here, via characterizing the cistrome maps, the authors reveal that transposon elements with transcription factor binding ability have the potential to make the contribution.
How highly inbred populations generate novel genetic variations upon which natural selection can act is unclear. Here, the authors reveal the effect of transposable elements on the genome-wide heterozygosity landscape across a natural inbreeding gradient of Arabidopsis lyrata and reducing the probability of inbreeding depression.
Codon usage bias of transposons (TEs) causes ribosome stalling, inducing truncated RNAs that are guided to siRNA bodies for epigenetically activated small interfering RNA (easiRNA) biogenesis. This process selectively targets TEs to the easiRNA biogenesis pathway for silencing and involves SGS3 phase separation.
MALE-ASSOCIATED ARGONAUTE-1 and -2 promote heat-induced phasiRNA production, which represses heat-activated retrotransposons and protects male fertility. This activity is regulated by heat-mediated hypophosphorylation of the Argonaute proteins.
Ryoichi Yano et al. report a Nanopore-based reference genome assembly of muskmelon—a fruit known for its many cultivated varieties, including cantaloupe and honeydew—using the Japanese Harukei-3 cultivar. They identify structural genetic variation by comparing the reference to several melon genome assemblies and investigate tissue-wide gene expression patterns by RNA sequencing.
Transposable element insertion polymorphisms (TIPs) are a potential source of large effect alleles. Here, the authors use genome resequencing data for 602 tomato accessions together with transcriptomic and extensive phenotypic information to investigate the contribution of TIPs to tomato diversity.
RNA-directed DNA methylation (RdDM) is thought to silence newly inserted transposable elements (TEs) with RNA-independent mechanisms becoming more prominent as TEs age. Here, the authors show that RdDM continues to silence the oldest intact distal TEs in tomato and Arabidopsis suggesting a second, later phase of RdDM.
Long-range cis-regulatory elements play important roles in regulating agronomic traits, but they are largely uncharacterized in crops. This study provides genetic, epigenomic and functional molecular evidence to support their widespread existence in the maize genome.
By examining chromatin accessibility and modification as well as sequence conservation in 13 plant species, this study characterizes thousands of putative cis-regulatory elements and reveals their prevalence, dynamic evolution and chromatin signatures.