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1. Genome‐wide analysis of flanking sequences reveals that  Tnt1 insertion is positively correlated with gene methylation in Medicago truncatula

   https://doi.org/10.1111/tpj.14291  

   Sun, Liang; Gill, Upinder S.; Nandety, Raja Sekhar; Kwon, Soonil; Mehta, Perdeep; Dickstein, Rebecca; Udvardi, Michael K.; Mysore, Kirankumar S.; Wen, Jiangqi (March 2019, The Plant Journal)

   Summary From a single transgenic line harboring fiveTnt1transposon insertions, we generated a near‐saturated insertion population inMedicago truncatula. Using thermal asymmetric interlaced‐polymerase chain reaction followed by sequencing, we recovered 388 888 flanking sequence tags (FSTs) from 21 741 insertion lines in this population.FSTrecovery from 14Tnt1lines using the whole‐genome sequencing (WGS) and/orTnt1‐capture sequencing approaches suggests an average of 80 insertions per line, which is more than the previous estimation of 25 insertions. Analysis of the distribution pattern and preference ofTnt1insertions showed thatTnt1is overall randomly distributed throughout theM. truncatulagenome. At the chromosomal level,Tnt1insertions occurred on both arms of all chromosomes, with insertion frequency negatively correlated with theGCcontent. Based on 174 546 filteredFSTs that show exact insertion locations in theM. truncatulagenome version 4.0 (Mt4.0), 0.44Tnt1insertions occurred per kb, and 19 583 genes containedTnt1with an average of 3.43 insertions per gene. Pathway and gene ontology analyses revealed thatTnt1‐inserted genes are significantly enriched in processes associated with ‘stress’, ‘transport’, ‘signaling’ and ‘stimulus response’. Surprisingly, gene groups with higher methylation frequency were more frequently targeted for insertion. Analysis of 19 583Tnt1‐inserted genes revealed that 59% (1265) of 2144 transcription factors, 63% (765) of 1216 receptor kinases and 56% (343) of 616 nucleotide‐binding site‐leucine‐rich repeat genes harbored at least oneTnt1insertion, compared with the overall 38% ofTnt1‐inserted genes out of 50 894 annotated genes in the genome. 

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2. Spontaneous homeotic mutants and genetic control of floral organ identity in a ranunculid

   https://doi.org/10.1111/ede.12357  

   Martínez‐Gómez, Jesús; Galimba, Kelsey D.; Coté, Erin Y.; Sullivan, Alessandra M.; Di Stilio, Verónica S. (November 2020, Evolution & Development)

   Abstract The regulation of floral organ identity was investigated using a forward genetic approach in five floral homeotic mutants ofThalictrum, a noncore eudicot. We hypothesized that these mutants carry defects in the floral patterning genes. Mutant characterization comprised comparative floral morphology and organ identity gene expression at early and late developmental stages, followed by sequence analysis of coding and intronic regions to identify transcription factor binding sites and protein–protein interaction (PPI) motifs. Mutants exhibited altered expression of floral MADS‐box genes, which further informed the function of paralogs arising from gene duplications not found in reference model systems. The ensuing modified BCE models for the mutants supported instances of neofunctionalization (e.g., B‐class genes expressed ectopically in sepals), partial redundancy (E‐class), or subfunctionalization (C‐class) of paralogs. A lack of deleterious mutations in the coding regions of candidate floral MADS‐box genes suggested thatcis‐regulatory ortrans‐acting mutations are at play. Consistent with this hypothesis, double‐flower mutants had transposon insertions or showed signs of transposon activity in the regulatory intron ofAGAMOUS(AG) orthologs. Single amino acid substitutions were also found, yet they did not fall on any of the identified DNA binding or PPI motifs. In conclusion, we present evidence suggesting that transposon activity and regulatory mutations in floral homeotic genes likely underlie the striking phenotypes of theseThalictrumfloral homeotic mutants. 

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3. Structure and Origin of the White Cap Locus and Its Role in Evolution of Grain Color in Maize

   https://doi.org/10.1534/genetics.116.198911  

   Tan, Bao-Cai; Guan, Jiahn-Chou; Ding, Shuo; Wu, Shan; Saunders, Jonathan W; Koch, Karen E; McCarty, Donald R (May 2017, Genetics)

   Abstract Selection for yellow- and white-grain types has been central to postdomestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that Wc is exclusive to maize, where it is prevalent in white-grain (y1) varieties. Moreover, Ccd1 copy number varies extensively among Wc alleles (from 1 to 23 copies), and confers a proportional range of Ccd1 expression in diverse organs. We propose that this dynamic source of quantitative variation in Ccd1 expression was created in maize shortly after domestication by a two-step, Tam3L transposon-mediated process. First, a chromosome segment containing Ccd1 and several nearby genes duplicated at a position 1.9 Mb proximal to the progenitor Ccd1r locus on chromosome 9. Second, a subsequent interaction of Tam3L transposons at the new locus created a 28-kb tandem duplication, setting up expansion of Ccd1 copy number by unequal crossing over. In this way, transposon-mediated variation in copy number at the Wc locus generated phenotypic variation that provided a foundation for breeding and selection of white-grain color in maize. 

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4. Mutator transposon insertions within maize genes often provide a novel outward reading promoter

   https://doi.org/10.1093/genetics/iyad171  

   Ellison, Erika L.; Zhou, Peng; Hermanson, Peter; Chu, Yi-Hsuan; Read, Andrew; Hirsch, Candice N.; Grotewold, Erich; Springer, Nathan M.; Birchler, ed., J. (October 2023, GENETICS)

   Abstract The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles that result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu-suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5′ UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and does not depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlight a strategy for transposons to co-exist with their host. 

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5. Mobilome impacts on physiology in the widely used non-toxic mutant Microcystis aeruginosa PCC 7806 ΔmcyB and toxic wildtype

   https://doi.org/10.1186/s12864-024-10839-5  

   Stark, Gwendolyn F; Truchon, Alexander R; Wilhelm, Steven W (December 2024, BMC Genomics)

   Abstract TheMicrocystismobilome is a well-known but understudied component of this bloom-forming cyanobacterium. Through genomic and transcriptomic comparisons, we found five families of transposases that altered the expression of genes in the well-studied toxigenic type-strain,Microcystis aeruginosaPCC 7086, and a non-toxigenic genetic mutant,Microcystis aeruginosaPCC 7806 ΔmcyB. Since its creation in 1997, the ΔmcyBstrain has been used in comparative physiology studies against the wildtype strain by research labs throughout the world. Some differences in gene expression between what were thought to be otherwise genetically identical strains have appeared due to insertion events in both intra- and intergenic regions. In our ΔmcyBisolate, a sulfate transporter gene cluster (sbp-cysTWA) showed differential expression from the wildtype, which may have been caused by the insertion of a miniature inverted repeat transposable element (MITE) in the sulfate-binding protein gene (sbp). Differences in growth in sulfate-limited media also were also observed between the two isolates. This paper highlights howMicrocystisstrains continue to “evolve” in lab conditions and illustrates the importance of insertion sequences / transposable elements in shaping genomic and physiological differences betweenMicrocystisstrains thought otherwise identical. This study forces the necessity of knowing the complete genetic background of isolates in comparative physiological experiments, to facilitate the correct conclusions (and caveats) from experiments. 

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