Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner's predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5′ and 3′ termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by PCR assays or by in silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously to our knowledge, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.A lthough transposable elements constitute the bulk of most sequenced eukaryotic genomes, their annotation has been hindered by their rapid evolutionary divergence. It is conceivable that a large fraction of the unannotated genome of most eukaryotes is made up of as yet unrecognized transposons. To date, elements have been assigned to a superfamily largely on the basis of terminal sequence homology to other elements that still encode vestiges of that superfamily's transposase (1). Helitrons are particularly challenging to identify because, unlike other DNA transposons, they do not end in inverted repeats or create target site duplications. These novel eukaryotic transposons were discovered only recently from a comparative bioinformatic analysis of several plant and animal genomes (2). Helitrons have attracted widespread attention because their remarkable ability to capture gene sequences, and intergenic regions containing potential regulatory elements, makes them of considerable potential evolutionary importance (3-10). Among carefully studied genomes, Helitron content has been estimated to be approximately 2% in Arabidopsis and maize (2, 11, 12) and 4.23% in silkworm (9). However, these values are most likely underestimates because Helitrons are hard to detect computationally given their lack of classical transposon structural features. As...

Maize Helitron transposons are intriguing because of their notable ability to capture gene fragments and move them around the genome. To document more extensively their variability and their contribution to the remarkable genome structure variation of present-day maize, we have analyzed their composition, copy number, timing of insertion, and chromosomal distribution. First, we searched 2.4 Gb of sequences generated by the Maize Genome Sequencing Project with our HelitronFinder program. We identified 2,791 putative nonautonomous Helitrons and manually curated a subset of 272. The predicted Helitrons measure 11.9 kb on average and carry from zero to nine gene fragments, captured from 376 different genes. Although the diversity of Helitron gene fragments in maize is greater than in other species, more than one-third of annotated Helitrons carry fragments derived from just one of two genes. Most members in these two subfamilies inserted in the genome less than one million years ago. Second, we conducted a BLASTN search of the maize sequence database with queries from two previously described agenic Helitrons not detected by HelitronFinder. Two large subfamilies of Helitrons or Helitron-related transposons were identified. One subfamily, termed Cornucopious, consists of thousands of copies of an Ϸ1.0-kb agenic Helitron that may be the most abundant transposon in maize. The second subfamily consists of >150 copies of a transposonlike sequence, termed Heltir, that has terminal inverted repeats resembling Helitron 3 termini. Nonautonomous Helitrons make up at least 2% of the maize genome and most of those tested show ؉/؊ polymorphisms among modern inbred lines.

Although maize (Zea mays) retrotransposons are recombinationally inert, the highly polymorphic structure of maize haplotypes raises questions regarding the local effect of intergenic retrotransposons on recombination. To examine this effect, we compared recombination in the same genetic interval with and without a large retrotransposon cluster. We used three different bz1 locus haplotypes, McC, B73, and W22, in the same genetic background. We analyzed recombination between the bz1 and stc1 markers in heterozygotes that differ by the presence and absence of a 26-kb intergenic retrotransposon cluster.To facilitate the genetic screen, we used Ds and Ac markers that allowed us to identify recombinants by their seed pigmentation. We sequenced 239 recombination junctions and assigned them to a single nucleotide polymorphism-delimited interval in the region. The genetic distance between the markers was twofold smaller in the presence of the retrotransposon cluster. The reduction was seen in bz1 and stc1, but no recombination occurred in the highly polymorphic intergenic region of either heterozygote. Recombination within genes shuffled flanking retrotransposon clusters, creating new chimeric haplotypes and either contracting or expanding the physical distance between markers. Our findings imply that haplotype structure will profoundly affect the correlation between genetic and physical distance for the same interval in maize.

The fall armyworm (FAW), native to the Americas, has rapidly invaded the whole of Southern China since January 2019. In addition, it can survive and breed in the key maize- and rice- growing area of the Yangtze River Valley. Furthermore, this pest is also likely to continue infiltrating other cropping regions in China, where food security is facing a severe threat. To understand the potential infestation area of newly-invaded FAW from the Yangtze River Valley, we simulated and predicted the possible flight pathways and range of the populations using a numerical trajectory modelling method combining meteorological data and self-powered flight behavior parameters of FAW. Our results indicate that the emigration of the first and second generations of newly-invaded FAW initiating from the Yangtze River Valley started on 20 May 2019 and ended on 30 July 2019. The spread of migratory FAW benefitted from transport on the southerly summer monsoon so that FAW emigrants from the Yangtze River Valley can reach northern China. The maize-cropping areas of Northeastern China, the Korean Peninsula and Japan are at a high risk. This study provides a basis for early warning and a broad picture of FAW migration from the Yangtze River Valley.