Aaron R. Leichty

The prolonged production of juvenile traits and an associated reduction or loss of adult traits during development (neoteny) can either arise from a change in genes that mediate the timing of the shift between juvenile and adult traits (timing genes) or from changes in genes that are necessary for the development of adult traits (target genes). To date, the relative contribution of each developmental mechanism to the origins of neoteny remain unclear. We examined this question in the plant genus, Acacia Mill., which contains species that undergo the juvenile-to-adult vegetative transition (vegetative phase change) early in shoot development, as well as species that remain permanently juvenile, or have delayed vegetative phase change. Mapping the timing of vegetative phase change onto a molecular phylogeny of Acacia revealed that permanent juvenility has evolved multiple times and is sometimes associated with a delay in vegetative phase change in related species. In three cases, the absence or delay in vegetative phase change was associated with either higher amounts or a delayed decline in the level of miR156, the master regulator of vegetative phase change in plants. These findings support the hypothesis that neoteny in Acacia has evolved not by a loss in the capacity to produce the adult leaf phenotype but by a change in the timing of genes that promote juvenile leaf identity.

Many citrus species show high levels of heterozygosity due to their hybrid origin and clonal propagation. This heterozygosity can both hinder and aid efforts to study and improve these cultivars, making it increasingly clear that diploid assemblies have significant advantages over the previous generation of haploid assemblies. In this work, we assemble both subgenomes of Mexican lime (Citrus × aurantifolia), an interspecific hybrid between Citrus hystrix var. micrantha and Citrus medica. The resulting diploid assembly is nearly telomere-to-telomere, spanning 680 Mb. Using subgenome-specific repeats, we were able to phase the 18 chromosomes based on their parent of origin. The resulting hystrix and medica haplotypes show a number of large structural variations, consistent with their distant hybrid ancestry. Despite divergence between haplotypes, syntenic gene pairs were identified for over 90% of the annotated protein coding genes. Within these genes, we find extensive divergence between haplotypes, with at least 89% harboring polymorphisms at an average rate of 13 per kilobase of coding sequence. Knowledge of this variation will be important for future efforts to improve this cultivar using genetic engineering technologies.

Clonally propagated crops have long been recognized for their high levels of heterozygosity both between subgenomes within a somatic cell and between cells within an individual clone. Recent developments in long read sequencing technologies have accelerated our ability to identify this diversity and it is increasingly clear that these sources of diversity are abundant in clonal varieties and can contribute to variation in traits of interest to breeders. In this work, we assemble both subgenomes of Mexican lime ( Citrus x aurantifolia ), an interspecific hybrid between C. hystrix var. micrantha and C. medica . Using this chromosome-level assembly, we find extensive divergence between haplotypes, with at least 89% of the annotated genes harboring polymorphisms at an average rate of 13 per kilobase of coding sequence. Additionally, using high coverage PacBio HiFi libraries from leaf tissue of four individuals we identified multiple large structural variants differing between thorned and thornless lineages, and evidence for mosaicism at hundreds of loci. Many of these variants are found in the promoters and bodies of genes and may act as standing variation for continued improvement of this cultivar.

The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. In this study, we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone, and using comparative analyses, confirm a whole-genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.

Abstrvact: The basic mechanisms of leaf development have been revealed through a combination of genetics and intense analyses in select model species. The genetic basis for diversity in leaf morphology seen in nature is also being unraveled through recent advances in techniques and technologies related to genomics and transcriptomics, which have had a major impact on these comparative studies. However, this has led to the emergence of new unresolved questions about the mechanisms that generate the diversity of leaf form. Here, we provide a review of the current knowledge of the fundamental molecular genetic mechanisms underlying leaf development with an emphasis on natural variation and conserved gene regulatory networks involved in leaf development. Beyond that, we discuss open questions/enigmas in the area of leaf development, how recent technologies can best be deployed to generate a unified understanding of leaf diversity and its evolution, and what untapped fields lie ahead.

A Grand Challenge in Development and Evodevo: Quantifying the Role of Development in Evolution

Summary: Plants transition through juvenile and adult phases of vegetative development in a process known as vegetative phase change (VPC). In poplars (genus Populus) the differences between these stages are subtle, making it difficult to determine when this transition occurs. Previous studies of VPC in poplars have relied on plants propagated in vitro, leaving the natural progression of this process unknown. We examined developmental morphology of seed‐grown and in vitro derived Populus tremula × alba (clone 717‐1B4), and compared the phenotype of these to transgenics with manipulated miR156 expression, the master regulator of VPC. In seed‐grown plants, most traits changed from node‐to‐node during the first 3 months of development but remained constant after node 25. Many traits remained unchanged in clones over‐expressing miR156, or were enhanced when miR156 was lowered, demonstrating their natural progression is regulated by the miR156/SPL pathway. The characteristic leaf fluttering of Populus is one of these miR156‐regulated traits. Vegetative development in plants grown from culture mirrored that of seed‐grown plants, allowing direct comparison between plants often used in research and those found in nature. These results provide a foundation for further research on the role of VPC in the ecology and evolution of this economically important genus.

Summary: Plants transition through juvenile and adult phases of vegetative development in a process known as vegetative phase change (VPC). In poplars (genus Populus ) the differences between these stages are subtle, making it difficult to determine when this transition occurs. Previous studies of VPC in poplars have relied on plants propagated in vitro , leaving the natural progression of this process unknown. We examined developmental morphology of seed-grown and in vitro derived Populus tremula x alba (clone 717-1B4), and compared the phenotype of these, to transgenics with manipulated miR156 expression, the master regulator of VPC. In seed-grown plants, most traits changed from node-to-node during the first 3 months of development but remained constant after node 25. Many traits remained unchanged in clones over-expressing miR156, or were enhanced when miR156 was lowered, demonstrating their natural progression is regulated by the miR156/SPL pathway. The characteristic leaf fluttering of Populus is one of these miR156-regulated traits. Vegetative development in plants grown from culture mirrored that of seed-grown plants, allowing direct comparison between plants often used in research and those found in nature. These results provide a foundation for further research on the role of VPC in the ecology and evolution of this economically important genus.

Age-dependent changes in plant defense against herbivores are widespread, but why these changes exist remains a mystery. We explored this question by examining a suite of traits required for the interaction between swollen thorn acacias (genus Vachellia ) and ants of the genus Pseudomyrmex . In this system, plants provide ants with refuge and food in the form of swollen stipular spines, protein-lipid–rich “Beltian” bodies, and sugar-secreting extrafloral nectaries—the “swollen thorn syndrome.” We show that this syndrome develops at a predictable time in shoot development and is tightly associated with the temporal decline in the microRNAs miR156 and miR157 and a corresponding increase in their targets—the SPL transcription factors. Growth under reduced light intensity delays both the decline in miR156/157 and the development of the swollen thorn syndrome, supporting the conclusion that these traits are controlled by the miR156-SPL pathway. Production of extrafloral nectaries by Vachellia sp. that do not house ants is also correlated with a decline in miR156/157, suggesting that this syndrome evolved by co-opting a preexisting age-dependent program. Along with genetic evidence from other model systems, these findings support the hypothesis that the age-dependent development of the swollen thorn syndrome is a consequence of genetic regulation rather than a passive developmental pattern arising from developmental constraints on when these traits can develop.