About

Michael Axtell is a Professor of Biology and holds the Louis and Hedwig Sternberg Chair in Plant Biology at Penn State University. His research focuses on the discovery and characterization of plant microRNAs and siRNAs, exploring their functions in the evolution of plant development. He is actively involved in genomics and bioinformatics related to microRNAs, siRNAs, and their targets, contributing to the understanding of RNA biology in plants. Axtell is affiliated with multiple research centers and graduate programs, including Bioinformatics and Genomics, Plant Biology, and Molecular, Cellular, and Integrative Biosciences. His work has significantly advanced knowledge in plant small RNA pathways, trans-species microRNA loci, and the molecular interactions between parasitic plants and their hosts. He has been recognized for his contributions through various honors, including being named the Louis and Hedwig Sternberg Chair and a distinguished professor of biology.

Research topics

• Genetics
• Biology
• Evolutionary biology
• Computational biology
• Chemistry
• Botany

Selected publications

• Antagonism in Orthotospoviruses Is Reflected in Plant Small RNA Profile

  Viruses · 2025-05-30

  articleOpen access

  Mixed infections of plant viruses are commonly found in natural patho-systems and present a valuable opportunity to understand how multiple viruses can co-infect the same host. Tomato spotted wilt orthotospovirus (TSWV) and impatiens necrotic spot orthotospovirus (INSV) are present in the same geographic areas and are closely related. More mixed infections of TSWV and INSV have been reported in recent years, and the INSV host range has been reported to be increasing. In a previous study, we isolated and characterized one strain of INSV and one of TSWV and found that they have an antagonistic relationship in their vectors. However, we were unable to determine whether this antagonism extends to the host plant or to uncover the underlying mechanisms and the host's contribution. Here, we show that TSWV and INSV exhibit antagonistic interactions in the host plant, as evidenced by a lower viral titer in mixed infections compared to single infections. Using small RNA sequencing, we identified that the host plant contributes to this antagonism through differential small RNA processing, which appears to regulate viral replication and the success of infection. This research advances our understanding of virus-virus and virus-host interactions and presents opportunities for leveraging these dynamics in integrated pest management strategies.

  PublisherOA PDFDOI

• Chromosome level assembly and annotation of <i>Cuscuta campestris</i> Yunck. (“field dodder”), a model parasitic plant

  G3 Genes Genomes Genetics · 2025-08-20 · 2 citations

  articleOpen access

  We present the first chromosome-level genome assembly and annotation for the genus Cuscuta, a twining and leafless parasitic plant of the morning glory family (Convolvulaceae). C. campestris, the study species, is a widely studied model parasite, due in part to its worldwide occurrence as a weed of agricultural and natural plant communities. The species has served as a model parasite for studies of parasite biology, haustorium development, growth responses to chemical and light stimuli, gene content and expression, horizontal gene transfer, and interspecies RNA movement and has a recently developed transformation system. The 505 Mb (1C) genome is assembled into 31 chromosomes and supports annotation of 47,199 protein-coding genes, 214 small RNA loci (including 146 haustoria-specific miRNAs), and 3,238 interspecies mobile mRNA loci. C. campestris is a recent tetraploid with a high retention of duplicated genes and chromosomes, with less than 8% nucleotide divergence between homoeologous chromosomes. We also show that transformation of C. campestris with the RUBY marker system allows visualization of transformed Cuscuta-derived fluorescent mobile molecules that have entered the host stem. This genome, with an associated genome browser and BLAST server, will be of value for scientists performing fundamental research in a wide range of molecular, developmental, population, and evolutionary biology, as well as serve as a research tool for studying interspecies mobile molecules, generating genetic markers for species and genotype identification, and developing highly specific herbicides.

  PublisherOA PDFDOI

• miRScore: A rapid and precise microRNA validation tool

  PLoS Computational Biology · 2025-11-03 · 3 citations

  articleOpen accessSenior authorCorresponding

  MicroRNAs (miRNAs) are small non-protein-coding RNAs that regulate gene expression in many eukaryotes. Next-generation sequencing of small RNAs (small RNA-seq) is central to the discovery and annotation of miRNAs. Newly annotated miRNAs and their longer precursors encoded by MIRNA loci are typically submitted to databases such as the miRBase microRNA registry following the publication of a peer-reviewed study. However, genome-wide scans using small RNA-seq data often yield high rates of false-positive MIRNA annotations, highlighting the need for more robust validation methods. miRScore was developed as an independent and efficient tool for evaluating new MIRNA annotations using sRNA-seq data. miRScore combines structural and expression-based analyses to provide rapid and reliable validation of new MIRNA annotations. By providing users with detailed metrics and visualization, miRScore enhances the ability to assess confidence in MIRNA annotations. miRScore has the potential to advance the overall quality of MIRNA annotations by improving accuracy of new submissions to miRNA databases and serving as a resource for re-evaluating existing annotations.

  PublisherDOI

• The parasitic plant <i>Cuscuta campestris</i> selectively loads <i>trans</i> -species miRNAs onto host Argonautes, but not self Argonautes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-16

  preprintOpen accessSenior authorCorresponding

  Abstract The obligate parasitic plant Cuscuta campestris delivers trans -species microRNAs (miRNAs) into host plants to silence host mRNAs. Here, the genetic requirements for biogenesis, movement, and function of these miRNAs were investigated. Primary miRNA transcript accumulation precedes mature miRNA accumulation by 24 to 48 hours. Trans- species miRNAs accumulate in host tissues a short distance from the site of parasite attachment. Trans- species miRNAs require C. campestris but not host Dicer-Like 1 ( DCL1 ) for accumulation. These miRNAs specifically avoid Argonaute (AGO) loading in C. campestris tissue where they instead accumulate as miRNA/miRNA* duplexes. After arrival and short-distance spreading in host tissues, they are selectively loaded into host AGO1. This study clarifies the transcription, dicing, delivery, and function of C. campestris trans -species miRNAs. We propose that selective avoidance of self AGO-loading is a mechanism to facilitate the delivery of these “export only” miRNAs to host tissues.

  PublisherOA PDFDOI

• <i>Trans</i>-Species Mobility of RNA Interference between Plants and Associated Organisms

  Plant and Cell Physiology · 2024-01-30 · 10 citations

  articleSenior author

  Trans-species RNA interference (RNAi) occurs naturally when small RNAs (sRNAs) silence genes in species different from their origin. This phenomenon has been observed between plants and various organisms including fungi, animals and other plant species. Understanding the mechanisms used in natural cases of trans-species RNAi, such as sRNA processing and movement, will enable more effective development of crop protection methods using host-induced gene silencing (HIGS). Recent progress has been made in understanding the mechanisms of cell-to-cell and long-distance movement of sRNAs within individual plants. This increased understanding of endogenous plant sRNA movement may be translatable to trans-species sRNA movement. Here, we review diverse cases of natural trans-species RNAi focusing on current theories regarding intercellular and long-distance sRNA movement. We also touch on trans-species sRNA evolution, highlighting its research potential and its role in improving the efficacy of HIGS.

  PublisherDOI

• miRScore: a rapid and precise microRNA validation tool

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-17 · 1 citations

  preprintSenior author

  Abstract MicroRNAs (miRNAs) are small non-protein-coding RNAs that regulate gene expression in many eukaryotes. Next-generation sequencing of small RNAs (small RNA-seq) has accelerated discovery and annotation of novel miRNAs. Newly discovered miRNAs are typically submitted to databases such as the miRBase microRNA registry following the publication of a peer-reviewed study. However, genome-wide scans using small RNA-seq data often yield high rates of false-positive miRNA annotations, highlighting the need for more robust validation methods. miRScore was developed as an independent and efficient tool for evaluating miRNA annotations using sRNA-seq data. miRScore combines structural and expression-based analyses to provide rapid and reliable validation of miRNA annotations. By providing users with detailed metrics and visualization, miRScore enhances the ability to assess confidence in novel and existing miRNA annotations. miRScore has the potential to advance the overall quality of miRNA annotations by improving accuracy of new submissions to miRNA databases and serving as a resource for re-evaluating existing annotations.

  PublisherDOI

• Focus on RNA biology

  The Plant Cell · 2023-03-21 · 1 citations

  editorialOpen access

  If DNA is the playbook of life, then RNA, in all its forms, is the company of actors that brings life into being. RNA is likely the original organic molecule that gave rise to DNA as well as enzymes and other proteins that create the flow of genetic information known as the central dogma (DNA -&gt; RNA -&gt; protein). Although the central dogma still holds true generally, our understanding has expanded the concept to encompass reverse transcription of RNA to DNA, regulatory functions of noncoding RNAs, and epigenetic modifications. In this focus issue, we highlight many of the forms and functions of RNA in plants.

  PublisherOA PDFDOI

• <i>Trans-</i> species microRNA loci in the parasitic plant <i>Cuscuta campestris</i> have a U6-like snRNA promoter

  The Plant Cell · 2023-03-10 · 18 citations

  articleOpen accessSenior author

  Small regulatory RNAs can move between organisms and regulate gene expression in the recipient. Whether the trans-species small RNAs being exported are distinguished from the normal endogenous small RNAs of the source organism is not known. The parasitic plant Cuscuta campestris (dodder) produces many microRNAs that specifically accumulate at the host-parasite interface, several of which have trans-species activity. We found that induction of C. campestris interface-induced microRNAs is similar regardless of host species and occurs in C. campestris haustoria produced in the absence of any host. The loci-encoding C. campestris interface-induced microRNAs are distinguished by a common cis-regulatory element. This element is identical to a conserved upstream sequence element (USE) used by plant small nuclear RNA loci. The properties of the interface-induced microRNA primary transcripts strongly suggest that they are produced via U6-like transcription by RNA polymerase III. The USE promotes accumulation of interface-induced miRNAs (IIMs) in a heterologous system. This promoter element distinguishes C. campestris IIM loci from other plant small RNAs. Our data suggest that C. campestris IIMs are produced in a manner distinct from canonical miRNAs. All confirmed C. campestris microRNAs with documented trans-species activity are interface-induced and possess these features. We speculate that RNA polymerase III transcription of IIMs may allow these miRNAs to be exported to hosts.

  PublisherOA PDFDOI

• Small RNA Analysis of Virus-virus Interaction between Two Orthotospoviruses

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-08-29

  preprintOpen access

  Abstract Mixed infections of plant viruses are commonly found in natural patho-systems and present a valuable opportunity to understand how multiple viruses can co-infect the same host. Tomato spotted wilt orthotospovirus (TSWV) and impatiens necrotic spot orthotospovirus (INSV) are present in the same geographic areas and are closely related. More mixed infections of TSWV and INSV have been reported in recent years, and the INSV host range has been reported to be increasing. In a previous study, we have isolated one strain of INSV and one of TSWV and showed that they have an antagonistic relationship in their vectors, but we were unable to determine, the underlying mechanisms governing their antagonism in planta and the contribution of the host to this. Here, we used small RNA sequencing to study TSWV-INSV antagonistic interaction and showed that INSV alters plant responses and the processing of TSWV.

  PublisherOA PDFDOI

• <i>Trans</i> -species microRNA loci in the parasitic plant <i>Cuscuta campestris</i> have a U6-like snRNA promoter

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-07-06 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Small regulatory RNAs can move between organisms during pathogenic interactions and regulate gene expression in the recipient. If and how such “ trans -species” small RNAs are distinguished from normal small RNAs is not known. The parasitic plant Cuscuta campestris produces a number of microRNAs that specifically accumulate at the interface between parasite and host, several of which have been demonstrated to have trans -species activity. We find that induction of C. campestris interface-induced microRNAs was similar regardless of host species, and can be replicated in haustoria stimulated to develop in the complete absence of a host. We also find that the loci encoding C. campestris interface-induced microRNAs are distinguished by a common 10 base-pair cis -regulatory element. This element is identical to a previously described upstream sequence element used by all plant small nuclear RNA loci. The sequence context of this element strongly suggests U6-like transcription by RNA polymerase III. The element promotes accumulation of interface-induced miRNAs in a heterologous system. This common promoter element distinguishes C. campestris interface-induced microRNA loci from other plant small RNAs; other plant small RNA loci are transcribed by polymerases II or IV, and lack any common promoter motifs. Our data suggest that C. campestris interface-induced miRNAs are produced in a manner distinct from canonical miRNAs. All confirmed C. campestris microRNAs with confirmed trans -species activity are interface-induced and possess these features. We speculate that this distinct production may allow these miRNAs to be exported to hosts.

  PublisherOA PDFDOI

Recent grants

• MRI: Acquisition of an Illumina HiSeq2000 as a core sequencing instrument for genomics and gene expression research

  NSF · $569k · 2012–2015

• Reference Annotations for Small RNA-producing Genes in Plants

  NSF · $907k · 2014–2019

• Functional and Evolutionary Genomics of Ancient Small RNAs

  NIH · $885k · 2009–2014

• Sequence Requirements for Small RNA Targeting in Plants

  NSF · $538k · 2011–2015

• Empirical Detection of Small RNA Targets

  NSF · $462k · 2007–2011

Frequent coauthors

• Pamela S. Soltis

  Florida Museum of Natural History

  34 shared

• David P. Bartel

  Whitehead Institute for Biomedical Research

  23 shared

• Hong Mā

  Lanzhou University of Technology

  18 shared

• Stephan C. Schuster

  Singapore Centre for Environmental Life Sciences Engineering

  17 shared

• Nathan Johnson

  Universidad Mayor

  15 shared

• José Fernandes Barbosa-Neto

  Universidade Federal do Rio Grande do Sul

  14 shared

• Ceyda Çoruh

  14 shared

• François Sabot

  Diversité, adaptation et développement des plantes

  14 shared

Labs

• Axtell LabPI

Awards & honors

• Louis and Hedwig Sternberg Chair in Plant Biology