The Small Subunit Ribosomal
Morphometric analysis is a common approach for comparing and categorizing botanical samples; however, completing a suite of analyses using existing tools may require a multi‐stage, multi‐program process. To facilitate streamlined analysis within a single program, Morphological Analysis of Size and Shape (
Exemplar samples were obtained from across a single tree (
Using
- NSF-PAR ID:
- 10460333
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Applications in Plant Sciences
- Volume:
- 7
- Issue:
- 9
- ISSN:
- 2168-0450
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract RNA gene (SSU rDNA ) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed asDNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate fourSSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) asDNA barcodes to distinguish among species of the genusBolivina , with particular emphasis onBolivina quadrata for which ten new sequences (KY468817 –KY468826 ) were obtained during this study. Our analyses show that a singleSSU rDNA hypervariable sequence is insufficient to resolve allBolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability ofDNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longerSSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus). -
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Premise The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associated
DNA sequencing (ddRAD seq) protocol usingDNA s from four genera extracted from both silica‐dried and herbarium tissue.Methods DNA s fromDraba ,Boechera ,Solidago , andIlex were processed with a ddRAD seq protocol. The effects ofDNA degradation, taxon, and specimen age were assessed.Results Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples.
Discussion These results suggest that herbarium samples can be incorporated into dd
RAD seq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRAD seq projects that minimize the expenses associated with fieldwork and sample evaluation. -
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Summary Many
Actinidia cultivars are characterized by anthocyanin accumulation, specifically in the inner pericarp, but the underlying regulatory mechanism remains elusive. Here we report two interacting transcription factors, AcMYB 123 and AcbHLH 42, that regulate tissue‐specific anthocyanin biosynthesis in the inner pericarp ofActinidia chinensis cv. Hongyang. Through transcriptome profiling analysis we identified fiveMYB and threebHLH transcription factors that were upregulated in the inner pericarp. We show that the combinatorial action of two of them, AcMYB 123 and AcbHLH 42, is required for activating promoters ofAcANS andAcF3GT1 that encode the dedicated enzymes for anthocyanin biosynthesis. The presence of anthocyanin in the inner pericarp appears to be tightly associated with elevated expression ofAcMYB123 andAcbHLH42 .RNA interference repression ofAcMYB123 ,AcbHLH42 ,AcF3GT1 andAcANS in ‘Hongyang’ fruits resulted in significantly reduced anthocyanin biosynthesis. Using both transient assays inNicotiana tabacum leaves orActinidia arguta fruits and stable transformation in Arabidopsis, we demonstrate that co‐expression ofAcMYB123 andAcbHLH42 is a prerequisite for anthocyanin production by activating transcription ofAcF3GT1 andAcANS or the homologous genes. Phylogenetic analysis suggests that AcMYB 123 or AcbHLH 42 are closely related toTT 2 orTT 8, respectively, which determines proanthocyanidin biosynthesis in Arabidopsis, and to anthocyanin regulators in monocots rather than regulators in dicots. All these experimental results suggest that AcMYB 123 and AcbHLH 42 are the components involved in spatiotemporal regulation of anthocyanin biosynthesis specifically in the inner pericarp of kiwifruit. -
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Premise Light is critical in the ability of plants to accumulate chlorophyll. When exposed to far‐red (
FR ) light and then grown in white light in the absence of sucrose, wild‐type seedlings fail to green in a response known as theFR block of greening (BOG ). This response is controlled by phytochrome A through repression of protochlorophyllide reductase‐encoding (POR ) genes byFR light coupled with irreversible plastid damage. Sigma (SIG ) factors are nuclear‐encoded proteins that contribute to plant greening and plastid development through regulating gene transcription in chloroplasts and impacting retrograde signaling from the plastid to nucleus.SIG s are regulated by phytochromes, and the expression of someSIG factors is reduced in phytochrome mutant lines, includingphyA . Given the association of phyA with theFR BOG and its regulation ofSIG factors, we investigated the potential regulatory role ofSIG factors in theFR BOG response.Methods We examined
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TE s) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed ofTE s. We developed an approach to define shared and variableTE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 andPH 207) with uniform structural annotations ofTE s. Among these genomes we identified approximately 400 000TE s that are polymorphic, encompassing 1.6 Gb of variableTE sequence. These polymorphicTE s include a combination of recent transposition events as well as deletions of olderTE s. There are examples of polymorphicTE s within each of the superfamilies ofTE s and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphicTE s within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variableTE s, providing evidence for the role ofTE s in contributing to the substantial differences in annotated gene content among these genotypes.TE s are highly variable in our survey of four temperate maize genomes, highlighting the major contribution ofTE s in driving variation in genome organization and gene content.Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at
https://github.com/SNAnderson/maizeTE_variation ;https://mcstitzer.github.io/maize_TEs .
