Ya Yang

Ya Yang
University of Minnesota Twin Cities | UMN · Plant and Microbial Biology

Ph.D.

About

59
Publications
17,474
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1,768
Citations
Additional affiliations
August 2005 - December 2011
University of Michigan

Publications

Publications (59)
Article
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Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons....
Article
C2 photosynthesis is characterized by recapturing photorespiratory CO2 by RuBisCO in Kranz‐like cells and is therefore physiologically intermediate between C3 and C4 photosynthesis. C2 can be interpreted as an evolutionary precursor of C4 and/or as the result of hybridization between a C3 and C4 lineage. ●We compared the expression of photosyntheti...
Preprint
Full-text available
Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons. Methods: We s...
Preprint
Full-text available
C2 photosynthesis is characterized by recapturing photorespiratory CO2 by RuBisCO in Kranz-like cells and is therefore physiologically intermediate between C3 and C4 photosynthesis. C2 is either interpreted as an evolutionary precursor of C4 or as the result of hybridization between a C3 and C4 lineage. We compared the expression of photosynthetic...
Article
Full-text available
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common...
Article
During the last few decades, biologists have made remarkable progress in understanding the fundamental processes that shape life. But despite the unprecedented level of knowledge now available, large gaps still remain in our understanding of the complex interplay of eco-evolutionary mechanisms across scales of life. Rapidly changing environments on...
Article
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Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a co...
Article
Full-text available
Hard fescue (Festuca brevipila Tracey, 2n = 6x = 42) is a cool season turfgrass with a fine leaf texture that performs well under low‐input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to...
Preprint
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Propiconazole is often used to remove fungal endophytes from turfgrass to study the effects of Epichloë endophytes. However, besides a fungicidal effect, propiconazole can bind to the genes in the cytochrome P450 family and affect the biosynthesis of brassinosteroids. For this reason, outside of fungicidal application, propiconazole has also been u...
Preprint
Full-text available
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci. Common approaches for processing paralogs in target enrichment datasets include...
Preprint
Full-text available
Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a co...
Preprint
Full-text available
Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform seque...
Preprint
Full-text available
Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform seque...
Preprint
Full-text available
Background Hard fescue ( Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform seque...
Article
Full-text available
Fine fescues (Festuca L., Poaceae) are turfgrass species that perform well in low-input environments. Based on morphological characteristics, the most commonly-utilized fine fescues are divided into five taxa: three are subspecies within F. rubra L. and the remaining two are treated as species within the F. ovina L. complex. Morphologically, these...
Preprint
Full-text available
Fine fescues ( Festuca L., Poaceae) are turfgrass species that perform well in low-input environments. Based on morphological characteristics, the most commonly-utilized fine fescues are divided into five taxa: three are subspecies within F. rubra L. and the remaining two are treated as species within the F. ovina L. complex. Morphologically, these...
Article
Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potenti...
Preprint
Full-text available
Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae of Madagascar, and high altitude Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae a...
Preprint
Full-text available
Motivation Quality of gene expression analyses using de novo assembled transcripts in species experienced recent polyploidization is yet unexplored. Results Five plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or bett...
Article
Full-text available
Aim Woody perennial plants on islands have repeatedly evolved from herbaceous mainland ancestors. Although the majority of species in Euphorbia subgenus Chamaesyce section Anisophyllum (Euphorbiaceae) are small and herbaceous, a clade of 16 woody species diversified on the Hawaiian Islands. They are found in a broad range of habitats, including the...
Article
Full-text available
Premise of the study: The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore t...
Article
Full-text available
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to r...
Article
Diverse natural products are synthesized in plants by specialized metabolic enzymes, which are often lineage-specific and derived from gene duplication followed by functional divergence. However, little is known about the contribution of primary metabolism to the evolution of specialized metabolic pathways. Betalain pigments, uniquely found in the...
Article
Full-text available
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potentia...
Article
Full-text available
Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. We assembled a...
Preprint
Full-text available
The role whole genome duplication (WGD) plays in the history of lineages is actively debated. WGDs have been associated with advantages including superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the po...
Article
Full-text available
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remai...
Preprint
Full-text available
Studies of the macroevolutionary legacy of paleopolyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. We assembl...
Article
Full-text available
Premise of the study: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. Methods and Results: A total of 216 frozen tissue samples of Caryop...
Preprint
Full-text available
The carnivorous members of the large, hyperdiverse Caryophyllales (e.g. Venus flytrap, sundews and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. To exp...
Preprint
Full-text available
Premise of the study: We describe a field and lab workflow developed for plant phylotranscriptomic projects, involving field collected cryogenic tissues, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. Methods and Results: 216 frozen tissue samples of Caryophyllales and other angiosperm...
Preprint
Full-text available
Aim The taxon cycle hypothesis describes the cyclic movement of taxa during range expansion and contraction, accompanied by an evolutionary shift from open and often coastal vegetation to closed, and often inland forest vegetation in island systems. The Hawaiian Archipelago is an ideal system to test this hypothesis given the linear fashion of isla...
Article
Full-text available
The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict ma...
Article
Full-text available
Betalain pigments are unique to the Caryophyllales and structurally and biosynthetically distinct from anthocyanins. Two key enzymes within the betalain synthesis pathway have been identified: 4,5-dioxygenase (DODA) that catalyzes the formation of betalamic acid and CYP76AD1, a cytochrome P450 gene that catalyzes the formation of cyclo-DOPA. We per...
Data
Table S2 Information for 14 newly sequenced transcriptomes: provenance, herbarium vouchers, type of material
Data
Table S3 List of 4,5-dioxygenase (DODA) gene accessions and corresponding taxa
Data
Table S4 List of CYP76AD1 gene accessions and corresponding taxa
Article
Full-text available
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales an...
Article
Full-text available
The mid-Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2 -concentrating mechanisms (CCMs)-CAM and C4 -evolved from the C3 photosynthetic pathway, enabling more efficient whole-plant function in such environments. Many angiosperm clades wi...
Article
Full-text available
Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies f...
Article
Full-text available
We aimed to disentangle the influence of environmental variables on the spatial patterns in stomatal occurrence and stomataltraits. We surveyed the stomatal occurrence and the stomatal length (SL), density (SD) and index (SI) of 99 species in 150grassland sites on the Tibetan and Inner Mongolian Plateau to explore their spatial patterns and evaluat...
Article
Full-text available
Background RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly of short reads cause noise in analyses and a large amount of missing data in the aligned matrix. To address these problems, we compare de novo assemblie...
Article
Full-text available
Euphorbia subg. Chamaesyce contains around 600 species and includes the largest New World radiation within the Old World-centered genus Euphorbia. It is one of the few plant lineages to include members with C3, C4 and CAM photosynthesis, showing multiple adaptations to warm and dry habitats. The subgenus includes North American-centered groups that...
Article
Euphorbia subg. Chamaesyce Raf. contains about 600 species and includes the largest New World radiation within the Old World-centered Euphorbia (Euphorbiaceae). It is one of the few plant lineages to include members with C3, C4 and CAM photosynthesis, showing multiple adaptations to warm and dry habitats. The subgenus includes North American-center...
Article
• The Chamaesyce clade of Euphorbia is the largest lineage of C(4) plants among the eudicots, with 350 species including both narrow endemics and cosmopolitan weeds. We sampled this group worldwide to address questions about subclade relationships, the origin of C(4) photosynthesis, the evolution of weeds, and the role of hybridization and long-dis...
Article
Full-text available
The name Euphorbia acuta Bellardi ex Colla was published in Herbarium Pedemontanum (Colla, l.c.), with a short and vague morphological description. The reference to "umbella 4-fida" is sufficient to place the species within Euphorbia L. subg. Esula Pers. because this is the only infrageneric taxon in northern Italy that possesses pseudoumbellate in...
Article
Neogrollea notabilis, Jackiella curvata, Goebelobryum unguiculatum and Herzogianthus vaginatus are four leafy liverworts found in New Zealand whose phylogenetic positions are uncertain. To determine their positions, we sequenced three chloroplast genes, atpB, rbcL and rps4, from these taxa, compiled a 3-gene data set for 78 taxa representing all ma...

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Projects (2)
Project
Constructing a better understanding of the relationships, genomics, and the evolution of this highly diverse angiosperm group.