@article{qi_an_hall_di_blischak_mckibben_hao_conant_pires_barker_2021, title={Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa}, volume={230}, ISSN={["1469-8137"]}, DOI={10.1111/nph.17194}, abstractNote={Summary}, number={1}, journal={NEW PHYTOLOGIST}, author={Qi, Xinshuai and An, Hong and Hall, Tara E. and Di, Chenlu and Blischak, Paul D. and McKibben, Michael T. W. and Hao, Yue and Conant, Gavin C. and Pires, J. Chris and Barker, Michael S.}, year={2021}, month={Apr}, pages={372–386} }
 @article{hao_mabry_edger_freeling_zheng_jin_vanburen_colle_an_abrahams_et al._2021, title={The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible}, volume={31}, ISSN={["1549-5469"]}, DOI={10.1101/gr.270033.120}, abstractNote={The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein–protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a “mix and match” model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.}, number={5}, journal={GENOME RESEARCH}, author={Hao, Yue and Mabry, Makenzie E. and Edger, Patrick P. and Freeling, Michael and Zheng, Chunfang and Jin, Lingling and VanBuren, Robert and Colle, Marivi and An, Hong and Abrahams, R. Shawn and et al.}, year={2021}, month={May}, pages={799–810} }
 @article{schoonmaker_hao_bird_conant_2020, title={A Single, Shared Triploidy in Three Species of Parasitic Nematodes}, volume={10}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077664460&partnerID=MN8TOARS}, DOI={10.1534/g3.119.400650}, abstractNote={Abstract}, number={1}, journal={G3-GENES GENOMES GENETICS}, author={Schoonmaker, Ashley and Hao, Yue and Bird, David McK. and Conant, Gavin C.}, year={2020}, month={Jan}, pages={225–233} }
 @article{hao_lee_baraboo_burch_maurer_somarelli_conant_2020, title={Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation}, volume={12}, ISSN={["1759-6653"]}, DOI={10.1093/gbe/evaa026}, abstractNote={Abstract}, number={3}, journal={GENOME BIOLOGY AND EVOLUTION}, author={Hao, Yue and Lee, Hyuk Jin and Baraboo, Michael and Burch, Katherine and Maurer, Taylor and Somarelli, Jason A. and Conant, Gavin C.}, year={2020}, month={Mar}, pages={35–47} }
 @article{osman_bolding_villalon_kaifer_lorson_tisdale_hao_conant_pires_pellizzoni_et al._2019, title={Functional characterization of SMN evolution in mouse models of SMA}, volume={9}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-019-45822-8}, abstractNote={Abstract}, journal={SCIENTIFIC REPORTS}, author={Osman, Erkan Y. and Bolding, Madeline R. and Villalon, Eric and Kaifer, Kevin A. and Lorson, Zachary C. and Tisdale, Sarah and Hao, Yue and Conant, Gavin C. and Pires, J. Chris and Pellizzoni, Livio and et al.}, year={2019}, month={Jul} }
 @article{an_qi_gaynor_hao_gebken_mabry_mcalvay_teakle_conant_barker_et al._2019, title={Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus}, volume={10}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-019-10757-1}, abstractNote={Abstract}, journal={NATURE COMMUNICATIONS}, author={An, Hong and Qi, Xinshuai and Gaynor, Michelle L. and Hao, Yue and Gebken, Sarah C. and Mabry, Makenzie E. and McAlvay, Alex C. and Teakle, Graham R. and Conant, Gavin C. and Barker, Michael S. and et al.}, year={2019}, month={Jun} }
 @article{hao_washburn_rosenthal_nielsen_lyons_edger_pires_conant_2018, title={Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived}, volume={10}, ISSN={["1759-6653"]}, DOI={10.1093/gbe/evy061}, abstractNote={Abstract Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes’ selective pressures. We analyzed two nested polyploidy events in Brassicaceae: the At-α genome duplication that is the most recent polyploidy in the model plant Arabidopsis thaliana and a more recent hexaploidy shared by the genus Brassica and its relatives. By comparing the strength and direction of the natural selection acting at the population and at the species level, we find evidence for continued intensified purifying selection acting on retained duplicates from both polyploidies even down to the present. The constraint observed in preferentially retained genes is not a result of the polyploidy event: the orthologs of such genes experience even stronger constraint in nonpolyploid outgroup genomes. In both the Arabidopsis and Brassica lineages, we further find evidence for segregating mildly deleterious variants, confirming that the population-level data uncover patterns not visible with between-species comparisons. Using the A. thaliana metabolic network, we also explored whether network position was correlated with the measured selective constraint. At both the population and species level, nodes/genes tended to show similar constraints to their neighbors. Our results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday’s polyploids still have distinct evolutionary trajectories.}, number={3}, journal={GENOME BIOLOGY AND EVOLUTION}, author={Hao, Yue and Washburn, Jacob D. and Rosenthal, Jacob and Nielsen, Brandon and Lyons, Eric and Edger, Patrick P. and Pires, J. Chris and Conant, Gavin C.}, year={2018}, month={Mar}, pages={999–1011} }
 @article{emery_willis_hao_barry_oakgrove_peng_schmutz_lyons_pires_edger_et al._2018, title={Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization}, volume={14}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1007267}, abstractNote={Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms’ successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers’ yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages’ history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.}, number={3}, journal={PLOS GENETICS}, author={Emery, Marianne and Willis, M. Madeline S. and Hao, Yue and Barry, Kerrie and Oakgrove, Khouanchy and Peng, Yi and Schmutz, Jeremy and Lyons, Eric and Pires, J. Chris and Edger, Patrick P. and et al.}, year={2018}, month={Mar} }