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Browsing by Author "Harkess, Alex"

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    The asparagus genome sheds light on the origin and evolution of a young Y chromosome
    (Nature Portfolio, 2017) Harkess, Alex; Zhou, Jinsong; Xu, Chunyan; Bowers, John E.; Van der Hulst, Ron; Ayyampalayam, Saravanaraj; Mercati, Francesco; Riccardi, Paolo; McKain, Michael R.; Kakrana, Atul; Tang, Haibao; Ray, Jeremy; Groenendijk, John; Arikit, Siwaret; Mathioni, Sandra M.; Nakano, Mayumi; Shan, Hongyan; Telgmann-Rauber, Alexa; Kanno, Akira; Yue, Zhen; Chen, Haixin; Li, Wenqi; Chen, Yanling; Xu, Xiangyang; Zhang, Yueping; Luo, Shaochun; Chen, Helong; Gao, Jianming; Mao, Zichao; Pires, J. Chris; Luo, Meizhong; Kudrna, Dave; Wing, Rod A.; Meyers, Blake C.; Yi, Kexian; Kong, Hongzhi; Lavrijsen, Pierre; Sunseri, Francesco; Falavigna, Agostino; Ye, Yin; Leebens-Mack, James H.; Chen, Guangyu; University of Georgia; Jiangxi Academy of Agricultural Sciences; Beijing Genomics Institute (BGI); Universita Mediterranea di Reggio Calabria; Consiglio Nazionale delle Ricerche (CNR); Istituto di Bioscienze e Biorisorse (IBBR-CNR); Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA); Donald Danforth Plant Science Center; University of Alabama Tuscaloosa; University of Delaware; Fujian Agriculture & Forestry University; Chinese Academy of Sciences; Institute of Botany, CAS; KWS Saat AG; Tohoku University; Chinese Academy of Tropical Agricultural Sciences; Yunnan Agricultural University; University of Missouri Columbia; Huazhong Agricultural University; Dalian University of Technology; University of Copenhagen; Bayer AG; Kasetsart University
    Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination. Dioecy has evolved recently within Asparagus and sex chromosomes are cytogenetically identical with the Y, harboring a megabase segment that is missing from the X. We show that deletion of this entire region results in a male-to-female conversion, whereas loss of a single suppressor of female development drives male-to-hermaphrodite conversion. A single copy anther-specific gene with a male sterile Arabidopsis knockout phenotype is also in the Y-specific region, supporting a two-gene model for sex chromosome evolution.
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    Dynamic genome evolution in a model fern
    (Nature Portfolio, 2021) Marchant, D. Blaine; Chen, Guang; Cai, Shengguan; Chen, Fei; Schafran, Peter; Jenkins, Jerry; Shu, Shengqiang; Plott, Chris; Webber, Jenell; Lovell, John T.; He, Guifen; Sandor, Laura; Williams, Melissa; Rajasekar, Shanmugam; Healey, Adam; Barry, Kerrie; Zhang, Yinwen; Sessa, Emily; Dhakal, Rijan R.; Wolf, Paul G.; Harkess, Alex; Li, Fay-Wei; Roessner, Clemens; Becker, Annette; Gramzow, Lydia; Xue, Dawei; Wu, Yuhuan; Tong, Tao; Wang, Yuanyuan; Dai, Fei; Hua, Shuijin; Wang, Hua; Xu, Shengchun; Xu, Fei; Duan, Honglang; Theissen, Guenter; McKain, Michael R.; Li, Zheng; McKibben, Michael T. W.; Barker, Michael S.; Schmitz, Robert J.; Stevenson, Dennis W.; Zumajo-Cardona, Cecilia; Ambrose, Barbara A.; Leebens-Mack, James H.; Grimwood, Jane; Schmutz, Jeremy; Soltis, Pamela S.; Soltis, Douglas E.; Chen, Zhong-Hua; Stanford University; Zhejiang Academy of Agricultural Sciences; Yangtze University; Zhejiang University; Western Sydney University; Hangzhou Normal University; Cornell University; Boyce Thompson Institute for Plant Research; HudsonAlpha Institute for Biotechnology; United States Department of Energy (DOE); Lawrence Berkeley National Laboratory; University of Arizona; University of Georgia; University of Florida; University of Alabama Huntsville; Auburn University; Justus Liebig University Giessen; Friedrich Schiller University of Jena; Huazhong Agricultural University; Guizhou University; University of Alabama Tuscaloosa; University of Texas Austin; New York Botanical Garden
    The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology. The genome of the model fern species Ceratopteris richardii reveals a history of remarkably dynamic genome evolution, including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago.
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    Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes
    (Frontiers, 2022) Timilsena, Prakash Raj; Wafula, Eric K.; Barrett, Craig F.; Ayyampalayam, Saravanaraj; McNeal, Joel R.; Rentsch, Jeremy D.; McKain, Michael R.; Heyduk, Karolina; Harkess, Alex; Villegente, Matthieu; Conran, John G.; Illing, Nicola; Fogliani, Bruno; Ane, Cecile; Pires, J. Chris; Davis, Jerrold, I; Zomlefer, Wendy B.; Stevenson, Dennis W.; Graham, Sean W.; Givnish, Thomas J.; Leebens-Mack, James; DePamphilis, Claude W.; Pennsylvania State University; Pennsylvania State University - University Park; West Virginia University; University of Georgia; Kennesaw State University; University of Alabama Tuscaloosa; University of Hawaii Manoa; HudsonAlpha Institute for Biotechnology; Universite Nouvelle Caledonie; University of Adelaide; University of Cape Town; University of Wisconsin Madison; University of Missouri Columbia; Cornell University; University of British Columbia; New York Botanical Garden; Virginia Polytechnic Institute & State University
    We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.