Zx-TIL18-REFERENCE-PanAnd-1.0 genome assembly
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PanAnd - Harnessing convergence and constraint to predict adaptations to abiotic stress for maize and sorghum

Project website: https://panandropogoneae.com
Research funded by NSF award 1822330.


ALL GENOMES ARE UNDER TORONTO AGREEMENT UNTIL PUBLICATION OF PAPER

Maize, sorghum, sugarcane, and Miscanthus are the most productive and water efficient crops and biofuels in the world. This productivity is due to a shared physiology and genetic ancestry over the last 15 million years. While these four crops are extensively used in this project, they are closely related to another 800 species that dominate grasslands across the world and are adapted to numerous environmental stresses including flooding, drought, heat, and frost. The project team will use modern genomics and machine learning to survey and analyze these related species, determining the most important genetic features they share that allow them to adapt to heat and drought. The results of this work will be used by commercial and public sector plant breeders to make maize and sorghum more productive and resilient to extreme weather. Key to this long-term impact is training the next generation of scientists in computational biology to address fundamental questions. These skills will be developed through hackathons and bioinformatics training workshops. The project will communicate this science to the general public through venues such as a traveling museum exhibit.


The Andropogoneae tribe of grasses contains a thousand species that collectively represent over a billion years of evolutionary history. It has used NADP-C4 photosynthesis and a wide range of adaptations to become a dominant clade on earth. This project will use the diversity and evolution across this tribe to understand the rules of adaptive convergence and constraint in plant genomes. The project team will sample and analyze the worldwide spectrum of genetic diversity in Andropogoneae to develop detailed models testing whether (1) quantitative estimates of evolutionary constraint improve predictions of fitness-related traits, and (2) convergent environmental adaptations shared across the Andropogoneae explain a substantial proportion of total adaptive variance. These hypotheses will be tested by assembling the gene and regulatory content of 57 species as well as whole genome sequencing of another 700 species. For eight species, diversity across their natural range of adaptation will be surveyed at the sequence level. Evolutionary and machine learning models will be used to quantify the disruptive impact of a mutation in every ancestral genomic element. The inter and intra-specific surveys will also permit an estimation of the prevalence of convergent evolution. This project addresses two key elements of the genotype to phenotype problem - how to quantify the disruptive impact of mutations and how to determine whether adaptive solutions to environmental stresses are convergently shared across species.



source: https://onlinelibrary.wiley.com/doi/epdf/10.1111/jse.12691

ALL GENOMES ARE UNDER TORONTO AGREEMENT UNTIL PUBLICATION OF PAPER

The genome assemblies and annotations will be released in two rounds:


Round 1 release: November 1, 2022
Av-Kellogg1287_8-REFERENCE-PanAnd-1.0 Anatherum virginicum, formerly Andropogon virginicus (Broomsedge)
Td-FL_9056069_6-DRAFT-PanAnd-1.0 Tripsacum dactyloides (FL, south) (Eastern gamagrass)
Td-KS_B6_1-DRAFT-PanAnd-1.0 Tripsacum dactyloides (KS, north)
Td-McKain334_5-DRAFT-PanAnd-1.0 Tripsacum dactyloides
Zd-Gigi-REFERENCE-PanAnd-1.0 Zea diploperennis
Zd-Momo-REFERENCE-PanAnd-1.0 Zea diploperennis
Zl-RIL003-REFERENCE-PanAnd-1.0 Zea luxurians [Genomic sequence only]
Zh-RIMHU001-REFERENCE-PanAnd-1.0 Zea mays - huehuetenagensis
Zn-PI615697-REFERENCE-PanAnd-1.0 Zea nicaraguensis
Zx-TIL18-REFERENCE-PanAnd-1.0 Zea mays - mexicana
Zx-TIL25-REFERENCE-PanAnd-1.0 Zea mays - mexicana
Zv-TIL01-REFERENCE-PanAnd-1.0 Zea mays - parviglumis
Zv-TIL11-REFERENCE-PanAnd-1.0 Zea mays - parviglumis


Round 2 release (coming in 2024)
Ac-Pasquet1232-DRAFT-PanAnd-1.0Andropogon chinensis
Ag-CAM1351-DRAFT-PanAnd-1.0Andropogon gerardii (Big bluestem)
Ab-Traiperm_572-DRAFT-PanAnd-1.0Andropogon burmanicus
Bl-K1279B-DRAFT-PanAnd-1.0Bothriochloa laguroides (Silver bluestem or Silver beard grass)
Cc-PI314907-DRAFT-PanAnd-1.0Cymbopogon citratus (Lemon grass)
Cr-AUB069-DRAFT-PanAnd-1.0Cymbopogon refractus (Barbed wire grass)
Cs-KelloggPI219580-DRAFT-PanAnd-1.0Chrysopogon serrulatus
Et-Layton_Zhong168-DRAFT-PanAnd-1.0Elionorus tripsacoides (Pan-American balsamscale)
Hc-AUB53_1-DRAFT-PanAnd-1.0Heteropogon contortus
Hp-KelloggPI404118-DRAFT-PanAnd-1.0Hemarthria compressa (Whip grass)
Ir-Pasquet1136-DRAFT-PanAnd-1.0Ischaemum rugosum (Saramollagrass)
Pi-Clark-DRAFT-PanAnd-1.0Pogonatherum paniceum (Baby bamboo)
Pp-Kellogg1297-DRAFT-PanAnd-1.0Poa pratensis ssp. angustifolia (Narrowleaf Kentucky bluegrass)
Rr-Malcomber3106-DRAFT-PanAnd-1.0Rhytachne rottboelloides
Rt-Layton_Zhong169-DRAFT-PanAnd-1.0 Rottboellia tuberculosa, also known as Coelorachis tuberculosa and Mnesithea tuberculosa (Florida joint tail grass)
Sm-PI203595-DRAFT-PanAnd-1.0Schizachyrium microstachyum
Ss-CAM1384-DRAFT-PanAnd-1.0Schizachyrium scoparium (Lttle bluestem)
Sn-CAM1369-DRAFT-PanAnd-1.0Sorghastrum nutans (Golden feather grass)
Te-Pasquet1246-DRAFT-PanAnd-1.0Thelopogon elegans
Tt-AUB21_1-DRAFT-PanAnd-1.0Themeda triandra (Kangaroo grass, Red grass, Red oat grass)
Tz-DC_05_58_3A-DRAFT-PanAnd-1.0Tripsacum zopolitense
Ud-Pasquet1171-DRAFT-PanAnd-1.0Urelytrum digitatum
Vc-Pasquet1098-DRAFT-PanAnd-1.0Vossia cuspidata (Hippo grass)

Research funded by NSF award 1822330.