TY - JOUR
T1 - Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff
AU - VanBuren, Robert
AU - Man Wai, Ching
AU - Wang, Xuewen
AU - Pardo, Jeremy
AU - Yocca, Alan E.
AU - Wang, Hao
AU - Chaluvadi, Srinivasa R.
AU - Han, Guomin
AU - Bryant, Douglas
AU - Edger, Patrick P.
AU - Messing, Joachim
AU - Sorrells, Mark E.
AU - Mockler, Todd C.
AU - Bennetzen, Jeffrey L.
AU - Michael, Todd P.
N1 - Funding Information:
We are indebted to Tsegaye Dabi at the Salk Institute for Biological Studies for introducing us to this amazing plant, and for inspiring generations of plant biologists. We thank Elliott Meer for assistance with PacBio sequencing, and the Monsanto Genomics Team (Randy Kerstetter, Mitch Sudkamp, Phil Latreille, Zijin Du, and Joe Zhou) for full-length sequenced fosmids. We thank James Schnable for his helpful comments and suggestions on the manuscript. This work is supported by funding from the National Science Foundation (MCB‐1817347 to R.V.), Department of Energy (DE-SC0012639 to T.C.M. and T.P.M.), and partial support from the Bill & Melinda Gates Foundation (T.C. M. and D.B.). This work is supported by the USDA National Institute of Food and Agriculture Hatch project to RV.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.
AB - Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.
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U2 - 10.1038/s41467-020-14724-z
DO - 10.1038/s41467-020-14724-z
M3 - Article
C2 - 32060277
AN - SCOPUS:85079360348
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 884
ER -
