New assembly of wheat progenitor offers clues to genome evolution

Date:12-22-2017

Following on the heels of the first nearly complete assembly of the hexaploid bread wheat genome, scientists from the University of California, Davis, the USDA Agricultural Research Service, Johns Hopkins University, and many other institutions recently published a high-quality genome assembly for one of wheat’s diploid ancestors. Both efforts incorporated SMRT Sequencing to improve contiguity of the assemblies. The new publication reveals that the ancestral plant’s genome has evolved more quickly than usual, driven largely by repeats.

The paper, “Genome sequence of the progenitor of the wheat D genome Aegilops tauschii,” comes from senior author Jan Dvořák; lead authors Ming-Cheng Luo, Yong Gu, Daniela Puiu, Hao Wang, and Sven Twardziok; and collaborators. “Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat,” the scientists note. “The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence.”

To tackle this difficult genome, the team used a number of genome analysis technologies, including SMRT Sequencing, BAC sequencing, optical mapping, and more. Scientists from Johns Hopkins contributed 35-fold PacBio coverage of the Ae. tauschii genome, which is a 4.3 Gb in size and organized into seven chromosomes.

With a high-quality assembly in hand, the team turned to exploring unique features of the ancestral wheat genome. “Compared to other sequenced plant genomes … the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences,” the scientists report. Transposable elements, including the frequent long terminal repeat retrotransposons, accounted for nearly 85% of the sequence.

“Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes,” the team writes. “We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.”

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