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Gingko Sequencing by BGI Team Reveals Large, Highly Repetitive Genome

NEW YORK (GenomeWeb) – A BGI-Shenzen-led team of researchers has sequenced the Ginkgo biloba genome and found it to be full of repeats, as well as gene clusters that may explain the tree's remarkable resilience.

This so-called 'living fossil' — the tree has changed little in the past 270 million years — is the sole living representative of one lineage of gymnosperms, and it has weathered glaciations and other adverse conditions over the ages. Researchers led by BGI's Wenbin Chen, Song Ge from the Chinese Academy of Sciences, and Chengxin Fu from Zhejiang University reported in GigaScience today that they've sequenced the more than 10-gigabase ginkgo genome to find a high number of repetitive sequences as well as a number of gene clusters that appear to be involved in defense mechanisms.

"Ginkgo represents one of the five living groups of seed plants, and has no living relatives," Zhejiang University's Yunpeng Zhao, a study co-author, said in a statement. "Such a genome fills a major phylogenetic gap of land plants, and provides key genetic resources to address evolutionary questions like [the] phylogenetic relationships of gymnosperm lineages."

For their study, the researchers extracted genomic DNA from the endosperm tissue of a ginkgo seed for sequencing, following a similar strategy as that used to sequence loblolly pine. They generated paired-end and mate-pair libraries, all using DNA from the same seed. After sequencing on the Illumina HiSeq 2000 and HiSeq 4000 platforms, the researchers generated 189.84X coverage with raw sequencing reads.

Using some of the mate-pair library reads as scaffolding, they assembled a draft ginkgo genome of some 10.6 gigabases in length. This, the researchers noted, is 80 times larger than the Arabidopsis thaliana genome as well as larger than the maize, orchid, and sorghum genomes.

"The large genome of ginkgo may have resulted from whole genome duplication and insertion of a remarkably high proportion of repetitive sequences," BGI's Chen said.

He and his colleagues reported that slightly more than three quarters of the G. biloba genome consists of repeats. This, they added, is a higher portion that what's found in other plant genomes, including the Norway spruce, orchid, and sorghum genomes. They also noted that long terminal repeat retrotransposons were particularly common amongst the repeat sequences of ginkgo.

By analyzing the reverse transcriptase genes tacked on to those long terminal repeats and comparing them to those in other land plants, the researchers found evidence that some of these repeats were conserved. Though the repeats largely accumulated slowly in the ginkgo genome, there was a period of repeat expansion that the researchers traced to between 16 million and 24 million years ago.

At the same time, the team reported that two whole-genome duplication events took place in ginkgo: one was an ancient duplication 515 million years to 735 million years ago that is common to seed plants, while the other was a more recent duplication specific to ginkgo.

Using protein sequence, transcriptome, and expressed sequence tag data from five other land plants — Selaginella moellendorffii, Picea abies, Pinus taeda, A. thaliana, and Oryza sativa — the researchers predicted gene models for ginkgo. Through this, they identified 41,840 ginkgo genes, of which 30,209 genes were assigned high confidence.

Some 2,100 gene families were unique to ginkgo, and many of those that harbored expansions were enriched for stimuli response functions, including defense. The researchers noted that ginkgo's defense mechanisms have been of interest to scientists as it employs multiple mechanisms to fend off insects and pathogens.

In particular, they uncovered a high level of gene duplications within the ginkgolide/bilobalide biosynthesis and flavonoid biosynthesis pathways, both of which produce defense metabolites — terpenic trilactones like ginkgolides and bilobalides, along with flavonoids, fend off herbivore attacks, they noted. These duplications, the researchers said, could have a dose effect that enhances resistance and adaptability.