The emergence of seed-producing plants more than 300 million years ago marked an evolutionary turning point, opening up new environments for plants and eventually giving rise to the flowering plants that light up our world and provide much of our food. But newly published DNA sequencing suggests it was less of a leap than it appears.
The genomes, taken from three species of ferns and cycads, one of the oldest types of seed-bearing plants, show that the key seed-making genes are the same as those in the spore-producing machinery of ferns, which appeared tens of millions of years ago. . They obviously existed in a common ancestor but were recruited to different reproductive functions as the plants diverged.
The genomes of ferns and cycads, published in a series of papers over the past several months, “fill the gap of gene flow during plant evolution,” says Xu Nong Bai, a plant developmental biologist emeritus at Peking University who helped sequence a member of the Maidenhair fern genus. Evolutionary innovation [can] They come from the alternative use of existing genes or networks, not new ones.” Genomes also teach a second surprising lesson: that plants acquired some of their genes not through mutation and selection, but directly from fungi or other microbes through a controversial process called horizontal gene transfer. .
Because of the sheer size of most fern genomes and the focus on crops such as rice, wheat, and maize, the majority of the more than 800 plant genomes sequenced to date have come from seed plants. So far, only two ferns have been – ferns with an unusually small genome. As a result, “we only had a small snapshot of plant evolution,” says Blaine Marchant, a plant evolutionary geneticist at Stanford University.
Thanks to advances in sequencing long stretches of DNA and reductions in costs, his team and three other groups have treated ferns with larger, typical genomes as well as a type of cycad, a non-flowering plant with bare seeds, like those found in pines and other conifers. “It’s great to finally see more and more diverse plant genomes being sequenced,” says Jennifer Wiskaffer, an evolutionary biologist at Purdue University.
The genomes of ferns, containing about 30,000 genes each, reveal a group of genes previously associated with flowering plants, which evolved more than 200 million years later. For example, Marchant and colleagues reported on September 1 in nature plants This water fern, Ceratopteris Ricciardihas 10 members of a genetic family known to control flowering time, seed germination, and flower shape in a small flowering plant, Arabidopsis. Their role in ferns is unclear, but seven of these genes are active in leaves where spores are produced, suggesting that they play a role in reproduction in ferns as well as in seed plants.
Jianbin Yan, a plant physiologist at the Agricultural Genomics Institute of the Chinese Academy of Agricultural Sciences, and colleagues found similar similarities in the maidenhair fern, Adiantum hair spring. Its DNA contains genes for transcription factors called EMS1 and TPD1, and proteins in maize and other seed plants that regulate genes involved in pollen development, Yan’s team reports in the same issue of nature plants. These pollen control genes are active in maidenhair sporangia, the tissue in which spores develop.
The genome of this fern also contains three genes that regulate seed growth in flowering plants, adds Hong Zhikong, an evolutionary plant evolutionary biologist at the Institute of Botany of the Chinese Academy of Sciences. Yan says Ferns are “evolutionarily pivotal to a comprehensive understanding of the origin and diversification of seeds.” The cycad genome contains similar networks, indicating that they were active in early seed plants, notes Shuzu Zhang, a botanist at the Fairy Lake Botanical Garden in Shenzhen, who led their sequencing.
The new genome highlights one reason why such ideas have been so slow: Fei-Wei Lee, a plant evolutionary biologist at Cornell University, says ferns are “known for having giant genomes.” The researchers hypothesized a process called whole genome replication, in which an organism’s DNA complement is doubled during reproduction, which explains the size of their genomes. “We’re not seeing the genome double the imprint we thought we would,” says Paul Wolf, a plant geneticist at the University of Alabama, Huntsville. Instead, ferns and cycads gained the bulk of their DNA from an accumulation of motile DNA — transposons and other genetic elements that infect the genome and replicate, or duplicate, short, transcribed sequences over and over.
The four new genomes are also changing views on whether plants experience horizontal gene transfer. Microbes are known to exchange genes all the time, helping them adapt to new conditions, but multicellular organisms seem to borrow genes in rare cases. However, the genomes of ferns and cycads contain an astonishing number of genes from bacteria and fungi. “It is remarkable that we see genes of both bacterial and fungal origin in vascular plants,” says Kong.
For example, the cycad sequence contains four copies of the innate cytotoxin gene, a protein that can bore holes in foreign cells, and Ceratoptris The genome contains 36 copies of another cytotoxin gene from a bacterium. These acquired genes may have enhanced their new host’s defenses against pathogens or herbivores.
Veronica de Stelio, a botanist at the University of Washington, Seattle, expects more surprises from the newly revealed genomes. “Having representative reference genomes for each of the major plant lineages opens up a lot of possibilities,” she says. “Genomes are tools, the tip of the iceberg.”