The evolution of land plants : a perspective from horizontal gene transfer

Recent studies suggest that horizontal gene transfer (HGT) played a significant role in the evolution of eukaryotic lineages. We here review the mechanisms of HGT in plants and the importance of HGT in land plant evolution. In particular, we discuss the role of HGT in plant colonization of land, phototropic response, C4 photosynthesis, and mitochondrial genome evolution.


Introduction
Horizontal gene transfer (HGT) refers to the movement of genetic information between distinct species.Being different from vertical genetic transmission from parent to offspring, HGT circumvents normal mating barriers and may introduce novel genes into recipient genomes.As such, HGT may not only accelerate the genome evolution of recipient organisms, but also allow recipients to explore new resources and niches [1][2][3][4].
HGT was once thought to be frequent only in prokaryotes and certain unicellular eukaryotes [2,5].During the past decade, horizontally acquired genes have been found in all major multicellular eukaryotic lineages (plants, animals, and fungi) [6][7][8][9], suggesting that HGT has occurred throughout the history of eukaryotic evolution and is critical for the adaptive evolution of some multicellular lineages.Here, we review cases of HGT in land plants, and discuss the genetic mechanisms and evolutionary importance of HGT in plant evolution.In particular, we focus on acquired genes of adaptive significance in plants, rather than genes that are selectively neutral or nearly neutral [10,11].Because intracellular gene transfer (IGT) from organelles (mitochondria and plastids) to the nucleus has been discussed in multiple other articles [12][13][14], it will not be considered here.

Mechanisms of HGT in plants
A complete and successful HGT requires that a foreign gene first enters cells of the recipient organism, be integrated into the recipient genome and then transmitted to the offspring [7].Because the physical isolation of germ cells may prevent foreign genes from being transmitted to the offspring [15,16], plants and animals were traditionally regarded to be resistant to HGT [3,15].Nevertheless, the occurrence of HGT in all major eukaryotic lineages suggests that no barrier to HGT is insurmountable in eukaryotes [7].Specifically for plants, their meristems, which represent the germline equivalent but can be formed through de-differentiation of somatic cells, are less protected and may result in a higher susceptibility to HGT [16].Several mechanisms have also been proposed regarding how HGT may occur in plants [6,7,[16][17][18] (Fig. 1).
INTIMATE PHYSICAL ASSOCIATION.Sustained contact such as symbiosis, parasitism, epiphytism, pathogen infection or plant grafting may offer opportunities to gene transfer.In particular, parasitism has been reported in several cases of HGT in plants [6,[18][19][20][21][22][23].In most of these documented examples, genes were transferred from host to parasitic plants.For instance, multiple mitochondrial and nuclear genes of Rafflesiaceae, a family of parasitic plants, were reportedly acquired from their host Tetrastigma (Vitaceae) [19][20][21].Similar cases have also been observed in other parasitic plants such as Cistanche deserticola (Orobanchaceae) [23], Orobanche aegyptiaca (Orobanchaceae) and Cuscuta australis (Convolvulaceae) [18], all of which acquired genes from their hosts.Considering the main direction of nutrient transmission from host to parasitic plants, it is possible that genetic material may be carried within, thus offering opportunities for HGT to parasitic plants.
However, even if gene transfer in the opposite direction (from parasitic to host plants) may be rare, there are still cases that have been reported.For instance, Mower and his colleagues described two HGT cases of the mitochondrial atp1 gene from parasitic flowering plants, Cuscuta and Bartsia (Orobanchaceae), to their host plants of Plantago (Plantaginaceae) [22].Therefore, the link between HGT direction and nutrient flow is not universal.ILLEGITIMATE POLLINATION.This hypothesis presumes that pollen grains of one flowering plant species may germinate on the stigma of another species and, after pollination, some genes from the former may happen to be integrated into the latter species [16,24,25].Such genetic materials may have been delivered to egg cells via elongated pollen tubes and, in some cases or under laboratory conditions, whole plastid and/or mitochondrial genomes are involved [24,26].Based on available data, HGT due to illegitimate pollination may happen between closely related species such as different Alloteropsis grasses [25], or even members from different genera of the grass family Poaceae [27,28].
TRANSFER AGENTS.Vectors such as viruses, bacteria, fungi or insects could transfer genes between organisms.Although concrete evidence is still scarce by now, the possibility that a vector with a wide host range may serve as a gene transfer agent between two unrelated plant species should not be dismissed prematurely [6,16].
MITOCHONDRIAL FUSION.HGT in land plant mitochondria is frequent and sometimes involves large pieces of DNA or even whole genomes (discussed below).Mitochondrial fusion has been suggested as a mechanism to explain these observations [29].The mitochondrial genomes of green plants may be incompatible with those of fungi or animals, thus limiting the donors of mitochondrial fusion events to other green plants [29].
THE WEAK-LINK MODEL.To explain how foreign genes may overcome the isolation of germ cells and reach the offspring, Huang recently proposed a weak-link model [7].This model suggests that foreign genes may enter recipient cells at weakly protected unicellular or early developmental stages of the lifecycle (e.g.zygotes, embryos or spores).These stages represent the weak link in recipient organisms for the entry of foreign genes.Subsequent cell proliferation and differentiation may spread foreign genes to other tissues, including germ cells.As such, foreign genes could ultimately be transmitted to the offspring and then fixed in the population through drift or positive selection on newly acquired functions [7].Some of the above mechanisms (e.g., illegitimate pollination) are only applicable to plants, whereas others (physical association and weak-link model) may explain HGT from miscellaneous donors such as viruses, fungi and prokaryotes.These mechanisms also are not mutually exclusive.For instance, the entry of weakly protected unicellular or early developmental stages of land plants may be facilitated by transfer agents or physical associations.In other words, transfer agents, intimate physical association, and illegitimate pollination concern how foreign genes may be carried from donor to recipient organisms, while the weak-link model focuses on how the barrier of germ cells may be circumvented and foreign genes be integrated into recipient genomes.Even boundaries of these mechanisms may not be clear-cut.For example, a common host plant could serve as an intermediate vector for horizontally transferred genes between different parasites [16,30].
Currently, our knowledge about how HGT happened in land plants is still limited.Future work and new technologies are needed in this research area.

HGT in plant colonization of land
Fossil data and molecular evidence suggest that land plants emerged from a pioneer green algal ancestor about 480-500 million years ago [31].Compared with aquatic environments, terrestrial habitats brought many challenges to early land plants (e.g., desiccation, UV radiation, and microbial attack).During their colonization of land, plants evolved some complex regulatory systems, body plans, and other phenotypic novelties that facilitated their adaptation and radiation in a hostile terrestrial environment [32,33].The origin and evolution of these novelties were aided through acquisition of genes from other organisms [32][33][34].
The phenylpropanoid pathway is responsible for the production of compounds such as flavonoids and lignin.The first and essential step of the phenylpropanoid pathway is catalyzed by phenylalanine ammonia lyase (PAL) [35,36].At 2009, Emiliani et al. reported that plants acquired the PAL gene from soil bacteria or fungi during their early stages of land colonization [32].Given the role of lignin in xylem formation and flavonoids in protecting plants from microbial infection and/or UV radiation, the acquisition of PAL might have been crucial for plant adaptation to terrestrial environments.A more comprehensive genome analysis of the moss Physcomitrella patens identified 57 gene families that were transferred from prokaryotes, fungi or viruses to the most recent common ancestors of land plants or green plants [33].These genes are involved in some essential or plant-specific activities such as xylem formation, plant defense or nitrogen recycling [33,34].Nineteen of these identified gene families also appear to be specific to mosses, suggesting that recent HGT events may not be rare.Further analyses also show that the origin of plant auxin biosynthesis was shaped by HGT [37].Since these acquired genes were identified based on analyses of a single genome using stringent phylogenomic approaches, it is reasonable to believe that more horizontally acquired genes will be found in land plants [34].
The origin of vascular tissues is a significant event in land plant evolution.By ensuring long-distance transport of water, nutrients and organic compounds and increasing the mechanical support for plants, vascular tissues enable land plants to overcome some of the major challenges in terrestrial habitats (e.g., anchorage of plants in the ground, absorption of water and nutrients, support for upright growth) [33,38].Several horizontally acquired genes are involved in the development of vascular tissues.For instance, the vein patterning 1 (VEP1) gene in land plants, presumably acquired from bacteria, is involved in vascular strand formation [33,39].Most recently, Yang et al. investigated the evolution of TAL-type transaldolase (TAL) gene and found that land plant TAL genes are derived from actinobacteria [40].TAL is ubiquitous in land plants and positively selected [40].Transgenic experiments in rice showed that TAL is specifically expressed in vascular tissues.Importantly, knockdown of TAL expression leads to fewer, smaller and immature vascular bundles in culms, suggesting that the acquisition of TAL genes have played a pivotal role in plant vascular development and, therefore, adaptation to land environments.

HGT in phototropic response and C 4 photosynthesis
Millions of years after the initial plant invasion of land, vascular plants arose (during Silurian) [41].Ferns dominated the earth's land surface antecedently, and their dominance was then replaced by angiosperms.Surprisingly, ferns did not die out.Instead, they mostly adapted to a shade-dwelling habit created by angiosperms-dominated forest canopies and then went through another round of diversification, which led to the emergence of the majority of living ferns.Neochrome, a novel chimeric photoreceptor derived from the fusion of red-sensing phytochrome and blue-sensing phototropin modules [42,43], is considered as a key innovation that allows ferns to thrive under low-light conditions [44,45].In order to understand the origin of fern neochrome, Li and his colleagues [46] performed some comprehensive phylogenetic analyses of neochrome and related gene families.After ruling out other causes (e.g., phylogenetic artifacts and independent origins), they concluded that neochrome originated in hornworts and then was transferred to ferns horizontally.This finding suggests that HGT may have had a profound evolutionary impact on the diversification of ferns and, without it, the fern lineages we see today would likely be dramatically different.
C 4 photosynthesis evolved multiple times from C 3 ancestors independently [47].HGT also has affected the evolution of C 4 photosynthesis in Poaceae [25].Alloteropsis, a genus of the grass family that includes five C 4 species and one C 3 subspecies (A.semialata subspecies eckloniana), is an excellent example for studying the evolution of C 4 photosynthesis [48,49].Christin and his colleagues [25] reported that two essential genes of the C 4 pathway in Alloteropsis grasses were acquired from other C 4 taxa within the same family (Poaceae).A reasonable mechanism for the gene transfer events in Alloteropsis grasses was illegitimate pollination.This study also demonstrates that, even without sustained physical associations like parasitism or epiphytism, occasional contact such as pollination may offer opportunities for HGT in flowering plants.

HGT in plant organellar genomes
Although HGT to plastid genomes has rarely been reported (but see [50,51]), mitochondrial genes of land plants are subject to widespread, sometimes in a large scale, gene transfers [24,52,53].For instance, up to 41% of mitochondrial genes in the parasitic family Rafflesiaceae were reportedly subject to HGT events [21].Such massive mitochondrial gene transfers in Rafflesiaceae are not entirely unexpected, considering the frequent reports of HGT in plant mitochondrial genes and in parasitic plants.
An unprecedented case of HGT in flowering plants is related to Amborella trichopoda (Amborellaceae), a basal flowering plant.The mitochondrial genome of Amborella reportedly contains six genome equivalents of foreign mitochondrial DNA, including entire mitochondrial genomes from three green algae and one moss [29].What makes Amborella so rich in foreign mitochondrial genes?The authors postulated that direct contact between Amborella and epiphytes, meristem regeneration through wounding, mitochondrial fusion, as well as a lower rate of DNA loss might have contributed to the large number of foreign genes in Amborella mitochondrial genome [17,29].On the other hand, the distinctive phylogenetic position of Amborella (it diverged the earliest from other lineages of flowering plants [54]) allows researchers to confidently detect genes acquired from other plants [17].The massive HGT in Amborella also highlights the tendency of plant mitochondrial genomes to take up foreign DNA, for there is no evidence of HGT in the chloroplast genome of Amborella [17,29].
HGT of mitochondrial genes is traditionally considered neutral or nearly neutral and, therefore, insignificant for plant adaptive evolution.However, because acquired mitochondrial genes can be transferred to the nucleus or recombine with endogenous organellar DNA fragments, they may increase genetic variation of the recipient plant taxon [14,55,56].Indeed, it has been demonstrated that gene acquisition and subsequent recombination/gene conversion led to some mosaic mitochondrial genes in plants [53,55,56].Therefore, it is premature to dismiss the functional implications of mitochondrial HGT.

Conclusions
The foregoing cases suggest that HGT happened in all major land plant lineages (mosses, ferns and flowering plants).The acquired genes may also be derived from different donor groups including viruses, bacteria, fungi, and other plants [6,33,57,58].Many other cases of HGT have been reported in land plants, but cannot be detailed here [37,52,[59][60][61][62][63][64].To sum up, while HGT in plants may not be as frequent as in prokaryotes or unicellular eukaryotes, it still plays an important role in some essential or plant-specific activities and has had a significant impact on the evolution of land plants.In the end, it should be noted that most of the HGT cases discussed above were detected through analyses of whole genomes or transcriptomic data.In view of the increasing amount of genomic data that become available, we will have a better understanding of the frequency and the role of HGT in land plants.

Fig. 1
Fig. 1 Mechanisms of HGT in land plants.Several mechanisms may facilitate HGT in plants, some of which are shown here.a The intimate physical association of the parasite Cuscuta with host plants offers opportunities for gene transfer.b Pollen germination on stigma of Cyananthus (as shown by image of fluorescence labeled callose.Photo courtesy of Yang Niu, Kunming Institute of Botany).Genetic materials may be delivered to egg cells via elongated pollen tubes.c Aphids may serve as a gene transfer agent between two plant species (photo courtesy of Jianwen Zhang, Kunming Institute of Botany).d Horizontal transfer of entire genomes between green plants may be explained by mitochondrial fusion.e Weakly protected zygote may serve as an entry point for foreign genes into the moss genome according to the weak-link model.