Polyploidy does not control all: Lineage‐specific average chromosome length constrains genome size evolution in ferns

Liu, Hongmei; Ekrt, Libor; Koutecký, Petr; Pellicer, Jaume; Hidalgo, Oriane; Marquardt, Jeannine; Pustahija, Fatima; Ebihara, Atsushi; Siljak‐Yakovlev, Sonja; Gibby, Mary; Leitch, Ilia J.; Schneider, Harald

doi:10.1111/jse.12525

Cited by 22 publications

(16 citation statements)

References 75 publications

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“…Polyploidy plays an important role in fern evolution (Vida, 1976; Wood et al ., 2009; Liu et al ., 2019). Most ferns use a mixed‐mating system (Haufler et al ., 2016), forming sporophytes by self‐fertilization (gametophytic selfing) or by exchanging gametes with other gametophytes (sporophytic selfing or outcrossing).…”

Section: Discussionmentioning

confidence: 99%

Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns

Hornych¹,

Testo

Sessa

et al. 2020

New Phytologist

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Sex expression of homosporous ferns is controlled by multiple factors, one being the antheridiogen system. Antheridiogens are pheromones released by sexually mature female fern gametophytes, turning nearby asexual gametophytes precociously male. Nevertheless, not all species respond. It is still unknown how many fern species use antheridiogens, how the antheridiogen system evolved, and whether it is affected by polyploidy and/or apomixis. We tested the response of 68 fern species to antheridiogens in cultivation. These results were combined with a comprehensive review of literature to form the largest dataset of antheridiogen interactions to date. Analyzed species also were coded as apomictic or sexual and diploid or polyploid. Our final dataset contains a total of 498 interactions involving 208 species (c. 2% of all ferns). About 65% of studied species respond to antheridiogen. Multiple antheridiogen types were delimited and their evolution is discussed. Antheridiogen responsiveness was not significantly affected by apomixis or polyploidy. Antheridiogens are widely used by ferns to direct sex expression. The antheridiogen system likely evolved multiple times and provides homosporous ferns with the benefits often associated with heterospory, such as increased rates of outcrossing. Despite expectations, antheridiogens may be beneficial to polyploids and apomicts.

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Section: Discussionmentioning

confidence: 99%

Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns

Hornych¹,

Testo

Sessa

et al. 2020

New Phytologist

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“…Whole-genome duplication or polyploidization is an important driver of adaptation and speciation in plants (Hovav et al, 2008;Liu et al, 2019). In the polyploid genome, there are a large number of duplicated genes and duplicated genes from different diploid ancestors.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Profile of the SNAT Gene Family in Tobacco (Nicotiana tabacum)

et al. 2020

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Melatonin plays key roles in development and confers stress tolerance to plants. Serotonin N-acetyltransferase (SNAT) is either the enzyme involved in the last step or the penultimate enzyme of phytomelatonin biosynthesis. To date, SNAT genes have not been characterized in tobacco (Nicotiana tabacum), an economically important plant species. The sequence of the Acetyltransf_7 conserved domain was used as a query sequence, and 12 NtSNAT candidate genes were in turn identified in the genome of tobacco. These NtSNATs could be divided into two groups based on the phylogenetic tree. NtSNAT1 and NtSNAT2 clustered together with the other typical SNATs, but the other 10 NtSNATs separately clustered outside of the typical SNATs. These 10 NtSNATs have only motif 1, whereas representative SNATs, such as NtSNAT1 and NtSNAT2 or a SNAT from cyanobacteria, have five motifs. In addition, NtSNAT1 and NtSNAT2 are highly homologous to the characterized OsSNAT1, 62.95 and 71.36%, respectively; however, the homology between the other 10 NtSNAT genes and OsSNAT1 is low. Concomitantly, it is hypothesized that NtSNAT1 and NtSNAT2 are the homolog of SNATs, whereas the other 10 candidates could be considered NtSNATlike genes. Furthermore, both Nicotiana tomentosiformis and Nicotiana sylvestris, two diploid ancestor species of N. tabacum, have two SNAT candidates; therefore, it is speculated that gene rearrangement or deletion during the process of genomic stabilization after whole-genome duplication or polyploidization led to the preservation of NtSNAT1 and NtSNAT2 during the evolution of tobacco from the ancestral diploid to the allotetraploid. NtSNAT and NtSNAT-like genes were differentially expressed in all organs under different stress conditions, indicating that these genes potentially associated with plant growth and development and stress resistance. Under different stress conditions, the expression of NtSNAT1 was significantly upregulated upon high-temperature and cadmium stresses, while the expression of NtSNAT2 did not significantly increase under any of the tested stress treatments. These results provide valuable information for elucidating the evolutionary relationship of SNAT genes in tobacco and genetic resources for improving tobacco production in the future.

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“…CYPs are the key set of enzymes involved in the biosynthesis of natural products catalyzing coveted pathway steps. Given that ferns do not undergo a typical genome downsizing following whole genome duplication events as observed for other plant lineages (Liu et al, 2019) it is not surprising that ferns possess such high incidences of CYP family blooms. Furthermore, as this analysis relied mainly on transcriptomic resources, the number of fern CYP genes may be vastly underestimated.…”

Section: The Existence Of 'Blooms' Of Cyp Familiesmentioning

confidence: 99%

“…From an evolutionary perspective, ferns hold an important position in plant evolution, lying in the sister clade to seed plants. Unlike seed plants, however, ferns do not undergo the typical genome downsizing following whole genome duplication events (Liu et al, 2019). This has resulted in ferns possessing relatively higher chromosome numbers and genome sizes compared with angiosperms (Sessa et al; Wolf et al, 2015; Clark et al, 2016; Li et al, 2018)).…”

Section: Introductionmentioning

confidence: 99%

The fern CYPome: Fern-specific cytochrome P450 family involved in convergent evolution of chemical defense

Thodberg

Hansen

Takos

et al. 2021

Preprint

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Plant natural products encompass an enormous chemical diversity bearing witness to great molecular innovation that occured throughout land plant evolution. Cytochrome P450 monooxygenases (CYPs) catalyze a wide variety of monooxygenation reactions essential to the metabolic repertoire of plants natural products. Ferns constitute the second largest group of vascular plants and hold a significant phylogenetic position in land evolution, lying sister to seed plants. To date, CYP diversity has not been described for this taxon and pathway discovery in ferns in general is scarce, despite possessing a rich diversity of natural products. We analysed over 8000 available fern CYPs, classifing and characterizing the landscape of this super-enzyme group. Fern CYPs are dominated by fern-specific families (∼60%), with the largest family – CYP981 – constituting approximately 15% of all predicted fern CYPs in the dataset. The abundancy and dynamics of the CYP981 family suggest a position equivalent to the CYP71 family present in seed plants, with potential roles in natural product biosynthesis. Ferns are the evolutionary oldest group to biosynthesize cyanogenic glycosides; amino acid-derived defense compounds. We show that CYP981F5 from the highly cyanogenic fern Phlebodium aureum catalyzes the conversion of phenylacetonitrile to mandelonitrile, an intermediate step in cyanogenic glycoside biosynthesis. The fern CYPome provides an important platform to further understand evolution of metabolite biosynthesis throughout the plant kingdom, and in ferns specifically.

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Polyploidy does not control all: Lineage‐specific average chromosome length constrains genome size evolution in ferns

Cited by 22 publications

References 75 publications

Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns

Insights into the evolutionary history and widespread occurrence of antheridiogen systems in ferns

Genome-Wide Identification and Expression Profile of the SNAT Gene Family in Tobacco (Nicotiana tabacum)

The fern CYPome: Fern-specific cytochrome P450 family involved in convergent evolution of chemical defense

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