FAD2 Gene Radiation and Positive Selection Contributed to Polyacetylene Metabolism Evolution in Campanulids1[OPEN]

Polyacetylenes (PAs) are bioactive, specialized plant defense compounds produced by some species in the eudicot clade campanulids. Early steps of PA biosynthesis are catalyzed by Fatty Acid Desaturase 2 (FAD2). Canonical FAD2s catalyze desaturation, but divergent forms can catalyze hydroxylation, conjugation, acetylenation, and epoxygenation. These alternate reactions give rise to valuable unusual fatty acids, including the precursors to PAs. The extreme functional diversity of FAD2 enzymes and the origin of PA biosynthesis are poorly understood from an evolutionary perspective. We focus here on the evolution of the FAD2 gene family. We uncovered a core eudicot-wide gene duplication event giving rise to two lineages: FAD2- a and FAD2-b. Independent neofunctionalizations in both lineages have resulted in functionally diverse FAD2-LIKEs involved in unusual fatty acid biosynthesis. We found significantly accelerated rates of molecular evolution in FAD2-LIKEs and use this metric to provide a list of uncharacterized candidates for further exploration of FAD2 functional diversity. FAD2-a has expanded extensively in Asterales and Apiales, two main clades of campanulids, by ancient gene duplications. Here, we detected positive selection in both Asterales and Apiales lineages, which may have enabled the evolution of PA metabolism in campanulids. Together, these findings also imply that yet uncharacterized FAD2-a copies are involved in later steps of PA biosynthesis. This work establishes a robust phylogenetic framework in which to interpret functional data and to direct future research into the origin and evolution of PA metabolism

\u3ci\u3eFAD2\u3c/i\u3e Gene Radiation and Positive Selection Contributed to Polyacetylene Metabolism Evolution in Campanulids

Polyacetylenes (PAs) are bioactive, specialized plant defense compounds produced by some species in the eudicot clade campanulids. Early steps of PA biosynthesis are catalyzed by Fatty Acid Desaturase 2 (FAD2). Canonical FAD2s catalyze desaturation, but divergent forms can catalyze hydroxylation, conjugation, acetylenation, and epoxygenation. These alternate reactions give rise to valuable unusual fatty acids, including the precursors to PAs. The extreme functional diversity of FAD2 enzymes and the origin of PA biosynthesis are poorly understood from an evolutionary perspective. We focus here on the evolution of the FAD2 gene family. We uncovered a core eudicot-wide gene duplication event giving rise to two lineages: FAD2- a and FAD2-b. Independent neofunctionalizations in both lineages have resulted in functionally diverse FAD2-LIKEs involved in unusual fatty acid biosynthesis. We found significantly accelerated rates of molecular evolution in FAD2-LIKEs and use this metric to provide a list of uncharacterized candidates for further exploration of FAD2 functional diversity. FAD2-a has expanded extensively in Asterales and Apiales, two main clades of campanulids, by ancient gene duplications. Here, we detected positive selection in both Asterales and Apiales lineages, which may have enabled the evolution of PA metabolism in campanulids. Together, these findings also imply that yet uncharacterized FAD2-a copies are involved in later steps of PA biosynthesis. This work establishes a robust phylogenetic framework in which to interpret functional data and to direct future research into the origin and evolution of PA metabolism

Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual <i>Kingdonia uniflora</i> (Circaeasteraceae, Ranunculales)

Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative ‘ancient asexuals’ usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated πN/πS ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality

Development and Application of Transcriptome-Derived Microsatellites in Actinidia eriantha (Actinidiaceae)

Actinidia eriantha Benth. is a diploid perennial woody vine native to China and is recognized as a valuable species for commercial kiwifruit improvement with high levels of ascorbic acid as well as having been used in traditional Chinese medicine. Due to the lack of genomic resources for the species, microsatellite markers for population genetics studies are scarce. In this study, RNASeq was conducted on fruit tissue of A. eriantha, yielding 5,678,129 reads with a total output of 3.41 Gb. De novo assembly yielded 69,783 non-redundant unigenes (41.3 Mb), of which 21,730 were annotated using protein databases. A total of 8,658 EST-SSR loci were identified in 7,495 unigene sequences, for which primer pairs were successfully designed for 3,842 loci (44.4%). Among these, 183 primer pairs were assayed for PCR amplification, yielding 69 with detectable polymorphism in A. eriantha. Additionally, 61 of the 69 polymorphic loci could be successfully amplified in at least one other Actinidia species. Of these, 14 polymorphic loci (mean N-A = 6.07 +/- 2.30) were randomly selected for assessing levels of genetic diversity and population structure within A. eriantha. Finally, a neighbor-joining tree and Bayesian clustering analysis showed distinct clustering into two groups (K = 2), agreeing with the geographical distributions of these populations. Overall, our results will facilitate further studies of genetic diversity within A. eriantha and will aid in discriminating outlier loci involved in local adaptation

Estimating the Potential Impacts of Climate Change on the Spatial Distribution of <i>Garuga forrestii</i>, an Endemic Species in China

Understanding how species have adapted and responded to past climate provides insights into the present geographical distribution and may improve predictions of how biotic communities will respond to future climate change. Therefore, estimating the distribution and potentially suitable habitats is essential for conserving sensitive species such as Garuga forrestii W.W.Sm., a tree species endemic to China. The potential climatic zones of G. forrestii were modelled in MaxEnt software using 24 geographic points and nine environmental variables for the current and future (2050 and 2070) conditions under two climate representative concentration pathways (RCP4.5 and RCP8.5) scenarios. The resulting ecological niche models (ENMs) demonstrated adequate internal assessment metrics, with all AUC and TSS values being >0.79 and a pROC of >1.534. Our results also showed that the distribution of G. forrestii was primarily influenced by temperature seasonality (% contribution = 12%), elevation (% contribution = 27.5%), and precipitation of the wettest month (% contribution = 35.6%). Our findings also indicated that G. forrestii might occupy an area of 309,516.2 km2 in southwestern China. We note that the species has a potential distribution in three provinces, including Yunnan, Sichuan, and Guangxi. A significant decline in species range is observed under the future worst case of high-emissions scenario (RCP8.5), with about 19.5% and 20% in 2050 and 2070, respectively. Similarly, higher elevations shift northward to southern parts of Sichuan province in 2050 and 2070. Thus, this study helps highlight the vulnerability of the species, response to future climate and provides an insight to assess habitat suitability for conservation management

Plastome Phylogenomic and Biogeographical Study on Thuja (Cupressaceae)

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja

Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant \u27tree of life\u27

To evaluate the phylogenetic patterns of the distribution and evolution of plant secondary metabolites (PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. A significant phylogenetic signal was detected in 17 of the 18 tested seed-plant clades for at least 1 of the 8 PSM classes using the D statistic. The phylogenetic signal, nevertheless, indicated weak clustering of PSMs compared to a random distribution across all seed plants. The observed signal suggests strong diversifying selection during seed-plant evolution and/or relatively weak evolutionary constraints on the evolution of PSMs. In the survey of the current phylogenetic distributions of PSMs, we found that multiple origins of PSM biosynthesis due to external selective forces for diverse genetic pathways may have played important roles. In contrast, a single origin of PSMs seems rather uncommon. The distribution patterns for PSMs observed in this study may also be useful in the search for natural compounds for medicinal purposes

Genome Sequencing of the Endangered \u3ci\u3eKingdonia uniflora\u3c/i\u3e (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization

Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment