GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba

Gu, Kai-Jie; Lin, Chen‐Feng; Wu, Junjie; Zhao, Yunpeng

doi:10.1093/database/baac046

Cited by 15 publications

(14 citation statements)

References 22 publications

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“…We launched a number of monitoring projects on the Ginkgo microhabitats, DBH growth rate, seedling survival and seed predators in Mt. Tianmu (Gu et al, 2021; Lin et al, 2022). Field and manipulative experiments were carried out to test a number of factors or processes speculated to be associated with the regeneration restriction.…”

Section: Conservation and Managementmentioning

confidence: 99%

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International Biological Flora:Ginkgo biloba

Lin

et al. 2022

Journal of Ecology

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This account presents information on all aspects of the biology of Ginkgo biloba L. (Ginkgo, Maidenhair tree) that are relevant to understanding its ecological characteristics. The main topics are presented within the standard framework of the International Biological Flora: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, reproductive and seed characters, herbivores and disease, history, conservation and global heterogeneity. Globally, Ginkgo survives a wide range of mean annual temperature (−3.3 to 23.3°C) and annual precipitation (34–3925 mm) conditions, according to a meta‐analysis. It prefers a warm, humid, open‐canopy and a well‐drained environment. The species shows strong tolerance to drought, freezing, fire, air pollution, heavy metals and low‐level salt, whereas it is intolerant to long‐time shade and waterlogging. Six Ginkgo trees even survived the atom bomb in Hiroshima, Japan, during World War II. Ginkgo is susceptible to few diseases. Those occurring in nursery seedlings and juvenile trees involve stem rot and leaf blight. The former is caused by Macrophomina phaseoli, which could lead to a mortality rate of 5%–12% (up to 31.8%) for seedlings. This disease can be mitigated by a 4‐h shading treatment and applying organic fertilisers. The pathogens inducing leaf blight include Alternaria alternata, Colletotrichum gloeosporioides and Pestalotia ginkgo, which may infect 100% juvenile trees in some regions. The application of 45% carbendazim or 50% Tuzet can effectively prevent leaf blight. Ginkgo biloba is one of the world’s most distinctive trees with an important position in plant evolution and human society. It is a tall deciduous dioecious tree native to China. Refugial populations were identified in three glacial refugia located in eastern, southern and south‐western China, respectively, with a patchy distribution pattern and a small population size. It typically grows along flood‐disturbed streamsides in warm‐temperate deciduous (and evergreen mixed) broadleaved forests. Ginkgo may have been introduced repeatedly out of China since the sixth century. It has been planted as a landscape tree world‐wide, except in Antarctica. Ginkgo is also of great value for edible nuts, herbal medicine, religion and art. It is a natural and cultural symbol of China.

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Section: Conservation and Managementmentioning

confidence: 99%

“…Data are available from the figshare repository: https://doi.org/10.6084/m9.figshare.19126583.v1 (Lin et al, 2022). The same data are also available on the GinkgoDB website: https://ginkgo.zju.edu.cn/project/survey_data/2022.xlsx(Gu et al, 2021).…”

Section: Peer Reviewmentioning

confidence: 99%

International Biological Flora:Ginkgo biloba

Lin

et al. 2022

Journal of Ecology

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“…Sequences of selected YTH-domain-containing proteins were downloaded from UniProt (Apweiler et al, 2004), TAIR (www.arabidopsis.org), phytozome (Goodstein et al, 2012) or GinkgoDB (Gu et al, 2022) and aligned with Clustal Omega (Sievers et al, 2011) webserver (https://www.ebi.ac.uk/Tools/msa/clustalo/) with default parameters. Evolutionary analyses were conducted in MEGA7 (Kumar et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

“…Amino acid sequences of selected YTH-domain proteins were downloaded from UniProt (Apweiler et al, 2004), TAIR (www.arabidopsis.org), phytozome (92) or GinkgoDB (93) and trimmed from their N-termini to discard intrinsically disordered regions with poor sequence conservation, thereby retaining only the regions with conservation to those structured in human YTHDF1 (62) ( SI Protein Sequences , Dataset S1). Trimmed sequences were aligned with MUSCLE (94, 95) with default parameters (Dataset S2).…”

Section: Methodsmentioning

confidence: 99%

Insights into the conservation and diversification of the molecular functions of YTHDF proteins

Flores-Tellez

Tankmar

Bülow

et al. 2022

Preprint

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YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A), the most common internal covalent modification in eukaryotic mRNA. Members of the YTHDF subclade can determine properties of m6A-containing mRNAs in the cytoplasm of animal and plant cells. Vertebrates encode three YTHDF proteins, and whether they perform specialized or redundant molecular functions is currently debated. In land plants, the YTHDF clade has expanded from just one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain found at the C-terminus following a long intrinsically disordered region (IDR) at the N-terminus. The origin and implications of YTHDF expansion in higher plants are not known, as it is unclear whether it involves acquisition of fundamentally different properties, in particular of their divergent IDRs. Here, we used the leaf formation defects in ect2/ect3/ect4 mutants to test whether the many Arabidopsis YTHDF proteins can perform the same function if expressed at similar levels in leaf primordia. We show that the ancestral molecular function of the m6A-YTHDF axis in land plants is conserved over YTHDF diversification, and currently present in all major clades of YTHDF proteins in flowering plants. Nevertheless, lineage-specific neo-functionalization of a few members also happened after late duplication events. ECT1, the closest homolog of ECT2/3/4, is one such divergent YTHDF protein. Accordingly, mutation of ECT1 does not aggravate the defective organogenesis of ect2/ect3/ect4 mutants, even though the four proteins are naturally expressed in the same population of primordial cells.

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“…In total, 164 full-length NAS sequences from 52 plant species were retrieved using an Expect value (E) cutoff of 10 -90 . Likewise, four NAS proteins were identified in the Ginkgo Database (https://ginkgo.zju.edu.cn/) (44) and seven NAS proteins in the PLAZA 5.0 database (https://bioinformatics.psb.ugent.be/plaza/) (45). Further amino acid sequences of NAS and NAS-like proteins from bacteria, archaea, and fungi were included based on published data (13,15,18,(46)(47)(48).…”

Section: Multiple Sequence Alignments and Phylogenetic Analysesmentioning

confidence: 99%

Arabidopsis Nicotianamine Synthases (NAS) comprise a common core-NAS domain fused to a variable auto-inhibitory C-terminus

Seebach

Radow

Brunek

et al. 2022

Preprint

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Nicotianamine Synthase (NAS) catalyzes the biosynthesis of nicotianamine (NA) from the 2-aminobutyrate moieties of three S-adenosylmethionine molecules. NA has central roles in metal nutrition and metal homeostasis of flowering plants. Despite the availability of crystal structures of archaeal and bacterial NAS-like proteins that carry out simpler aminobutanoyltransferase reactions, the enzymatic function of NAS remains poorly understood. Here we report amino acids essential for the activity of AtNAS1 based on structural modeling and site-directed mutagenesis. An enzyme-coupled continuous activity assay allowed us to compare differing NAS proteins identified through multiple sequence alignments and phylogenetic analyses. In most class Ia and b NAS proteins of dicotyledonous and monocotyledonous angiosperm plants, respectively, the core-NAS domain is fused to a variable C-terminal domain. Compared to fungal and moss NAS (class III) that consist merely of the core-NAS domain, NA biosynthetic activities of the four paralogous Arabidopsis NAS proteins were far lower. Yet their C-terminally trimmed core-NAS variants exhibited strongly elevated activities. Out of 320 amino acids of AtNAS1, twelve, 287-TRGCMFMPCNCS-298, accounted for the auto-inhibitory effect of the C-terminus, with approximately one third contributed by N296 within a CNCS motif that is conserved in Arabidopsis. No detectable NA biosynthesis was mediated by two representatives of groups of plant NAS proteins that naturally lack the C-terminal domain, class Ia Arabidopsis halleri NAS5, and Medicago truncatula NAS2 of class II which is found in dicots and diverged early during the evolution of flowering plants. Our results suggest that NAS activity is under stringent post-translational control in plants.

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GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba

Cited by 15 publications

References 22 publications

International Biological Flora:Ginkgo biloba

International Biological Flora:Ginkgo biloba

Insights into the conservation and diversification of the molecular functions of YTHDF proteins

Arabidopsis Nicotianamine Synthases (NAS) comprise a common core-NAS domain fused to a variable auto-inhibitory C-terminus

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