Recent advances on phylogenomics of gymnosperms and a new classification

Yang, Yong; Ferguson, David K.; Liu, Bing; Mao, Kangshan; Gao, Lian‐Ming; Zhang, Shouzhou; Wan, Tao; Rushforth, Keith; Zhang, Zhixiang

doi:10.1016/j.pld.2022.05.003

Cited by 55 publications

(35 citation statements)

References 57 publications

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“…High-level classification for fungi, gymnosperms, angiosperms and pteridophytes follows Tedersoo et al 2018, Yang et al 2022, APG IV (APG IV 2016, and PPG I (PPG I 2016), respectively. For algae, we used specific classification systems for each division (Cavalier-Smith and Chao 1996, Cavalier-Smith 1998, Lewis and McCourt 2004, Cavalier-Smith 2016, Kamiya et al 2017, Garcia-Pichel et al 2019 following Algaebase (Guiry and Guiry 2015).…”

Section: Methodsmentioning

confidence: 99%

12,500+ and counting: biodiversity of the Brazilian Pampa

Andrade¹,

Dröse²,

Aguiar³

et al. 2023

Frontiers of Biogeography

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Knowledge on biodiversity is fundamental for conservation strategies. The Brazilian Pampa region, located in subtropical southern Brazil, is neglected in terms of conservation, and knowledge of its biodiversity is fragmented. We aim to answer the question: how many, and which, species occur in the Brazilian Pampa? In a collaborative effort, we built species lists for plants, animals, bacteria, and fungi that occur in the Brazilian Pampa. We included information on distribution patterns, main habitat types, and conservation status. Our study resulted in referenced lists totaling 12,503 species (12,854 taxa, when considering infraspecific taxonomic categories [or units]). Vascular plants amount to 3,642 species (including 165 Pteridophytes), while algae have 2,046 species (2,378 taxa) and bryophytes 316 species (318 taxa). Fungi (incl. lichenized fungi) contains 1,141 species (1,144 taxa). Animals total 5,358 species (5,372 taxa). Among the latter, vertebrates comprise 1,136 species, while invertebrates are represented by 4,222 species. Our data indicate that, according to current knowledge, the Pampa holds approximately 9% of the Brazilian biodiversity in an area of little more than 2% of Brazil's total land. The proportion of species restricted to the Brazilian Pampa is low (with few groups as exceptions), as it is part of a larger grassland ecoregion and in a transitional climatic setting. Our study yielded considerably higher species numbers than previously known for many species groups; for some, it provides the first published compilation. Further efforts are needed to increase knowledge in the Pampa and other regions of Brazil. Considering the strategic importance of biodiversity and its conservation, appropriate government policies are needed to fund studies on biodiversity, create accessible and constantly updated biodiversity databases, and consider biodiversity in school curricula and other outreach activities.

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Section: Methodsmentioning

confidence: 99%

12,500+ and counting: biodiversity of the Brazilian Pampa

Andrade¹,

Dröse²,

Aguiar³

et al. 2023

Frontiers of Biogeography

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“…Columns on the right side show the number of analyzed species in each order and the number of species possessing the conserved motifs in KNL1 (FFGPVS) and NDC80 (RMKRE). The phylogenetic tree was drawn according to The Angiosperm Phylogeny Group 2016 (Yang et al 2022). Fig.…”

Section: Authors Contributionmentioning

confidence: 99%

KNL1 and NDC80 represent new universal markers for the detection of functional centromeres in plants

Oliveira,

Neumann,

Mata-Sucre

et al. 2023

Preprint

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Centromere is the chromosomal site of kinetochore assembly and microtubule attachment for chromosome segregation. Given its importance, markers that allow specific labeling of centromeric chromatin throughout the cell cycle and across all chromosome types are sought for facilitating various centromere studies. Antibodies against the N-terminal region of CENH3 are commonly used for this purpose, since CENH3 is the near-universal marker of functional centromeres. However, because the N-terminal region of CENH3 is highly variable among plant species, antibodies directed against this region usually function only in a small group of closely related species. As a more versatile alternative, we present here antibodies targeted to the conserved domains of two outer kinetochore proteins, KNL1 and NDC80. Sequence comparison of these domains across more than 350 plant species revealed a high degree of conservation, particularly within a six amino acid motif, FFGPVS in KNL1, suggesting that both antibodies would function in a wide range of plant species. This assumption was confirmed by immunolabeling experiments in angiosperm (monocot and dicot) and gymnosperm species, including those with mono-, holo-, and meta-polycentric chromosomes. In addition to centromere labeling on condensed chromosomes during cell division, both antibodies detected the corresponding regions in the interphase nuclei of most species tested. These results demonstrated that KNL1 and NDC80 are better suited for immunolabeling centromeres than CENH3, because antibodies against these proteins offer incomparably greater versatility across different plant species which is particularly convenient for studying the organization and function of the centromere in non-model species.

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“…[ 13 ] and Ginkgo L. [ 14 ]. To our knowledge, some miRNAs studies have also been conducted on several Cupressaceae trees, such as Platycladus orientalis (L.) Franco and Chinese fir ( C. lanceolata ) [ 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Further Mining and Characterization of miRNA Resource in Chinese Fir (Cunninghamia lanceolata)

Deng

Huang

et al. 2022

Genes

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In this study, we aimed to expand the current miRNA data bank of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) regarding its potential value for further genetic and genomic use in this species. High-throughput small RNA sequencing successfully captured 140 miRNAs from a Chinese fir selfing family harboring vigor and depressed progeny. Strikingly, 75.7% (n = 106) of these miRNAs have not been documented previously, and most (n = 105) of them belong to the novel set with 6858 putative target genes. The new datasets were then integrated with the previous information to gain insight into miRNA genetic architecture in Chinese fir. Collectively, a relatively high proportion (62%, n = 110) of novel miRNAs were found. Furthermore, we identified one MIR536 family that has not been previously documented in this species and four overlapped miRNA families (MIR159, MIR164, MIR171_1, and MIR396) from new datasets. Regarding the stability, we calculated the secondary structure free energy and found a relatively low R2 value (R2 < 0.22) between low minimal folding free energy (MFE) of pre-miRNAs and MFE of its corresponding mature miRNAs in most datasets. When in view of the conservation aspect, the phylogenetic trees showed that MIR536 and MIR159 sequences were highly conserved in gymnosperms.

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Recent advances on phylogenomics of gymnosperms and a new classification

Cited by 55 publications

References 57 publications

12,500+ and counting: biodiversity of the Brazilian Pampa

12,500+ and counting: biodiversity of the Brazilian Pampa

KNL1 and NDC80 represent new universal markers for the detection of functional centromeres in plants

Further Mining and Characterization of miRNA Resource in Chinese Fir (Cunninghamia lanceolata)

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