Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi

Guohua Xiao; Guirong Tang; Chengshu Wang

doi:10.3390/jof6030134

Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi

Journal of Fungi ◽

10.3390/jof6030134 ◽

2020 ◽

Vol 6 (3) ◽

pp. 134

Author(s):

Guohua Xiao ◽

Guirong Tang ◽

Chengshu Wang

Keyword(s):

Protein Content ◽

Clustering Analysis ◽

Evolutionary Rate ◽

Fungal Species ◽

Phylogenomic Analysis ◽

Genome Wide ◽

Whole Genomes ◽

Data Explosion ◽

Relationship Of ◽

Varied Level

Amid the genomic data explosion, phylogenomic analysis has resolved the tree of life of different organisms, including fungi. Genome-wide clustering has also been conducted based on gene content data that can lighten the issue of the unequal evolutionary rate of genes. In this study, using different fungal species as models, we performed phylogenomic and protein-content (PC)-based clustering analysis. The obtained sequence tree reflects the phylogenetic trajectory of examined fungal species. However, 15 PC-based trees constructed from the Pfam matrices of the whole genomes, four protein families, and ten subcellular locations largely failed to resolve the speciation relationship of cross-phylum fungal species. However, lifestyle and taxonomic associations were more or less evident between closely related fungal species from PC-based trees. Pairwise congruence tests indicated that a varied level of congruent or discordant relationships were observed between sequence- and PC-based trees, and among PC-based trees. It was intriguing to find that a few protein family and subcellular PC-based trees were more topologically similar to the phylogenomic tree than was the whole genome PC-based phylogeny. In particular, a most significant level of congruence was observed between sequence- and cell wall PC-based trees. Cophylogenetic analysis conducted in this study may benefit the prediction of the magnitude of evolutionary conservation, interactive associations, or networking between different family or subcellular proteins.

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Re-assessing the phylogenetic status and evolutionary relationship of Forest Owlet [Athene blewitti (Hume 1873)] using genomic data

10.1101/2021.10.09.463762 ◽

2021 ◽

Author(s):

K.L Vinay ◽

Meghana Natesh ◽

Prachi Mehta ◽

Rajah Jayapal ◽

Shomita Mukherjee ◽

...

Keyword(s):

Evolutionary Relationship ◽

Phylogenetic Position ◽

List Type ◽

Tree Construction ◽

Genome Wide ◽

Whole Genomes ◽

Divergence Dating ◽

Phylogenetic Status ◽

Taxonomic Affiliation ◽

Relationship Of

ABSTRACTPhylogenetic relationships are often challenging to resolve in recent/younger lineage when only a few loci are used. Ultra Conserved Elements (UCE) are highly conserved regions across taxa that help resolve shallow and deep divergences. We utilized UCEs harvested from whole genomes to assess the phylogenetic position and taxonomic affiliation of an endangered endemic owlet in the family Strigidae – the Forest Owlet Athene blewitti. The taxonomic placement of this species has been revised multiple times. A multigene study attempted to address the question but showed a discrepancy across datasets in its placement of the species within genus Athene. We assembled a dataset of 5018 nuclear UCE loci with increased taxon sampling. Forest Owlet was found to be an early split from the Athene clade but sister to other Athene; and consistent across three approaches - maximum likelihood, bayesian, and the multispecies coalescence. Divergence dating using fossil calibrations suggest that the Athene lineage split from its ancestor about 7.6Mya, and the Forest Owlet diverged about 5.2Mya, consistent with previous multigene approaches. Despite osteological differences from other Athene, we suggest the placement of the Forest Owlet as a member of the Athene to emphasize its evolutionary relationship.Graphical AbstractHIGHLIGHTSPhylogenomics using genome-wide nuclear markers yielded a well-supported topology for Athene and Glaucidium lineages.Three different methods of phylogenetic tree construction showed that Forest Owlet is an early split from all other Athene species.Divergence dating in the bayesian framework puts the Forest Owlet age between 5.0my to 5.5my.

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Genome-wide association study identified candidate genes for seed size and seed composition improvement in M. truncatula

Scientific Reports ◽

10.1038/s41598-021-83581-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhijuan Chen ◽

Vanessa Lancon-Verdier ◽

Christine Le Signor ◽

Yi-Min She ◽

Yun Kang ◽

...

Keyword(s):

Association Study ◽

Protein Content ◽

Seed Size ◽

Seed Protein ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Strong Positive Correlation ◽

Seed Composition ◽

Seed Traits ◽

Genome Wide

AbstractGrain legumes are highly valuable plant species, as they produce seeds with high protein content. Increasing seed protein production and improving seed nutritional quality represent an agronomical challenge in order to promote plant protein consumption of a growing population. In this study, we used the genetic diversity, naturally present in Medicago truncatula, a model plant for legumes, to identify genes/loci regulating seed traits. Indeed, using sequencing data of 162 accessions from the Medicago HAPMAP collection, we performed genome-wide association study for 32 seed traits related to seed size and seed composition such as seed protein content/concentration, sulfur content/concentration. Using different GWAS and postGWAS methods, we identified 79 quantitative trait nucleotides (QTNs) as regulating seed size, 41 QTNs for seed composition related to nitrogen (i.e. storage protein) and sulfur (i.e. sulfur-containing amino acid) concentrations/contents. Furthermore, a strong positive correlation between seed size and protein content was revealed within the selected Medicago HAPMAP collection. In addition, several QTNs showed highly significant associations in different seed phenotypes for further functional validation studies, including one near an RNA-Binding Domain protein, which represents a valuable candidate as central regulator determining both seed size and composition. Finally, our findings in M. truncatula represent valuable resources to be exploitable in many legume crop species such as pea, common bean, and soybean due to its high synteny, which enable rapid transfer of these results into breeding programs and eventually help the improvement of legume grain production.

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High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis

Nature Communications ◽

10.1038/s41467-020-20490-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Qiu Sun ◽

Alan Perez-Rathke ◽

Daniel M. Czajkowsky ◽

Zhifeng Shao ◽

Jie Liang

Keyword(s):

High Resolution ◽

Single Cell ◽

3D Models ◽

Computational Method ◽

Midblastula Transition ◽

Genome Wide ◽

Large Ensembles ◽

Chromatin Folding ◽

Function Relationship ◽

Relationship Of

AbstractSingle-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis in Drosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5–6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore, >50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the midblastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.

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CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2018.2878564 ◽

2020 ◽

Vol 17 (3) ◽

pp. 981-989

Author(s):

Qiwen Kang ◽

Neil Moore ◽

Christopher L. Schardl ◽

Ruriko Yoshida

Keyword(s):

Phylogenomic Analysis ◽

Analysis Method ◽

Genome Wide ◽

Branch Lengths

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Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route

10.1101/2020.04.27.20081349 ◽

2020 ◽

Cited By ~ 3

Author(s):

Lehai Zhang ◽

Shifu Wang ◽

Qian Ren ◽

Junjie Yang ◽

Yanqin Lu ◽

...

Keyword(s):

Molecular Detection ◽

Detection Efficiency ◽

Evolutionary Relationship ◽

Clinical Manifestations ◽

Coding Region ◽

Gene Coding ◽

Genome Wide ◽

Group A ◽

Group B ◽

Relationship Of

AbstractIn the epidemic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the issues of mutation, origin, typing and the effect of mutation on molecular detection remain to be unrevealed. In order to identify the evolutionary relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are currently used in different countries, we retrieved genomic sequences of 373 SARS-CoV-2 strains from multiple databases and performed genome-wide variation analysis. According to the nucleotide C28144T variation, the SARS-CoV-2 can be divided into group A (117 strains) and group B (256 strains). The spike protein gene (S gene) coding region 1841 (total 23403) A1841G, formed a B1 subgroup (40 strains) in group B, of which 30 strains were from European and American countries in March (especially Washington, USA). These mutations are likely to be influenced by the environment or the immunization selection pressure of different populations. Although the mutation is not in the receptor binding region (RBD) and alkaline cleavage region, it may also affect the ability of transmission and pathogenicity; however, the significance is not yet clear. As the ratio of A / B strains in the epidemic months showed an increasing trend (0.35: 1 in January, 0.62: 1 in February and 0.76: 1 in March), it seems that the transmissibility of group A strains becomes stronger with time. Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. By comparing the detection capabilities of primers in different countries, the SARS-CoV-2 nucleotide variation may only affect molecular detection of very few strains. The differences in the transmissibility, pathogenicity and clinical manifestations of different types of strains require further investigations.

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Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery

Biotechnology for Biofuels ◽

10.1186/s13068-019-1569-6 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Stephen J. Mondo ◽

Diego Javier Jiménez ◽

Ronald E. Hector ◽

Anna Lipzen ◽

Mi Yan ◽

...

Keyword(s):

Wheat Straw ◽

Purifying Selection ◽

Reticulate Evolution ◽

Phylogenomic Analysis ◽

Lignocellulolytic Enzymes ◽

Genome Expansion ◽

Lack Of Information ◽

Genome Wide ◽

A Genome ◽

Furanic Compounds

Abstract Background Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). Results The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source. Conclusions We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and “eco-enzymology” of lignocellulolytic Coniochaeta species.

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Korean Genome Project: 1094 Korean personal genomes with clinical information

Science Advances ◽

10.1126/sciadv.aaz7835 ◽

2020 ◽

Vol 6 (22) ◽

pp. eaaz7835 ◽

Cited By ~ 2

Author(s):

Sungwon Jeon ◽

Youngjune Bhak ◽

Yeonsong Choi ◽

Yeonsu Jeon ◽

Seunghoon Kim ◽

...

Keyword(s):

Genome Wide Association Study ◽

Imputation Accuracy ◽

Clinical Information ◽

Genome Project ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

Whole Genomes ◽

Personal Genomes

We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.

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Genome-wide analysis of the aquaporin genes in melon (Cucumis melo L.)

Scientific Reports ◽

10.1038/s41598-020-79250-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Alvaro Lopez-Zaplana ◽

Juan Nicolas-Espinosa ◽

Micaela Carvajal ◽

Gloria Bárzana

Keyword(s):

Cucumis Melo ◽

Evolutionary Relationship ◽

Physiological Importance ◽

Genome Wide ◽

Related Plant ◽

Complete Set ◽

The Individual ◽

Almost All ◽

Relationship Of ◽

Cucumis Melo L

AbstractMelon (Cucumis melo L.) is a very important crop throughout the world and has great economic importance, in part due to its nutritional properties. It prefers well-drained soil with low acidity and has a strong demand for water during fruit set. Therefore, a correct water balance—involving aquaporins—is necessary to maintain the plants in optimal condition. This manuscript describes the identification and comparative analysis of the complete set of aquaporins in melon. 31 aquaporin genes were identified, classified and analysed according to the evolutionary relationship of melon with related plant species. The individual role of each aquaporin in the transport of water, ions and small molecules was discussed. Finally, qPCR revealed that almost all melon aquaporins in roots and leaves were constitutively expressed. However, the high variations in expression among them point to different roles in water and solute transport, providing important features as that CmPIP1;1 is the predominant isoform and CmTIP1;1 is revealed as the most important osmoregulator in the tonoplast under optimal conditions. The results of this work pointing to the physiological importance of each individual aquaporin of melon opening a field of knowledge that deserves to be investigated.

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Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet

Scientific Reports ◽

10.1038/s41598-020-76230-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mahesh Pujar ◽

S. Gangaprasad ◽

Mahalingam Govindaraj ◽

Sunil S. Gangurde ◽

A. Kanatti ◽

...

Keyword(s):

Association Study ◽

Protein Content ◽

Pearl Millet ◽

Genome Wide Association Study ◽

Breeding Strategy ◽

Genome Wide Association ◽

Late Embryogenesis Abundant Protein ◽

Pentatricopeptide Repeat ◽

Genome Wide ◽

Population Structure Analysis

Abstract Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

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