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

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 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-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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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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Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria

Scientific Reports ◽

10.1038/s41598-019-54637-6 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Madelyne Xiao ◽

Mercer R. Brugler ◽

Michael B. Broe ◽

Luciana C. Gusmão ◽

Marymegan Daly ◽

...

Keyword(s):

Hydrothermal Vents ◽

Phylogenetic Reconstruction ◽

Evolutionary Relationship ◽

Molecular Data ◽

Sea Anemone ◽

Trophic Levels ◽

Phylogenetic Position ◽

Sea Anemones ◽

Sister Relationship ◽

Relationship Of

AbstractRelicanthus daphneae (formerly Boloceroides daphneae) was first described in 2006 as a giant sea anemone based on morphology. In 2014, its classification was challenged based on molecular data: using five genes, Relicanthus was resolved sister to zoanthideans, but with mixed support. To better understand the evolutionary relationship of Relicanthus with other early-branching metazoans, we present 15 newly-sequenced sea anemone mitochondrial genomes and a mitogenome-based phylogeny including all major cnidarian groups, sponges, and placozoans. Our phylogenetic reconstruction reveals a moderately supported sister relationship between Relicanthus and the Actiniaria. Morphologically, the cnidae of Relicanthus has apical flaps, the only existing synapomorphy for sea anemones. Based on both molecular and morphological results, we propose a third suborder (Helenmonae) within the Actiniaria to accommodate Relicanthus. Although Relicanthus shares the same gene order and content with other available actiniarian mitogenomes, it is clearly distinct at the nucleotide level from anemones within the existing suborders. The phylogenetic position of Relicanthus could reflect its association with the periphery of isolated hydrothermal vents, which, although patchy and ephemeral, harbor unique chemosynthetic communities that provide a relatively stable food source to higher trophic levels over long evolutionary timescales. The ability to colonize the deep sea and the periphery of new vent systems may be facilitated by Relicanthus’ large and extremely yolky eggs.

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Genome-wide protein phylogenies for four African cichlid species

10.1101/110510 ◽

2017 ◽

Author(s):

Ajay Ramakrishnan Varadarajan ◽

Rohini Mopuri ◽

J. Todd Streelman ◽

Patrick T. McGrath

Keyword(s):

Protein Function ◽

Evolutionary Relationship ◽

Trait Variation ◽

Cichlid Species ◽

Genome Wide ◽

A Genome ◽

History Of ◽

Astatotilapia Burtoni ◽

African Cichlids ◽

Relationship Of

ABSTRACTBackgroundThe thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species.ResultsWe used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented.ConclusionThese phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species.

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Genome-wide identification and expression analysis of tomato ADK gene family during development and stress

10.21203/rs.3.rs-57426/v1 ◽

2020 ◽

Author(s):

Lu Yang ◽

Haohao Cao ◽

Xiaoping Zhang ◽

Liangxian Gui ◽

Qiang Chen ◽

...

Keyword(s):

Energy Homeostasis ◽

Functional Characterization ◽

Evolutionary Relationship ◽

Hormone Treatment ◽

Motif Analysis ◽

Element Analysis ◽

Real Time Quantitative Pcr ◽

Cis Element ◽

Genome Wide ◽

Relationship Of

Abstract Background: Adenylate kinase (ADK) is widely distributed in organisms and plays an important role in cellular energy homeostasis. In plants, ADK has important functions in plant growth and development regulation as well as adaptation to the environment. However, little information is available about the ADK genes in tomato (Solanum lycopersicum), an important economic crop.Results: To investigate the characteristics and functions of ADK genes in tomato, a total of 11 ADK genes were identified and named according to their chromosomal locations. The ADK family was divided into five groups and motif analysis revealed that each SlADK protein contained five to eight conserved motifs. Sequence analysis revealed 4-19 exons in all SlADKs and most members possessed four. The 11 SlADKs were randomly distributed on nine of the 12 tomato chromosomes. A cis-element analysis inferred that several stress response elements were found on the promoters of SlADKs. The online TomExpress platform prediction revealed that SlADKs were expressed in various tissues and organs, basically consistent with the data obtained from real-time quantitative PCR (qPCR). The qPCR verification was also used to determine the expression level of SlADKs and demonstrated that the genes responded to multiple abiotic stresses, such as drought, salt and cold. For example, almost all SlADKs contained two expression peaks at 9 and 48 h following salt treatment. The qPCR results showed that SlADK transcription was responsive to most of the applied hormone treatment: methyl jasmonate, ethylene, salicylic acid, indole 3-acetic acid and abscisic acid. Notably, SlADK2 and 4 exhibited significant changes under multiple stress treatments.Conclusions: These results provide valuable information for clarifying the evolutionary relationship of the tomato ADK family and in aiding functional characterization of SlADKs in further research.

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Genomic analyses of the extinct Sardinian dhole (Cynotherium sardous) reveal its evolutionary history

10.1101/2021.02.26.432714 ◽

2021 ◽

Author(s):

Marta Maria Ciucani ◽

Julie Kragmose Jensen ◽

Mikkel-Holger S. Sinding ◽

Oliver Smith ◽

Saverio Bartolini Lucenti ◽

...

Keyword(s):

Small Body ◽

Evolutionary Relationship ◽

Population Connectivity ◽

Phylogenetic Position ◽

Dental Morphology ◽

Genome Wide ◽

Morphometric Analyses ◽

Hunting Dog ◽

High Level ◽

Canid Species

SummaryThe Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species of canid that was endemic of Sardinia and Corsica until it became extinct at the end of the Late Pleistocene2–5. Given its peculiar dental morphology, small body size and high level of endemism, several canids have been proposed as possible ancestors of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor 3,6–9. Morphometric analyses3,6,8–12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca 21,100 year old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found it represents a separate taxon from all other living canids from Eurasia, Africa and North America, and that the Sardinian and Asian dhole lineages diverged ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, that ended approximately 500-300 ka, when the landbridge between Sardinia and mainland Italy was broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids - probably a result of the long-term isolation - that could have contributed to the subsequent extinction of the Sardinian dhole.

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Relationship of the Pine Growth Promoting Pantoea eucalypti FBS135 with Type Strains P. eucalypti LMG 24197T and P. vagans 24199T

Life ◽

10.3390/life11070608 ◽

2021 ◽

Vol 11 (7) ◽

pp. 608

Author(s):

Chunyue Wei ◽

Zhongwen Song ◽

Yiming Lu ◽

Yinjuan Zhao ◽

Ben Fan

Keyword(s):

Endophytic Bacterium ◽

Pinus Massoniana ◽

Comparative Genomic ◽

Circular Chromosome ◽

Single Chromosome ◽

Whole Genomes ◽

Phylogenetic Status ◽

Relationship Of ◽

Low Nitrogen Tolerance ◽

Type Strains

Endophytes in woody plants are much less understood. Pantoea strain FBS135 is an endophytic bacterium isolated from Pinus massoniana with the ability to promote pine growth significantly. In this study, we demonstrated that FBS135 has the astonishing ability of low nitrogen tolerance but no ability of nitrogen fixation. To exactly determine the phylogenetic status of FBS135, we sequenced the whole genomes of P. eucalypti LMG 24197T and P. vagans 24199T, type strains of two Pantoea species, which are evolutionarily closest to FBS135. P. eucalypti LMG 24197T contained a single chromosome of 4,035,995 bp (C+G, 54.6%) plus three circular plasmids while LMG 24199T comprises a single circular chromosome of 4,050,173 bp (C+G, 55.6%) and two circular plasmids. With the genomic information, FBS135 was finally identified as a P. eucalypti strain, although it showed some different physiological traits from the two type strains. Comparative genomic analyses were performed for the three strains, revealing their common molecular basis associated with plant lifecycle as well as the differences in their gene arrangements relating to nitrogen utilization.

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Genome-Wide Identification of Stress-Associated Proteins (SAPs) Encoding A20/AN1 Zinc Finger in Almond (Prunus dulcis) and Their Differential Expression during Fruit Development

Plants ◽

10.3390/plants11010117 ◽

2021 ◽

Vol 11 (1) ◽

pp. 117

Author(s):

Sidra Fatima ◽

Zeeshan Zafar ◽

Alvina Gul ◽

Muhammad Faraz Bhatti

Keyword(s):

Zinc Finger ◽

Developmental Stages ◽

Evolutionary Relationship ◽

Prunus Dulcis ◽

Regulatory Elements ◽

Genome Wide ◽

Upstream Promoter ◽

Associated Proteins ◽

Upstream Promoter Region ◽

Relationship Of

Stress-associated proteins (SAPs) are zinc finger proteins involved in the regulation of various stresses in a variety of plant species. A total of nine PdSAP genes were identified in Prunus dulcis. Phylogenetic and synteny analyses were performed to analyze the homology and evolutionary relationship of PdSAP genes. The functions of PdSAP genes were assessed by further analyses, including cis-regulatory elements, gene duplication, gene ontology, gene structure, subcellular localization, and motif pattern. This study found that PdSAP genes were unevenly distributed on chromosomes 2, 3, 6, and 7. Phylogenetic analysis of PdSAP genes with Arabidopsis thaliana and Oryza sativa suggested that six subgroups have a similar pattern of AN1 and A20 domains in each subgroup. PdSAP genes lacked duplicated blocks. The majority of PdSAP genes were localized in the nucleus region. Three hormonal and five stress cis-regulatory elements were found in the upstream promoter region of the PdSAP gene family. RNA-seq analysis revealed differential gene expression of PdSAP genes at days 12, 17, 22, 27, 32, and 37 of fruitlet development after flowering. This study identifies the SAP genes in P. dulcis and also provides insights into the expression of PdSAP genes in abnormal fruitlets with diapause atrophic growth at various developmental stages.

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Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79s.1.20 ◽

2019 ◽

Vol 79 (01S) ◽

Author(s):

Pawan Kumar Jayaswal ◽

Asheesh Shanker ◽

Nagendra Kumar Singh

Keyword(s):

Evolutionary Relationship ◽

Genomic Data ◽

Gene Clusters ◽

Species Trees ◽

Model Species ◽

Tubulin Gene ◽

Tubulin Genes ◽

Eukaryotic Species ◽

Relationship Of ◽

Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

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