Phylogenetic analyses to uncover the evolutionary relationship of a newly sequenced mitochondrial genome from an Eastern spinebill (Acanthorhynchus tenuirostris)

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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The evolution of brain size among the Homininae and selection at ASPM and MCPH1 genes

Biosis:Biological Systems ◽

10.37819/biosis.002.02.0104 ◽

2021 ◽

Vol 2 (2) ◽

pp. 293-310

Author(s):

Sandra Leyva-Hernández ◽

Ricardo Fong-Zazueta ◽

Luis Medrano-González ◽

Ana Julia Aguirre-Samudio

Keyword(s):

Positive Selection ◽

Nucleotide Substitution ◽

Brain Size ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Brain Evolution ◽

Haplotype Blocks ◽

Accelerated Evolution ◽

Relationship Of ◽

The Brain

We examined the evolutionary relationship of the ASPM (abnormal spindle-like microcephaly associated) and MCPH1 (microcephalin-1) genes with brain volume among humans and other primates. We obtained sequences of these genes from 14 simiiform species including hominins. Two phylogenetic analyses of ASPM exon 3 and MCPH1 exons 8 and 11 were performed to maximize taxon sampling or sequence extension to compare the nucleotide substitution and encephalization rates, and examine signals of selection. Further assessment of selection among humans was done through the analysis of non-synonymous and synonymous substitutions (dN/dS), and linkage disequilibrium (LD) patterns. We found that the accelerated evolution of brain size in hominids, is related to synchronic acceleration in the substitution rates of ASPM and MCPH1, and to signals of positive selection, especially in hominins. The dN/dS and LD analyses in Homo detected sites under positive selection and some regions with haplotype blocks at several candidate sites surrounded by blocks in LD-equilibrium. Accelerations and signals of positive selection in ASPM and MCPH1 occurred in different lineages and periods being ASPM more closely related with the brain evolution of hominins. MCPH1 evolved under positive selection in different lineages of the Catarrhini, suggesting independent evolutionary roles of this gene among primates.

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Complete Mitogenome of Endangered and Endemic Nicobar Treeshrew (Tupaia Nicobarica) and Comparison with Other Scandentians

10.21203/rs.3.rs-880056/v1 ◽

2021 ◽

Author(s):

Shantanu Kundu ◽

Avas Pakrashi ◽

Manokaran Kamalakannan ◽

Devkant Singha ◽

Kaomud Tyagi ◽

...

Keyword(s):

Mitochondrial Genome ◽

Biomedical Research ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Andaman Sea ◽

Nicobar Island ◽

Taxonomic Rank ◽

Strong Negative Selection ◽

Complete Mitogenome

Abstract The Nicobar treeshrew (Tupaia nicobarica) is an endangered smaller mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate evolutionary relationship. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (ML and BA) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (11.4 to 18.8 MYR) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. The present study suggests the assembly of whole-genome to improve the understanding of evolutionary relationships of treeshrews and its implication in biomedical research.

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Comparative analysis of prophages carried by human and animal-associated Staphylococcus aureus strains spreading across the European regions

10.21203/rs.3.rs-409259/v1 ◽

2021 ◽

Author(s):

Romen Singh Naorem ◽

Gunajit Goswami ◽

Schneider Gyorgy ◽

Csaba Fekete

Keyword(s):

Staphylococcus Aureus ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Genomic Islands ◽

European Regions ◽

Pathogenic Potential ◽

Host Interactions ◽

Relationship Of ◽

Clustering Patterns

Abstract Staphylococcus aureus is a major human and animal pathogen although the animal-associated S. aureus can be a potential risk of human zoonoses. Acquisition of phage-related genomic islands determines the diversity of the S. aureus species and contributes to adapt to various host conditions. This study characterized and compared the genome architecture, distribution nature, and evolutionary relationship of 65 complete prophages carried by human and animal-associated S. aureus strains spreading across the European regions. The genomes of the analyzed prophages showed mosaic architecture with extensive variation in genome size and displayed low sequence similarity in their functional modules. The phylogenetic analyses generated seven clades in which prophages of the animal-associated S. aureus scattered in all the clades and showed slightly different clustering patterns than human-associated S. aureus prophages. The presence of various virulence factors in prophages of animal-associated S. aureus suggested that these prophages could have more pathogenic potential than prophages of human-associated S. aureus. This study showed that the S. aureus phages are dispersed among the several S. aureus serotypes and around the European regions. Further, understanding the phage functional genomics is necessary for the phage-host interactions and could be used for tracing the S. aureus strains transmission.

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Comparative analysis of prophages carried by human and animal-associated Staphylococcus aureus strains spreading across the European regions

Scientific Reports ◽

10.1038/s41598-021-98432-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Romen Singh Naorem ◽

Gunajit Goswami ◽

Schneider Gyorgy ◽

Csaba Fekete

Keyword(s):

Staphylococcus Aureus ◽

Clonal Complex ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Genomic Islands ◽

Genome Architecture ◽

European Regions ◽

Pathogenic Potential ◽

Host Interactions ◽

Relationship Of

AbstractStaphylococcus aureus is a major human and animal pathogen although the animal-associated S. aureus can be a potential risk of human zoonoses. Acquisition of phage-related genomic islands determines the S. aureus species diversity. This study characterized and compared the genome architecture, distribution nature, and evolutionary relationship of 65 complete prophages carried by human and animal-associated S. aureus strains spreading across the European regions. The analyzed prophage genomes showed mosaic architecture with extensive variation in genome size. The phylogenetic analyses generated seven clades in which prophages of the animal-associated S. aureus scattered in all the clades. The S. aureus strains with the same SCCmec type, and clonal complex favored the harboring of similar prophage sequences and suggested that the frequency of phage-mediated horizontal gene transfer is higher between them. The presence of various virulence factors in prophages of animal-associated S. aureus suggested that these prophages could have more pathogenic potential than prophages of human-associated S. aureus. This study showed that the S. aureus phages are dispersed among the several S. aureus serotypes and around the European regions. Further, understanding the phage functional genomics is necessary for the phage-host interactions and could be used for tracing the S. aureus strains transmission.

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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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Nucleotide sequence of the Syrian hamster intracisternal A-particle gene: close evolutionary relationship of type A particle gene to types B and D oncovirus genes.

Journal of Virology ◽

10.1128/jvi.55.2.387-394.1985 ◽

1985 ◽

Vol 55 (2) ◽

pp. 387-394 ◽

Cited By ~ 57

Author(s):

M Ono ◽

H Toh ◽

T Miyata ◽

T Awaya

Keyword(s):

Nucleotide Sequence ◽

Syrian Hamster ◽

Evolutionary Relationship ◽

Type A ◽

Intracisternal A Particle ◽

Relationship Of

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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

Scientific Reports ◽

10.1038/s41598-019-57065-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Rajasree Chakraborty ◽

Priya Prasad ◽

Shantanu Kundu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Gene Arrangement ◽

Sister Relationship ◽

Protein Coding ◽

Relationship Of ◽

Rna Genes ◽

Boundary Mapping ◽

Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

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Complete mitochondrial genome of Black Drongo Dicrurus macrocercus (Passeriformes: Dicruridae) and phylogenetic analyses

Mitochondrial DNA Part B ◽

10.1080/23802359.2021.1920490 ◽

2021 ◽

Vol 6 (8) ◽

pp. 2442-2444

Author(s):

Haibo Zhang ◽

Xue Gou ◽

Shize Li ◽

Cheng Wang ◽

Caichun Peng ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome

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Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

Scientific Reports ◽

10.1038/s41598-021-81622-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kun Zhang ◽

Kehua Zhu ◽

Yifan Liu ◽

Hua Zhang ◽

Li Gong ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Rearrangement ◽

Tandem Duplication ◽

Mitochondrial Gene ◽

Gene Arrangement ◽

Protein Coding ◽

Muraenesox Cinereus ◽

Complete Mitogenome ◽

Relationship Of ◽

Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

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