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Genomes reveal pervasive distant hybridization in nature among cyprinid fishes
<h4>Background</h4>Genomic data have unveiled a fascinating aspect of the evolutionary past, showing that the mingling of different species through hybridization has left its mark on the histories of numerous life forms. However, the relationship between …
Read PDFThe center of wheat domestication drives diversity of <i>Clavibacter</i> pathogens
Microbial plant pathogens possess higher diversity in the center of domestication of their host plants than in the introduced geographic area of the corresponding crops. In this study, the center of wheat, barley, and oat …
Read PDFUnraveling genomic features and phylogenomics through the analysis of three Mexican endemic <i>Myotis</i> genomes
<h4>Background</h4>Genomic resource development for non-model organisms is rapidly progressing, seeking to uncover molecular mechanisms and evolutionary adaptations enabling thriving in diverse environments. Limited genomic data for bat species hinder insights into their evolutionary processes, particularly …
Read PDFFirst Plastome Sequences of Two Endemic Taxa of <i>Orbea</i> Haw. from the Arabian Peninsula: Comparative Genomics and Phylogenetic Relationships Within the Tribe Ceropegieae (Asclepiadoideae, Apocynaceae)
<i>Orbea</i> is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of <i>Orbea sprengeri</i> subsp. <i>commutata</i> and <i>O. wissmannii</i> …
Read PDFComprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships
BACKGROUND: The Poaceae is one of the world’s most ecologically and economically important plant families, encompassing major food crops and forage grasses. Despite its agricultural significance, systematic analyses of chloroplast genome evolution across this diverse …
Read PDFPhylogeny and evolution of streptophyte algae
The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of …
Read PDFComplete mitochondrial genome of a golden orb-web spider <i>Trichonephila clavata</i> (Chelicerata, Arachnida) from South Korea
The mitochondrial genome of a golden orb-web spider <i>Trichonephila clavata</i> (L. Koch, 1878) from South Korea is determined and characterized in detail, which is the second mitochondrial genome reported from this species: the first was …
Read PDFUPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics
Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a …
Read PDFThe adaptive evolution of Quercus section Ilex using the chloroplast genomes of two threatened species
Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, …
Read PDFHidden in the Pangenome? Machine Learning-Driven Discovery of Antimicrobial Potential in <i>Corynebacterium glutamicum</i>
Antimicrobial resistance poses an increasing global challenge, driving the urgent need for alternative strategies to identify novel therapeutic agents. Microbial natural products encoded by biosynthetic gene clusters (BGCs) remain among the most promising sources of …
Read PDFSynteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae
Large genomic data sets are becoming the new normal in phylogenetic research, but the identification of true orthologous genes and the exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such …
Read PDFPlastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae)
Well-resolved phylogenetic relationships within the diverse Neotropical orchid genus Lepanthes are presented based on a genome skimming approach that yielded nine newly sequenced chloroplast genomes. We complemented this with 17-86 plastome coding genes for 26 …
Read PDFRepeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group
Mitochondrial introgression is common among animals and is often first identified through mitonuclear discordance-discrepancies between evolutionary relationships inferred from mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA). Over recent decades, genomic data have also revealed extensive …
Read PDFBursts of Rapid Diversification, Dispersals Out of Southern Africa, and Two Origins of Dioecy Punctuate the Evolution of Asparagus
The genus Asparagus arose ∼9 to 15 million years ago (Ma), and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3 to 4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining …
Read PDFTwo New Steroidal Saponins with Potential Anti-Inflammatory Effects from the Aerial Parts of <i>Gnetum formosum</i> Markgr
<i>Gnetum formosum</i> Markgr., a member of the Gnetaceae family, is distributed in Vietnam. This plant remains a botanical enigma with an unexplored diversity of chemical constituents and pharmacological effects. In this study, two new steroidal …
Read PDF<i>Glissandra oviformis</i> n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs
Culturing protists offers a powerful approach to exploring eukaryotic diversity, especially for deep-branching lineages. In this study, we cultured and described a novel protist species, named <i>Glissandra oviformis</i> n sp. within the poorly studied and …
Read PDFWhole-genome analysis of a novel <i>Pandoraea sputorum</i> lineage causing high-mortality bloodstream infections
<b>Background.</b> <i>Pandoraea sputorum</i> is an emerging multidrug-resistant pathogen primarily associated with cystic fibrosis. Bloodstream infections (BSIs) are rare but linked to high mortality. The genomic characteristics and evolutionary history of <i>P. sputorum</i> lineages causing BSIs …
Read PDFPhylogenomics, taxonomy and morphological characters of the Microdochiaceae (Xylariales, Sordariomycetes)
Species of the family Microdochiaceae (Xylariales, Sordariomycetes) have been reported from worldwide, and collected from different plant hosts. The proposed new genus and two new species, <i>viz.</i>, <i>Macroidriella</i> <b>gen. nov.</b>, <i>M.bambusae</i> <b>sp. nov.</b> and <i>Microdochiumaustrale</i> …
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