Biology subjects

Karimi, N.

Publications and source records attributed to Karimi, N..

7 recordsLinked to original sources

bioRxiv2026

Madagascar as an evolutionary source for the Paleotropical flora: New insights from the biogeography of Grewia (Malvaceae)

Oceanic islands are natural laboratories for investigating the processes that generate, maintain, and redistribute biodiversity through time. An ideal flowering plant system to investigate these processes is Grewia L. (Malvaceae, Grewioideae), comprising ca. 283 species, of which nearly 30% are endemic to Madagascar, where they display considerable morphological diversity. Using Angiosperms353 target-capture sequencing for 171 accessions (119 Grewia spp.), we reconstructed the first densely sampled phylogeny of Grewia and performed divergence-time estimation, diversification analyses, and ancestral-range reconstruction. Our results support a Malagasy origin of the crown group around 27 million years ago, followed by extensive in situ diversification of Grewia. Repeated dispersal events from Madagascar to continental Africa subsequently contributed to the establishment of new African lineages, whereas colonization of the western Indian Ocean islands was more recent and resulted in anagenetic dispersals. Africa acted as the principal source of dispersal toward Arabia and into tropical Asia, suggesting the presence of a Miocene Afro-Arabian migration corridor under warm and humid conditions. Subsequent eastward dispersal from Asia to Australia is consistent with the stepping stone pathway provided by the Sunda and Sahul regions during the Miocene. This complex dispersal history was likely aided by fleshy fruits adapted for endozoochory. Our new evolutionary framework provides a robust basis for future taxonomic revision of this morphologically and ecologically diverse genus, and for identifying which characters have contributed to its exceptional diversification.

evolutionary biology↗

bioRxiv2026

Chloroplast Genome Evolution, Heteroplasmy, and Inverted Repeat Dynamics in the Elymus Complex (Triticeae, Poaceae): Insights from Single-Molecule Sequencing of Elymus ciliaris and Comparative Analysis of St-Genome Lineages

Background/ObjectivesElymus sensu lato (Poaceae) is arguably the largest and most complex genus in the tribe Triticeae. It includes hybrids and polyploids based on x=7 chromosomes, all including the St genome, forming a valuable genepool for forage grass and cereal breeding. Analysis of chloroplast genome diversity and structural dynamics is critical for resolving maternal lineages, reticulate evolution and biodiversity across this agronomically important complex, refining their taxonomy, conservation and exploitation. MethodsWe sequenced the complete chloroplast genome (plastome) of Elymus ciliaris (4x=2n=28; StStYY genome composition) using ultra-long Oxford Nanopore single-molecule reads and compared it to 76 additional chloroplast genomes representing major St-genome lineages in Elymus s.l. (Pseudoroegneria St; Elymus s.s. StH, StY; Thinopyrum StJ/E; Campeiostachys StYH; Kengyilia StYP). We analyzed structure, nucleotide diversity, inverted repeat (IR) dynamics, and phylogenetic signal. ResultsThe E. ciliaris chloroplast genome was 135,004 bp long (38.3% GC) with a canonical quadripartite structure. Single-molecule reads (n=74) revealed heteroplasmy: two Small-Single-Copy (SSC) orientations at 30%:70% frequency, indicating an inversion polymorphism. Across the Elymus group, comparative analysis of chloroplast assemblies showed high structural conservation but lineage-specific IR-boundary shifts. Kengyilia exhibits exceptional IR expansion. Nucleotide diversity hotspots localize to the large single-copy region, especially in StY lineages. Phylogenies recover a monophyletic St-containing clade but do not delineate genera, reflecting reticulate evolution, with North American/Southeast Asian and Eurasian geographic sub-clades. ConclusionsSingle-molecule sequencing uncovered heteroplasmy with an inversion polymorphism in a single plant of Elymus ciliaris, hidden in short read assemblies. There were no other polymorphisms, as expected for chloroplast sequences (except for technical homopolymer variation). Our analyses showed that a Pseudoroegneria-like St chloroplast genome predominates as the maternal donor across Elymus polyploids. Variable regions and IR dynamics offer strong models for chloroplast genome evolution in reticulate lineages and suggest exploiting plastome variation to complement nuclear biodiversity studies.

genomics↗

bioRxiv2025

How much can reticulate evolution entangle plant systematics? Revisiting subfamilial classification of the Malvatheca clade (Malvaceae) on the basis of phylogenomics

Reticulate evolution (RE), involving hybridization and related processes, generates network-like rather than strictly bifurcating relationships among lineages and can obscure phylogenetic relationships. Detecting ancient hybridization is particularly challenging, as genomic signals may erode over time. The Malvatheca clade (Malvaceae), marked by multiple paleopolyploidy events since its estimated origin 66 my, offers a useful model for examining RE. Its three subfamilies--Bombacoideae (with high chromosome numbers, mostly trees), Malvoideae (lower chromosome numbers, mostly herbs), and the recently described Matisioideae--show unresolved relationships, with several taxa of uncertain placement. We conducted a phylogenomic analysis of 62 Malvatheca species via complete plastomes, 35S rDNA cistrons, and comparative repeatome data. All datasets consistently resolved three main clades: (i) Bombacoideae, (ii) Malvoideae, and (iii) a heterogeneous assemblage including most of the recently assigned Matisioideae and several incertae sedis taxa, suggesting a more complex evolutionary history and circumscription than previously recognized. Chromosome numbers were negatively correlated with repeatome diversity: Bombacoideae presented higher counts but lower repeat diversity, possibly reflecting slower repeat evolution associated with woody growth forms. In contrast, clade III showed marked heterogeneity in both chromosome number and repeat composition, which is consistent with a reticulate origin. Overall, our results show evidence of ancient hybridization and polyploidy, predominantly allopolyploidy, in shaping Malvatheca evolution. These results highlight that reticulation and genome dynamics, rather than taxonomic boundaries alone, are central to understanding the diversification of Malvatheca.

genomics↗

bioRxiv2025

Proteomic and lipidomic profiling of immune cell-derived subpopulations of extracellular vesicles

IntroductionExtracellular vesicles (EVs) are a heterogeneous group of membrane-enclosed vesicles released by cells. They play important roles in intercellular communication and contribute to several physiological and pathological processes. Cells release subpopulations of EVs with distinct biogenesis and functions, however, we currently have few markers to differentiate them. This study, therefore, aimed to determine proteomic and lipidomic differences among four EV subpopulations of varying sizes and densities. MethodsLarge and small EVs (L-EVs and S-EVs) were isolated from two immune cell lines by differential ultracentrifugation at 16,500 x g and 118,000 x g, respectively. The crude EVs were then further separated by density cushion centrifugation. EVs were isolated from the interphase between 1.079-1.146 and 1.146-1.185 g/ml, hereafter referred to as low density (LD) and high density (HD), respectively. This resulted in four subpopulations of EVs: L-EVs LD, L-EVs HD, S-EVs LD, and S-EVs HD. The morphology, size, and yield of EVs were determined by nanoparticle tracking analysis, electron microscopy, and western blot. The proteome and lipidome of the four subpopulations of EVs were determined with mass spectrometry. ResultsA total of 5364 proteins were quantified in the dataset. L-EV and S-EVs as well as LD and HD were well separated. Briefly, L-EVs LD were enriched in mitochondrial proteins such as the TIMM/TOMM complex, MICOS, and ATP5 proteins. In contrast, L-EVs HD were enriched in proteins associated with the cytoskeleton, such as KIF proteins. Furthermore, S-EVs LD were enriched in tetraspanins and ESCRT machinery proteins, while S-EVs HD were enriched in histones, CCT proteins, and proteins from the complement pathway. Proteins such as flotillins, RABs, annexins, and integrins were enriched in two or several subpopulations. Furthermore, 107 lipids were quantified, and the most abundant lipids in EVs were phosphatidylcholine (PC), sphingomyelin, and phosphatidylethanolamine (PE). The most profound difference was that PE was less abundant in L-EVs LD as compared to the other EV subtypes, and ceramides were enriched in L-EVs as compared to S-EVs. ConclusionThis study demonstrates that the proteome and lipidome differ in EV subpopulations separated based on size and density. Furthermore, it validates several protein groups that have previously been suggested to be enriched in either S-EVs or L-EVs.

molecular biology↗

bioRxiv2024

Chromosome-level baobab (Adansonia digitata) genome illuminates its evolutionary insights

AbstractBaobab, Adansonia digitata, is a long-lived tree endemic to Africa that holds great economic, ecological, and cultural value. However, our knowledge of its genomic features, evolutionary history, and diversity is limited, rendering it orphaned scientifically. We generated a haploid chromosome-level reference genome anchored into 42 chromosomes for A. digitata, as well as draft assemblies for a sibling tree, two trees from distinct locations in Africa, and a related species, A. za from Madagascar. Unlike any other plant to date, DNA transposable elements (TEs) make up 33% of the A. digitata genome compared to only 10% long terminal repeat retrotransposons (LTR-RTs), which are usually predominant in plant genomes. Baobab has undergone a whole genome duplication (WGD) shared with the Malvoideae [~]30 million years ago (MYA), as well as a confirmed autotetraplody event 3-4 million MYA that coincides with the most recent burst of TE insertions. Resequencing 25 A. digitata trees from Africa revealed three subpopulations that suggest gene flow through most of West Africa but separated from East Africa. Gene enrichment analysis for baobab-specific and high fixation index (Fst) suggested baobab may have retained multiple copies of circadian, light and growth genes to coordinate genome protection for longevity through the UV RESISTANCE LOCUS 8 (UVR8) and synchronizing flower development with pollinators. This study lays the groundwork for the creation of breeding resources and the conservation of baobab biodiversity.

genomics↗

bioRxiv2021

Improving germline transmission efficiency in chimeric chickens using a multi-stage injection approach

Although different strategies have been developed to generate transgenic poultry, low efficiency of germline transgene transmission has remained a challenge in poultry transgenesis. Herein, we developed an efficient germline transgenesis method using a lentiviral vector system in chickens through multiple injections of transgenes into embryos at different stages of development. The embryo chorioallantoic membrane (CAM) vasculature was successfully used as a novel route of gene transfer into germline tissues. We established a new method of eggshell windowing for embryo manipulation at different developmental stages. Compared to the other routes of viral vector administration, the embryos bloodstream at Hamburger-Hamilton (HH) stages 14-15 achieved the highest rate of germline transmission (GT), 7.7%. Single injection of viral vectors into the CAM vasculature resulted in a GT efficiency of 2.7%, which was significantly higher than the 0.4% obtained by injection into embryos at the blastoderm stage. Double injection of viral vectors into the bloodstream at HH stages 14-15 and through CAM was the most efficient method for producing germline chimeras, giving a GT rate of 13.6%. The authors suggest that the new method described in this study could be efficiently used to produce transgenic poultry in virus-mediated gene transfer systems.

developmental biology↗

bioRxiv2020

Focus-tunable microscope for imaging small neuronal processes in freely moving animals

Miniature 1-photon microscopes have been widely used to image neuronal assemblies in the brain of freely moving animals over the last decade. However, these systems have important limitations for imaging in-depth fine neuronal structures. We present a novel subcellular imaging 1-photon device that uses an electrically tunable liquid crystal lens to enable a motion-free depth scan in the search of such structures. Our miniaturized microscope is compact (10 mm x 17 mm x 12 mm), lightweight ({approx} 1.4 g), provides fast acquisition rate (30-50 frames/second), high magnification (8.7x) and high resolution (1.4 m) that allow imaging of calcium activity of fine neuronal processes in deep brain regions during a wide range of behavioural tasks of freely moving mice.

neuroscience↗