Genome size‐dependent pcna gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism

Hou, Yubo; Ji, Nanjing; Zhang, Huan; Shi, Xinguo; Han, Hansen; Lin, Senjie

doi:10.1111/jpy.12815

Cited by 16 publications

(9 citation statements)

References 47 publications

(60 reference statements)

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“…All 26 dinoflagellates have DVNP genes but their copy numbers vary with species. Although larger genomes usually mirror more gene duplications 3,20 , the number of DVNP genes does not scale with genome size (Fig 1A). Between the two major parasitic genera from the order Syndiniales, Hematodinium has a 40-fold larger genome and ∼3-fold greater gene repertoire relative to Amoebophrya .…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics illuminates adaptive evolution of DVNP with lifestyle and with loss of histone H1 in dinoflagellates

Wang,

Li,

et al. 2024

Preprint

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About ten years ago dinoﬂagellate/viral nucleoprotein (DVNP) was discovered in dinoflagellates, an ecologically important and evolutionarily enigmatic group of aquatic protists. Apparently acquired from a viral origin, the appearance of DVNP coincided with the loss of nucleosome, a rare event in eukaryote evolution. Despite the potential importance of DVNP as the substitute of histones, its evolutionary trajectory and adaptive significance remain elusive. Here, we conducted comparative analyses using existing dinoflagellate genomes and transcriptomes from 26 species ranging from ancestral to later-diverging lineages to investigate the pattern of sequence and structural divergence. Results showed that the functional domestication of DVNP in ancestral dinoflagellates coincided with the loss of histone H1, while subsequent DVNP differentiation was accompanied by the yet another genomic innovation: acquisition of bacterial-originated histone-like protein. Furthermore, our data split DVNP into two major groups: the core DVNP that resembles histone H1 and shows consistently high levels of expression and the non-core DVNP with higher sequence variability and showing lower yet variable levels of expression. In addition, we observed a trend in DVNP evolution tracing that in lifestyle differentiation. This work offers insights into the adaptive evolution of DVNP, laying the foundation for further inquiries of evolutionary drivers and functional innovation of DVNP to enhance our understanding of dinoflagellate evolution and ecological success.

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Section: Resultsmentioning

confidence: 99%

Comparative genomics illuminates adaptive evolution of DVNP with lifestyle and with loss of histone H1 in dinoflagellates

Wang,

Li,

et al. 2024

Preprint

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“…Are replication origins associated with the TADs in the genome? A high number of replication origins would explain how dinoflagellates are able to maintain similar duration of the S (DNA synthesis) phase of the cell cycle as typical eukaryotes despite their enormous genomes and would be consistent with the unusually high copy number of proliferating cell nuclear antigen gene (Hou et al 2018).…”

Section: Topologically Associated Domains (Tads) Distinct From Eukaryotic Counterpartsmentioning

confidence: 85%

“…Both the genome size and chromosome number vary substantially among dinoflagellates, with genomes ranging from 0.1 to ˜250 Gb (Veldhuis et al 1997, John et al 2019). Both transposons (John et al 2019) and retrotransposons (Slamovits and Keeling 2008, Song et al 2017, Hou et al 2018) have been proposed as potential mechanisms. The latter is supported by genes with an SL sequence encoded in the genome, as well as by high numbers of genes associated with reverse transcription, DNA integration, DNA replication, and transposition (Lin et al 2015, Nand et al 2021.…”

Section: Topologically Associated Domains (Tads) Distinct From Eukaryotic Counterpartsmentioning

confidence: 99%

Spatial organization of dinoflagellate genomes: Novel insights and remaining critical questions

Lin

Song²,

Morse

2021

Journal of Phycology

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As is true for many other aspects, genome architecture, evolution, and function in dinoflagellates are enigmatic and, in the meantime, continuous inspiration for scientific quests. Recent third‐generation sequencing and Hi‐C linkage analyses brought new insights into the spatial organization of symbiodiniacean genomes, revealing the topologically associated domains, discrete gene clusters and their cis and trans orientations, and relationships with transcription. Where do these new findings bring us in dinoflagellate genomics? Here, we aim to place these new results in the backdrop of the long history of research on this topic and in the context of what critical questions remain to be pursued in the future. The new data suggest, pending verification of other complete chromosome assemblies, a potential evolutionary trend in chromosome number decrease and length increase within the Symbiodiniaceae. While questions remain about the mechanics of the three‐dimensional chromosome structure and cell cycle‐related DNA replication, the mechanisms of gene transcription and genome size evolution, these latest findings set new starting points for further inquiries.

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“…32) PCNA plays critical roles in eukaryotic DNA replication and replication-associated processes. 33) Bcl-2 is the first inhibitor of apoptosis through the regulation of mitochondrial outer membrane permeabilization leading to the irreversible release of intermembrane space proteins and subsequent caspase activation and apoptosis. 34) CDK4 belongs to the cyclin-dependent kinase family and plays an important role in regulating the cell cycle.…”

Section: Discussionmentioning

confidence: 99%

Extract of <i>Salvia przewalskii</i> Repair Tissue Damage in Chronic Hypoxia Maybe through the RhoA–ROCK Signalling Pathway

Wang

Duo

Yan

et al. 2020

Biological & Pharmaceutical Bulletin

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Salvia przewalskiiMaxim is a traditional Chinese herbal medicine and is known to have antibacterial, antiviral, anti-oxidant, anti-thrombotic and anti-depressant properties. However, the major active components of S. przewalskii and its anti-hypoxic effects are still unclear. This study probed the major active component and anti-hypoxic activity of S. przewalskii. The major active components of S. przewalskii were detected by HPLC. The anti-hypoxic effects of S. przewalskii were detected in mice and a rat model of hypoxic preconditioning. The results showed that there are eight active components, including sodium danshensu, rosmarinic acid, lithospermic acid, salvianolic acid B, dihydrotanshinone I, cryptotanshinone, tanshinone I and tanshinone IIA, and each component showed a certain anti-hypoxic effect. Moreover, S. przewalskii enhanced anti-hypoxia in mice, which was manifested as prolonged survival time in acute hypoxic preconditioning and the amelioration of acute hypoxia-induced changes in the activity of superoxide dismutase (SOD) and lactate dehydrogenase (LDH). In addition, S. przewalskii also repaired tissue damage in chronic hypoxia by downregulating hypoxia inducible factor-1α (HIF-1α), proliferating cell nuclear antigen (PCNA), Bcl-2, CDK4, CyclinD1 and P27Kip1 and inhibiting pro-inflammatory cytokines and the RhoA-Rho-associated protein kinase (ROCK) signalling pathway. Our findings provide new insight into the anti-hypoxic effect of S. przewalskii as a promising agent for high-altitude pulmonary hypertension treatment.

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Genome size‐dependent pcna gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism

Abstract: Proliferating cell nuclear antigen (PCNA) is most widely known as a processivity factor for DNA polymerases d in eukaryotic cells, forming a ring-like clamp to enclose the polymerase and single-1

Cited by 16 publications

References 47 publications

Comparative genomics illuminates adaptive evolution of DVNP with lifestyle and with loss of histone H1 in dinoflagellates

Comparative genomics illuminates adaptive evolution of DVNP with lifestyle and with loss of histone H1 in dinoflagellates

Spatial organization of dinoflagellate genomes: Novel insights and remaining critical questions

Extract of <i>Salvia przewalskii</i> Repair Tissue Damage in Chronic Hypoxia Maybe through the RhoA–ROCK Signalling Pathway

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