Homology of Nonrepeated DNA Sequences in Phylogeny of Fungal Species
S. K. Dutta in DNA Systematics, 2019
The DNA content per cell, estimated by chemical means in a large number of organisms, agrees well with the accepted notion that the genetic complexity or genome size increased as the complex cellular organization of higher forms evolved. 19 Britten and Kohne20 and Wetmur and Davidson21 extensively studied the rate of reassociation of complementary DNA strands after dissociation and showed that the kinetics of renaturation was directly proportional to the sequence complexity of the reacting DNA molecules. Britten and Kohne20 used the term “Cot ½” to express the concentrations of reacting nucleotides expressed in mol/sec at which 50% reassociation occurred. The Cot ½ value was found to be directly proportional to the sequence complexity of the genome. Thus, by known and unknown genomes, the Cot ½ value of the unknown was used to determine its sequence complexity. Earlier, we reviewed the genome size of fungi representing different taxonomic groups.22 Since then a few more fungi have been added to the list. In general, they all fall within a narrow range of approximately 1.4 to 3 × 107 nucleotide pairs. Although the genome sizes seem to follow the monophyletic origin of fungi, the narrow range of variation makes any definite conclusion difficult.
Other Double-Stranded DNA Viruses
Paul Pumpens, Peter Pushko, Philippe Le Mercier in Virus-Like Particles, 2022
The HcDNAV, a large dsDNA virus of the single species Heterocapsa circularisquama DNA virus 01 from the unassigned genus Dinodnavirus, was isolated from Japanese coastal waters in August 1999 during a H. circularisquama bloom (Tarutani et al. 2001). The virus was icosahedral, lacking a tail, approximately 180–210 nm in diameter and contained an electron-dense core. Its genome size was estimated to be about 356 kb. In fact, this was the first report that has been isolated and maintained in culture of a virus infecting dinoflagellates. Later, Takano et al. (2018) performed detailed observation of the HcDNAV particle, and its infection process was conducted via field emission scanning electron microscopy and epifluorescence microscopy. Each 5-fold vertex of the icosahedral virion was decorated with a protrusion, which may be related to the entry process of HcDNAV into the host. The transverse groove of host cells is proposed to be the main virus-entry site.
Dengue Fever: A Viral Hemorrhagic Fever of Global Concern
Jagriti Narang, Manika Khanuja in Small Bite, Big Threat, 2020
According to the virus classification of Baltimore, dengue virus comes under Group IV because it is a +ssRNA virus. The dengue virus belongs to the Arthropod family consisting a large group and to the family Flaviviridae. The size of a single virion is 50 nm and has about 1.23 g/cc density (Rusell et al., 1980). The total genome size is 11,000 bases. The genome of the virus codes for 10 different proteins, namely, three structural proteins and seven nonstructural proteins. Structural proteins are designated as nucleocapsid protein, membrane-linked protein M and envelope protein E (Fig. 4.4), and seven nonstructural proteins are designated as NS1, NS2a, NS2b, NS3, NS4a, NS4b, and NS5 (Henchal and Putnak, 1990). This was first documented by Rice et al. in 1985 and 1986. In viral genome, capping was found at the 5’ end of ssRNA (Cleaves and Dublin, 1979; Wengler et al., 1978), while at the 3” end, there is absence of poly A tail (Hahn et al., 1988; Irie et al., 1989; Rice et al., 1985). It has a single open reading frame.
Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome
Published in Gut Microbes, 2022
Hao Jin, Lijun You, Feiyan Zhao, Shenghui Li, Teng Ma, Lai-Yu Kwok, Haiyan Xu, Zhihong Sun
The completeness and contamination of each of the recovered genomes were estimated using CheckM (v1.0.18)60 lineage-workflows with default parameters. 16S rRNA genes were predicted using barrnap (v.0.9, https://github.com/tseemann/barrnap). The estimated genome size was adjusted to account for its completeness and contamination: Estimated genome size = (genome size)/(completeness + contamination). The genome replication rate was calculated using the GRiD software (version 1.3).61 This method calculated the genome growth rate from reference genomes at ultra-low sequencing coverage (>0.2x) based on estimating the ratio between coverage at the peak (ori) and the terminus (ter) for the reference bacterial genome using redescending M estimator with Tukey’s biweight function. The GRiD value was directly proportional to the growth rate.
Blautia—a new functional genus with potential probiotic properties?
Published in Gut Microbes, 2021
Xuemei Liu, Bingyong Mao, Jiayu Gu, Jiaying Wu, Shumao Cui, Gang Wang, Jianxin Zhao, Hao Zhang, Wei Chen
The high performance and efficiency of next-generation sequencing technology have allowed novel insights into the whole genome of several bacteria.35 Bioinformatics is widely used to analyze bacterial genome information, enabling the research direction shift from phenotypic assessments to genomic evaluations and even prediction of potential probiotic functions.36 Compared with the abundance of well-known probiotics such as Bifidobacterium and Lactobacillus species and of their genomic data, fewer Blautia species have been isolated, so information on their genome is limited. Currently, there are 12 isolated Blautia species with a total of 195 genome assemblies according to the NCBI database. The genome size varies greatly and ranges from 3.17 to 6.07 Mb with a median of 3.49 Mb. The median GC content is 44.25%, and the median protein count is 3205 (These data were obtained from the NCBI database on September 1, 2020, and detailed information is presented in Table 3).
Suggested doses of proton ions and gamma-rays for mutation induction in 20 plant species
Published in International Journal of Radiation Biology, 2021
Sang Hoon Kim, Sun Young Kim, Jaihyunk Ryu, Yeong Deuk Jo, Hong-Il Choi, Jin-Baek Kim, Si-Yong Kang
Lentil (8,251 Mbp), naked barley (14,410 Mbp), and wheat (33,908 Mbp) have large genome sizes greater than 8,000 Mbp (https://cvalues.science.kew.org/). These plant species showed relatively low LD50 values in response to proton ions and γ-rays: the LD50 values in response to proton ions and γ-rays were 85.5 Gy (lentil), 57.7 Gy (naked barley), and 77.3 Gy (wheat) and 217.7 Gy (lentil), 120.8 Gy (naked barley), and 176.6 Gy (wheat), respectively (Table 1; Figure 3). In the 11 plant species with genome sizes smaller than 2,500 Mbp, however, there was no clear correlation between genome size and estimated LD50 value in response to proton ions and γ-rays (Figure 3). For example, rice and watermelon have similar genome sizes (rice, 980 Mbp; watermelon, 882 Mbp) (https://cvalues.science.kew.org/) but displayed extremely different LD50 values in response to proton ions and γ-rays: 151.4 Gy (rice) and 1,000.2 Gy (watermelon) in response to proton ions and 254.7 Gy (rice) and 1,061.7 Gy (watermelon) in response to γ-rays (Table 1; Figure 3).
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