Increasing Microbial Biofuel Production by In-silico Comparative Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

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The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽

10.3390/genes12040483 ◽

2021 ◽

Vol 12 (4) ◽

pp. 483

Author(s):

Wen-Juan Ma ◽

Paris Veltsos

Keyword(s):

Sex Determination ◽

Sex Chromosomes ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Comparative Genomic ◽

Ancestral State ◽

Heteromorphic Sex Chromosomes ◽

Genomic Studies ◽

Evolutionary Trajectories ◽

Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

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Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach

BMC Genomics ◽

10.1186/1471-2164-12-456 ◽

2011 ◽

Vol 12 (1) ◽

Cited By ~ 4

Author(s):

Luz B Gilbert ◽

Lee Chae ◽

Takao Kasuga ◽

John W Taylor

Keyword(s):

In Silico ◽

Evolutionary Relationships ◽

Comparative Genomic

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Identification of RD5-EncodedMycobacterium tuberculosisProteins As B-Cell Antigens Used for Serodiagnosis of Tuberculosis

Clinical and Developmental Immunology ◽

10.1155/2012/738043 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 5

Author(s):

Miao-Miao Zhang ◽

Jun-Wei Zhao ◽

Zhan-Qiang Sun ◽

Jun Liu ◽

Xiao-Kui Guo ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Detection Sensitivity ◽

Comparative Genomic ◽

Healthy Controls ◽

Specific Diagnosis ◽

Pulmonary Tb ◽

Genomic Studies ◽

Immunodominant Antigens ◽

Genomic Regions ◽

Hiv Negative

Comparative genomic studies have identified severalMycobacterium tuberculosis-specific genomic regions of difference (RDs) which are absent in the vaccine strains ofMycobacterium bovisBCG and which may be useful in the specific diagnosis of tuberculosis (TB). In this study, all encoded proteins from DNA segment RD5 ofMycobacterium tuberculosis, that is, Rv3117–Rv3121, were recombined and evaluated by enzyme-linked immunosorbent assays for antibody reactivity with sera from HIV-negative pulmonary TB patients (n=60) and healthy controls (n=32). The results identified two immunodominant antigens, that is, Rv3117 and Rv3120, both of which revealed a statistically significant antigenic distinction between healthy controls and TB patients (P<0.05). In comparison with the well-known early-secreted antigen target 6 kDa (ESAT-6) (sensitivity 21.7%, specificity 90.6%), the higher detection sensitivity and higher specificity were achieved (Rv3117: sensitivity 25%, specificity 96.9%; Rv3120: sensitivity 31.7%, specificity 96.9%). Thus, the results highlight the immunosensitive and immunospecific nature of Rv3117 and Rv3120 and indicate promise for their use in the serodiagnosis of TB.

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In silico Analysis of Phylogeny and Virulence Genes in STEC Strains Associated with Outbreaks

Türk Mikrobiyoloji Cemiyeti Dergisi ◽

10.5222/tmcd.2021.07769 ◽

2021 ◽

Author(s):

Mehmet Demirci ◽

Akın Yiğin ◽

Fadile Yıldız Zeyrek

Keyword(s):

Foodborne Pathogens ◽

In Silico ◽

Virulence Genes ◽

Genomic Analysis ◽

In Silico Analysis ◽

Comparative Genomic ◽

Phylogeny Analysis ◽

In Silico Study ◽

The World ◽

Different Parts

Objective: Shiga toxin-producing E. coli (STEC) strains are important foodborne pathogens. Significant outbreaks with STEC strains can be encountered, even if the geography, time or resources were different. The aim of our in silico study was to compare the virulance factors and phylogeny of STEC strains such as EDL933 and Sakai, which have been identified as an agent in important outbreaks in different parts of the world and whole genomic data were in open databases. Method: Genomic NCBI data of eight strains were included in our study, including seven different STEC strains associated with significant epidemics in different parts of the world, and one supershedder strain obtained from cattle feces. Results: According to phylogeny analysis, the most similar strain to EDL933 strain was TW14588, with 96.4% similarity. The most distant similarity was Sakai strains with 79.2%. According to the virulence genes analysis; the presence of 333 genes that constitute virulence factors under nine headings were detected. In the first STEC origin, EDL933, 45% of all virulence genes were found to be active. Adherence genes such as Ecp, Elf, Hcp and toxin genes such as clyA were active in all strains except stx genes. Conclusion: In our in silico study of comparative genomic analysis of STEC strains which are associated with outbreaks, it was determined that STEC strains used different virulence genes besides the stx gene. Indeed, they used certain virulence genes, even their sources, time and locations were different, in the pathogenesis

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Unexpected cryptic species among streptophyte algae most distant to land plants

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.2168 ◽

2021 ◽

Vol 288 (1963) ◽

Author(s):

Iker Irisarri ◽

Tatyana Darienko ◽

Thomas Pröschold ◽

Janine M. R. Fürst-Jansen ◽

Mahwash Jamy ◽

...

Keyword(s):

Land Plants ◽

Comparative Genomic ◽

Future Studies ◽

Form And Function ◽

Genomic Studies ◽

Plant Form ◽

Phylogenomic Analyses ◽

And Function ◽

Shed Light ◽

Green Lineage

Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one billion years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp. and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes.

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Versatile templates from cellulose nanofibrils for photosynthetic microbial biofuel production

Journal of Materials Chemistry A ◽

10.1039/c7ta11164a ◽

2018 ◽

Vol 6 (14) ◽

pp. 5825-5835 ◽

Cited By ~ 11

Author(s):

M. Jämsä ◽

S. Kosourov ◽

V. Rissanen ◽

M. Hakalahti ◽

J. Pere ◽

...

Keyword(s):

Green Algae ◽

Cellulose Nanofibrils ◽

Biofuel Production ◽

Microbial Biofuel

Porous, transparent plant-based template constructed from cellulose nanofibrils acts as a versatile matrix for immobilization of H2-producing cyanobacteria and green algae.

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Evolution of multicellularity in Dictyostelia

The International Journal of Developmental Biology ◽

10.1387/ijdb.190108ps ◽

2019 ◽

Vol 63 (8-9-10) ◽

pp. 359-369 ◽

Cited By ~ 2

Author(s):

Yoshinori Kawabe ◽

Qingyou Du ◽

Christina Schilde ◽

Pauline Schaap

Keyword(s):

Life Cycle ◽

Experimental Studies ◽

Evolutionary Conservation ◽

Comparative Genomic ◽

Camp Signalling ◽

Life Styles ◽

Phenotypic Complexity ◽

Genomic Studies ◽

Developmental Programme ◽

Differentiation Pathways

The well-orchestrated multicellular life cycle of Dictyostelium discoideum has fascinated biologists for over a century. Self-organisation of its amoebas into aggregates, migrating slugs and fruiting structures by pulsatile cAMP signalling and their ability to follow separate differentiation pathways in well-regulated proportions continue to be topics under investigation. A striking aspect of D. discoideum development is the recurrent use of cAMP as chemoattractant, differentiation inducing signal and second messenger for other signals that control the developmental programme. D. discoideum is one of >150 species of Dictyostelia and aggregative life styles similar to those of Dictyostelia evolved many times in eukaryotes. Here we review experimental studies investigating how phenotypic complexity and cAMP signalling co-evolved in Dictyostelia. In addition, we summarize comparative genomic studies of multicellular Dictyostelia and unicellular Amoebozoa aimed to identify evolutionary conservation and change in all genes known to be essential for D. discoideum development.

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