whole genome sequence
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2022 ◽  
Vol 12 ◽  
Author(s):  
Lidia De los Ríos-Pérez ◽  
Tom Druet ◽  
Tom Goldammer ◽  
Dörte Wittenburg

Pikeperch (Sander lucioperca) has emerged as a high value species to the aquaculture industry. However, its farming techniques are at an early stage and its production is often performed without a selective breeding program, potentially leading to high levels of inbreeding. In this study, we identified and characterized autozygosity based on genome-wide runs of homozygosity (ROH) on a sample of parental and offspring individuals, determined effective population size (Ne), and assessed relatedness among parental individuals. A mean of 2,235 ± 526 and 1,841 ± 363 ROH segments per individual, resulting in a mean inbreeding coefficient of 0.33 ± 0.06 and 0.25 ± 0.06 were estimated for the progeny and parents, respectively. Ne was about 12 until four generations ago and at most 106 for 63 generations in the past, with varying genetic relatedness amongst the parents. This study shows the importance of genomic information when family relationships are unknown and the need of selective breeding programs for reproductive management decisions in the aquaculture industry.


2022 ◽  
Author(s):  
Shruthy Priya Prakash ◽  
Vaidheki Chandrasekar ◽  
Selvi Subramanian ◽  
Rahamatthunnisha Ummar

Banana being a major food crop all around the world, attracts various research interests in crop improvement. In banana, complete genome sequences of Musa accuminata and Musa balbisiana are available. However, the mitochondrial genome is not sequenced or assembled. Mitochondrial (mt) genes play an important role in flower and seed development and in Cytoplasmic Male Sterility. Unraveling banana mt genome architecture will be a foundation for understanding inheritance of traits and their evolution. In this study, the complete banana mt genome is assembled from the whole genome sequence data of the Musa acuminata subsp. malaccensis DH-Pahang. The mt genome sequence acquired by this approach was 409574 bp and it contains, 54 genes coding for 25 respiratory complex proteins 15 ribosomal proteins, 12 tRNA genes and two ribosomal RNA gene. Except atpB, rps11 and rps19 other genes are in multiple copies. The copy number is 12 in tRNA genes. In addition, nearly 25% tandem repeats are also present in it. These mt proteins are identical to the mt proteins present in the other members of AA genome and share 98% sequence similarity with M. balbisiana. The C to U RNA editing is profoundly higher (87 vs 13%) in transcripts of M. balbisiana (BB) compared to M. accuminata (AA). The banana AA mitochondrial genome is tightly packed with 233 genes, with less rearrangements and just 5.3% chloroplast DNA in it. The maintenance of high copy number of functional mt genes suggest that they have a crucial role in the evolution of banana.


Author(s):  
Afri Herlambang ◽  
Yong Guo ◽  
Yusuke Takashima ◽  
Kazuhiko Narisawa ◽  
Hiroyuki Ohta ◽  
...  

Some mucoromycotan fungi establish symbiotic associations with endohyphal bacteria. Here, the genome of Entomortierella parvispora E1425 (synonymously known as Mortierella parvispora E1425), which harbors a cultured Burkholderiaceae -related endobacterium (BRE) designated Mycoavidus sp. Strain B2-EB, was sequenced. We provide genomic information to elucidate fungal-BRE symbiotic features.


2022 ◽  
Author(s):  
Sonalika Mahajan ◽  
Karikalan Mathesh ◽  
Vishal Chander ◽  
Abhijit M Pawde ◽  
G Saikumar ◽  
...  

We report patho-morphological and virological characterization of SARS-CoV-2 in naturally infected, free ranging Indian Leopard (Panthera pardus fusca). Whole genome sequence analysis confirmed infection of Delta variant of SARS-CoV-2, possibly spill over from humans, but the case was detected when infection level had dropped significantly in human population. This report underlines the need for intensive screening of wild animals for keeping track of the virus evolution and development of carrier status of SARS-CoV-2 among wildlife species.


2022 ◽  
Author(s):  
Fangyuan Xu ◽  
Liqiang Liu ◽  
Jun Liu ◽  
Wei He ◽  
Kang Liao

Abstract Wild apricot in Yili wild fruit forest in Xinjiang have been seriously affected by leaf spot-hole disease, with the incidence reaching 100%. To identify the pathogen of apricot perforation in the Yili wild fruit forest, two bacterial strains with strong virulence were obtained by the dilution separation method. The bacterial strains were gram-negative bacteria with yellow colonies, smooth surfaces and neat edges. The results of the pathogenicity test showed that the bacteria could cause symptoms of leaf spot-hole disease in wild apricot, similar to the symptoms in the field, and could cause HR in tobacco. Based on the 16S rDNA gene sequence and multilocus sequence analysis of fusA, gyrB, leuS, pyrG, rpoB and rlpB, combined with the physiological and biochemical characteristics, the isolated strain was identified as Pantoea agglomerans. The pathogen causing bacterial leaf spot-hole disease in wild apricot was determined to be P. agglomerans in the wild fruit forest of Yili, Xinjiang. The whole genome of the pathogen strain GL9-2 was sequenced based on the Illumina HiSeq500 and PacBio RS platforms. The genome size was 4765392 bp, and the G+C value was 55.27%. There was one chromosome and two plasmids in the genome, and 4353 CDs were identified. The annotation results showed that 52 glycoside hydrolase-related genes, 38 bacterial secretory system-related genes and 600 toxin-related genes were predicted.


Author(s):  
Ebrahim Osdaghi ◽  
Geraldine Taghouti ◽  
Cecile Dutrieux ◽  
S. Mohsen Taghavi ◽  
Amal Fazliarab ◽  
...  

Curtobacterium flaccumfaciens complex species in the family Microbacteriaceae encompasses a group of plant pathogenic actinobacterial strains affecting annual crops and ornamental plants. The species includes five pathovars namely C. flaccumfaciens pv. betae, C. flaccumfaciens pv. flaccumfaciens, C. flaccumfaciens pv. ilicis, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. Despite the economic importance of C. flaccumfaciens, its members have rarely been investigated for their phylogenetic relationships, molecular characteristics and virulence repertories due in part to the lack of whole genome resources. Here we present the whole genome sequence of 17 C. flaccumfaciens strains representing members of four pathovars isolated from different plant species in a diverse geographical and temporal span. The genomic data presented in this study will pave the way of research on the comparative genomics, phylogenomics and taxonomy of C. flaccumfaciens, and extend our understanding of the virulence features of the species.


2022 ◽  
Vol 10 (1) ◽  
pp. 142
Author(s):  
Hye Won Kim ◽  
Na Kyung Kim ◽  
Alex P. R. Phillips ◽  
David A. Parker ◽  
Ping Liu ◽  
...  

Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO2 fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.


PLoS Genetics ◽  
2022 ◽  
Vol 18 (1) ◽  
pp. e1009604
Author(s):  
Jiru Han ◽  
Jacob E. Munro ◽  
Anthony Kocoski ◽  
Alyssa E. Barry ◽  
Melanie Bahlo

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).


2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Hussain Bahbahani ◽  
Faisal Almathen

AbstractDromedary camels in the Arabian Peninsula distribute along different geographical and ecological locations, e.g. desert, mountains and coasts. Here, we are aiming to explore the whole genome sequence data of ten dromedary populations from the Arabian Peninsula to assess their genetic structure, admixture levels, diversity and similarity indices. Upon including reference dromedary and Bactrian camel populations from Iran and Kazakhstan, we characterise inter-species and geographic genetic distinction between the dromedary and the Bactrian camels. Individual-based alpha genetic diversity profiles are found to be generally higher in Bactrian camels than dromedary populations, with the exception of five autosomes (NC_044525.1, NC_044534.1, NC_044540.1, NC_044542.1, NC_044544.1) at diversity orders (q ≥ 2). The Arabian Peninsula camels are generally homogenous, with a small degree of genetic distinction correlating with three geographic groups: North, Central and West; Southwest; and Southeast of the Arabian Peninsula. No significant variation in diversity or similarity indices are observed among the different Arabian Peninsula dromedary populations. This study contributes to our understanding of the genetic diversity of Arabian Peninsula dromedary camels. It will help conserve the genetic stock of this species and support the design of breeding programmes for genetic improvement of favorable traits.


2022 ◽  
Author(s):  
Benjamin Sobkowiak ◽  
Kamila Romanowski ◽  
Inna Sekirov ◽  
Jennifer L Gardy ◽  
James Johnston

Pathogen genomic epidemiology is now routinely used worldwide to interrogate infectious disease dynamics. Multiple computational tools that reconstruct transmission networks by coupling genomic data with epidemiological modelling have been developed. The resulting inferences are often used to inform outbreak investigations, yet to date, the performance of these transmission reconstruction tools has not been compared specifically for tuberculosis, a disease process with complex epidemiology that includes variable latency periods and within-host heterogeneity. Here, we carried out a systematic comparison of seven publicly available transmission reconstruction tools, evaluating their accuracy in predicting transmission events in both simulated and real-world Mycobacterium tuberculosis outbreaks. No tool was able to fully resolve transmission networks, though both the single-tree and multi-tree input implementations of TransPhylo identified the most epidemiologically supported transmission events and the fewest false positive links. We observed a high degree of variability in the transmission networks inferred by each approach. Our findings may inform the choice of tools in future tuberculosis transmission analyses and underscore the need for caution when interpreting transmission networks produced using probabilistic approaches.


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