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Plant Genome 2021 Apr 5:e20075. Epub 2021 Apr 5.

Department of Agronomy, Kansas State University, Manhattan, KS, USA.

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in western Africa (WA) has diversified across a mosaic of cultures and end uses and along steep precipitation and photoperiod gradients. Read More

Vet Med Sci 2021 Feb 11. Epub 2021 Feb 11.

Ecole Inter-Etats des Sciences et Médecine Vétérinaires de Dakar, Dakar, Senegal.

Mycoplasma mycoides subsp. mycoides (Mmm) is the aetiological agent of contagious bovine pleuropneumonia (CBPP). The aim of the present study was to identify the profiles of the Mmm strains isolated in Niger using the 'Multilocus Sequence Analysis' (MLSA) typing technique based on polymorphism analysis of housekeeping and non-coding genes. Read More

Microbiol Res 2021 Apr 6;245:126694. Epub 2021 Jan 6.

School of Biology and Biological Engineering, South China University of Technology, No. 382 Waihuan East Rd, Guangzhou Higher Education Mega Center, Guangzhou 510006, China. Electronic address:

Epigenetic studies on secondary metabolites (SMs) mainly relied so far on non-selective epigenetic factors deletion or feeding epigenetic inhibitors in Aspergillus niger. Although technologies developed for epigenome editing at specific loci now enable the direct study of the functional relevance of precise gene regulation and epigenetic modification, relevant assays are limited in filamentous fungi. Herein, we show that CRISPR/dCas9-mediated histone epigenetic modification systems efficiently reprogramed the expression of target genes in A. Read More

Genes (Basel) 2020 Dec 30;12(1). Epub 2020 Dec 30.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.

A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2. Read More

J Fungi (Basel) 2020 Dec 17;6(4). Epub 2020 Dec 17.

Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná 86057-970, Brazil.

Diversity of species within clade, currently represented by and , was investigated combining three-locus gene sequences, , secondary metabolites profile and morphology. Firstly, approximately 700 accessions belonging to this clade were investigated using calmodulin gene sequences. Based on these sequences, eight haplotypes were clearly identified as ( = 247) and 17 as ( = 403). Read More

Microorganisms 2020 Dec 11;8(12). Epub 2020 Dec 11.

National Institute of Chemistry, SI-1000 Ljubljana, Slovenia.

Aegerolysins are small lipid-binding proteins particularly abundant in fungi. Aegerolysins from oyster mushrooms interact with an insect-specific membrane lipid and, together with MACPF proteins produced by the same organism, form pesticidal pore-forming complexes. The specific interaction with the same membrane lipid was recently demonstrated for nigerolysin A2 (NigA2), an aegerolysin from . Read More

Ecol Evol 2020 Dec 27;10(23):13403-13411. Epub 2020 Oct 27.

CIRAD, UMR AGAP Montpellier France.

To study the genetic diversity and structure of the forest species Poir., seventeen polymorphic nuclear microsatellite markers were isolated and characterized, using next-generation sequencing. Three hundred and sixty-five (365) individuals were analyzed within fifteen (15) West African populations. Read More

Evol Appl 2020 Sep 24;13(8):1818-1840. Epub 2020 Feb 24.

Institut des Sciences de l'Évolution UMR 5554 CNRS/Université de Montpellier/IRD/EPHE CC065 Équipe Dynamique de la Biodiversité, Anthropo-écologie Université - Montpellier Montpellier Cedex 5 France.

Crop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here, we combined population genetics and ethnobotany to investigate date palm ( L.) diversity in Siwa Oasis, Egypt. Read More

Genes (Basel) 2020 09 1;11(9). Epub 2020 Sep 1.

International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, India.

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross-RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. Read More

Am J Hum Genet 2020 09 10;107(3):473-486. Epub 2020 Aug 10.

College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda. Electronic address:

Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Read More

PeerJ 2020 7;8:e9425. Epub 2020 Jul 7.

Department of Genetic Research, Department of Epidemic Diseases Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudia Arabia.

Background: Extracellular production of fungal lipases especially the lipases obtained from the has gained immense interest in recent years due to its diverse biotechnological applications. In this study, we focused on determining the fermentation parameters required for the optimal lipase production.

Methods: A total of 256 fungal isolates were obtained from oil seeds. Read More

BMC Genomics 2020 Apr 10;21(1):289. Epub 2020 Apr 10.

College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda.

Background: Copy number variation is an important class of genomic variation that has been reported in 75% of the human genome. However, it is underreported in African populations. Copy number variants (CNVs) could have important impacts on disease susceptibility and environmental adaptation. Read More

PLoS Comput Biol 2020 03 27;16(3):e1007653. Epub 2020 Mar 27.

Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel.

Social insect colonies exhibit colony-level phenotypes such as social immunity and task coordination, which are produced by the individual phenotypes. Mapping the genetic basis of such phenotypes requires associating the colony-level phenotype with the genotypes in the colony. In this paper, we examine alternative approaches to DNA extraction, library construction, and sequencing for genome wide association studies (GWAS) of colony-level traits using a population sample of Cataglyphis niger ants. Read More

J Microbiol Methods 2019 08 18;163:105655. Epub 2019 Jun 18.

School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, Guangdong, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology Guangzhou, Guangzhou 510006, Guangdong, China. Electronic address:

Aspergillus niger is an important industrial producer of enzymes due to its high capacity for producing exocellular secretory proteins. The CRISPR/Cas9 system has been developed as a genetic manipulation tool in A. niger. Read More

Ecol Evol 2019 May 23;9(10):6038-6051. Epub 2019 Apr 23.

Department of Agronomy Kansas State University Manhattan Kansas.

Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum ( L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. Read More

Fungal Biol Biotechnol 2019 1;6. Epub 2019 May 1.

Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby, Denmark.

Background: CRISPR technology has revolutionized fungal genetic engineering by increasing the speed and complexity of the experiments that can be performed. Moreover, the efficiency of the system often allows genetic engineering to be introduced in non-model species. The efficiency of CRISPR gene editing is due to the formation of specific DNA double-strand breaks made by RNA guided nucleases. Read More

Mol Biol Rep 2019 Apr 9;46(2):2473-2484. Epub 2019 Mar 9.

Laboratory of Animal Genetics and Evolution (LEGAL), Department of Genetics, Federal University of Amazonas (UFAM), Manaus, Amazonas, Brazil.

We isolated and characterized 10 new microsatellites loci for Paleosuchus trigonatus using ION TORRENT Sequencing Technology. We tested the transferability of these loci to three related species of the subfamily Caimaninae, and used these bi-parental markers to test population structure and genetic diversity of two populations of P. trigonatus impacted by hydroelectric dam construction on the Madeira (N = 16) and Xingu (N = 16) rivers. Read More

Appl Plant Sci 2019 Feb 30;7(2):e01215. Epub 2019 Jan 30.

Department of Environmental Sciences Mills College 5000 MacArthur Blvd. Oakland California 94613 USA.

Premise Of The Study: The endangered subsp. (Brassicaceae) is endemic to a single peninsula in California and threatened by fragmentation. We developed microsatellite markers to investigate genetic diversity in the two extant populations and the degree to which they have diverged from one another. Read More

PLoS One 2019 17;14(1):e0210243. Epub 2019 Jan 17.

Joint Bioenergy Institute, Emeryville, CA, United States of America.

Aspergillus niger and other filamentous fungi are widely used in industry, but efficient genetic engineering of these hosts remains nascent. For example, while molecular genetic tools have been developed, including CRISPR/Cas9, facile genome engineering of A. niger remains challenging. Read More

Med Mycol 2019 Aug;57(6):773-780

BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium.

Aspergillus section Nigri is a taxonomically difficult but medically and economically important group. In this study, an update of the taxonomy of A. section Nigri strains within the BCCM/IHEM collection has been conducted. Read More

Ecol Evol 2018 Nov 23;8(22):10638-10654. Epub 2018 Oct 23.

USDA Forest Service Northern Research Station Hardwood Tree Improvement and Regeneration Center West Lafayette Indiana.

Dispersal of seeds by scatter-hoarding rodents is common among tropical and temperate tree species, including chestnuts in the genus . Backcrossed (BC) interspecific hybrid chestnuts exhibit wide variation in seed traits: as the parent species ( and ) have distinct seed phenotypes and tend to be handled differently by seed dispersers, phenotypic variation in BC trees is likely due to inheritance of genes that have undergone divergent evolution in the parent species. To identify candidate genomic regions for interspecific differences in seed dispersal, we used tagged seeds to measure average dispersal distance for seeds of third-generation BC chestnuts and sequenced pooled whole genomes of mother trees with contrasting seed dispersal: high caching rate/long distance; low caching rate/short distance; no caching. Read More

PLoS One 2018 25;13(10):e0201635. Epub 2018 Oct 25.

DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France.

Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Read More

Front Microbiol 2018 8;9:878. Epub 2018 May 8.

Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.

In filamentous fungi, growth and protein secretion occurs predominantly at the tip of long, thread like cells termed hyphae. This requires coordinated regulation of multiple processes, including vesicle trafficking, exocytosis, and endocytosis, which are facilitated by a complex cytoskeletal apparatus. In this study, functional analyses of the small GTPase ArfA from demonstrate that this protein functionally complements the , and that this protein is essential for . Read More

Biotechnol Biofuels 2018 17;11:142. Epub 2018 May 17.

2State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China.

Background: The ascomycete fungus was widely used as a biotechnological workhorse for production of cellulases and recombinant proteins due to its large capacity of protein secretion. Transgenesis by random integration of a gene of interest (GOI) into the genome of can generate series of strains that express different levels of the indicated transgene. The insertion site of the GOI plays an important role in the ultimate production of the targeted proteins. Read More

Genes (Basel) 2018 May 11;9(5). Epub 2018 May 11.

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.

Pearl millet is a climate-resilient nutritious crop requiring low inputs and is capable of giving economic returns in marginal agro-ecologies. In this study, we report large-effect iron (Fe) and zinc (Zn) content quantitative trait loci QTLs) using diversity array technology (DArT) and simple sequence repeats (SSRs) markers to generate a genetic linkage map using 317 recombinant inbred line (RIL) population derived from the (ICMS 8511-S1-17-2-1-1-B-P03 × AIMP 92901-S1-183-2-2-B-08) cross. The base map [seven linkage groups (LGs)] of 196 loci was 964. Read More

Theor Appl Genet 2018 Jul 21;131(7):1509-1529. Epub 2018 Apr 21.

Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India.

Key Message: Four genetic regions associated with water use traits, measured at different levels of plant organization, and with agronomic traits were identified within a previously reported region for terminal water deficit adaptation on linkage group 2. Close linkages between these traits showed the value of phenotyping both for agronomic and secondary traits to better understand plant productive processes. Water saving traits are critical for water stress adaptation of pearl millet, whereas maximizing water use is key to the absence of stress. Read More

BMC Plant Biol 2018 Apr 17;18(1):65. Epub 2018 Apr 17.

Institute of Plant Breeding, Seed Science and Population Genetics, Fruwirthstr University of Hohenheim, 21, D-70599, Stuttgart, Germany.

Background: Pearl millet (Pennisetum glaucum (L.) R. Br. Read More

Fungal Biol Biotechnol 2018 8;5. Epub 2018 Feb 8.

1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Xiqidao 32, Tianjin Airport Economic Area, Tianjin, 300308 China.

Background: promoters have been used for single guide RNA (sgRNA) transcription in the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) genome editing system. However, no available promoters have been identified in which is an important industrial platform for organic acid and protein production. Two CRISPR/Cas9 systems established in have recourse to the RNA polymerase II promoter or in vitro transcription for sgRNA synthesis, but these approaches generally increase cloning efforts and genetic manipulation. Read More

Genome 2018 Apr 12;61(4):223-232. Epub 2018 Feb 12.

a Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA.

Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. Read More

Cell 2017 04;169(3):497-509.e13

Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

The environmentally widespread polysaccharide chitin is degraded and recycled by ubiquitous bacterial and fungal chitinases. Although vertebrates express active chitinases from evolutionarily conserved loci, their role in mammalian physiology is unclear. We show that distinct lung epithelial cells secrete acidic mammalian chitinase (AMCase), which is required for airway chitinase activity. Read More