scholarly journals The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Fengchao Cui ◽  
Geli Taier ◽  
Manli Li ◽  
Xiaoxia Dai ◽  
Nan Hang ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Agronomic Traits ◽  
Warm Season ◽  
Genomic Research ◽  
Functional Genomic ◽  
Evolutionary Analysis ◽  
Ecological Significance ◽  
Genomic Resources ◽  
Transcriptome Comparison ◽  
Genomic Basis

AbstractCynodon species can be used for multiple purposes and have high economic and ecological significance. However, the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood, partially due to the limited availability of genomic resources. In this study, we report a chromosome-scale genome assembly of a diploid Cynodon species, C. transvaalensis, obtained by combining Illumina and Nanopore sequencing, BioNano, and Hi-C. The assembly contains 282 scaffolds (~423.42 Mb, N50 = 5.37 Mb), which cover ~93.2% of the estimated genome of C. transvaalensis (~454.4 Mb). Furthermore, 90.48% of the scaffolds (~383.08 Mb) were anchored to nine pseudomolecules, of which the largest was 60.78 Mb in length. Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates, typically with dry summers. The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily, in particular, the Cynodonteae tribe, but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.

Functional genomic resources for potato

2008 ◽  
Vol 88 (4) ◽  
pp. 573-581 ◽  
Author(s):  
Xiu-Qing Li ◽  
Rebecca Griffiths ◽  
David De Koeyer ◽  
Charlotte Rothwell ◽  
Vicki Gustafson ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Genetic Maps ◽  
Genomic Research ◽  
Functional Genomic ◽  
Entire Genome ◽  
Future Directions ◽  
Genomic Resources ◽  
Expressed Sequence ◽  
Selection Of ◽  
Made In

Considerable functional genomic resources have been developed by the potato research community in the past decade, including expressed sequence tag (EST) libraries, SAGE libraries, microarrays, molecular-function maps, and mutant populations. This article reviews the types, characteristics, strengths, limitations, and appropriate applications of these resources for genomic research and discusses perspectives on future directions. This wide selection of resources available to potato researchers complements efforts to sequence the entire genome and advances made in the development of saturated genetic maps. Key words: Solanum, potato, genomics, expressed sequence tag, microarray, longSAGE, data mining

scholarly journals Next-generation microbiology: from comparative genomics to gene function

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Carolin M. Kobras ◽  
Andrew K. Fenton ◽  
Samuel K. Sheppard
Keyword(s):  
Data Science ◽  
Genetic Basis ◽  
Turning Point ◽  
Functional Genomic ◽  
Bacterial Cells ◽  
Next Generation ◽  
New Techniques ◽  
Molecular Microbiology ◽  
Genetic Complexity ◽  
Generation Sequencing

AbstractMicrobiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology.

scholarly journals Molecular evolutionary analysis of human primary microcephaly genes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nashaiman Pervaiz ◽  
Hongen Kang ◽  
Yiming Bao ◽  
Amir Ali Abbasi
Keyword(s):  
Evolutionary History ◽  
Genetic Basis ◽  
Brain Size ◽  
Primate Species ◽  
Evolutionary Analysis ◽  
Australopithecus Afarensis ◽  
Primary Microcephaly ◽  
Modern Humans ◽  
History Of ◽  
The Brain

Abstract Background There has been a rapid increase in the brain size relative to body size during mammalian evolutionary history. In particular, the enlarged and globular brain is the most distinctive anatomical feature of modern humans that set us apart from other extinct and extant primate species. Genetic basis of large brain size in modern humans has largely remained enigmatic. Genes associated with the pathological reduction of brain size (primary microcephaly-MCPH) have the characteristics and functions to be considered ideal candidates to unravel the genetic basis of evolutionary enlargement of human brain size. For instance, the brain size of microcephaly patients is similar to the brain size of Pan troglodyte and the very early hominids like the Sahelanthropus tchadensis and Australopithecus afarensis. Results The present study investigates the molecular evolutionary history of subset of autosomal recessive primary microcephaly (MCPH) genes; CEP135, ZNF335, PHC1, SASS6, CDK6, MFSD2A, CIT, and KIF14 across 48 mammalian species. Codon based substitutions site analysis indicated that ZNF335, SASS6, CIT, and KIF14 have experienced positive selection in eutherian evolutionary history. Estimation of divergent selection pressure revealed that almost all of the MCPH genes analyzed in the present study have maintained their functions throughout the history of placental mammals. Contrary to our expectations, human-specific adoptive evolution was not detected for any of the MCPH genes analyzed in the present study. Conclusion Based on these data it can be inferred that protein-coding sequence of MCPH genes might not be the sole determinant of increase in relative brain size during primate evolutionary history.

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals Two highly representative rice BAC libraries of japonica cv Tainung 67 suitable for rice structural and functional genomic research

Plant Science ◽  
2006 ◽  
Vol 170 (4) ◽  
pp. 889-896
Author(s):  
Yann-Rong Lin ◽  
Teh-Yuan Chow ◽  
Meizhong Luo ◽  
Dave Kudrna ◽  
Chih-Chi Lin ◽  
...  
Keyword(s):  
Genomic Research ◽  
Functional Genomic ◽  
Bac Libraries

Boosting dsRNA delivery in plant and insect cells with peptide- and polymer-based carriers: case-based current status and future perspectives.

2021 ◽  
pp. 102-116
Author(s):  
Kristof de Schutter ◽  
Olivier Christiaens ◽  
Clauvis Nji Tizi Taning ◽  
Guy Smagghe
Keyword(s):  
Plant Cell Wall ◽  
Endosomal Escape ◽  
Genomic Research ◽  
Current Status ◽  
Functional Genomic ◽  
Future Perspectives ◽  
Agricultural Industry ◽  
Efficient Delivery ◽  
Rnai Response ◽  
Carrier Systems

Abstract Since the discovery of this naturally occurring endogenous regulatory and defence mechanism, RNA interference (RNAi) has been exploited as a powerful tool for functional genomic research. In addition, it has evolved as a promising candidate for a sustainable, specific and ecofriendly strategy for pest management and plant improvement. A key element in this technology is the efficient delivery of dsRNAs into the pest or plant tissues. While several examples using transgenic plants expressing the dsRNAs have proved the potential of this technology, nontransgenic approaches are investigated as alternatives, allowing flexibility and circumventing technical limitations of the transgenic approach. However, the efficacy of environmental RNAi is affected by several barriers, such as extracellular degradation of the dsRNA, inefficient internalization of the dsRNA in the cell and low endosomal escape into the cytoplasm, resulting in variable or low RNAi responses. In the medical field, carrier systems are commonly used to enhance RNA delivery and these systems are being rapidly adopted by the agricultural industry. Using four case studies, this chapter demonstrates the potential of carriers to improve the RNAi response in pest control for aquatic-living mosquito larvae and RNAi-resilient Lepidoptera and to cross the plant cell wall, allowing efficient environmental RNAi in plants.

Pharmacogenomics of childhood acute lymphoblastic leukemia (ALL)

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. s3-s3
Author(s):  
William E. Evans ◽  
Mary V. Relling
Keyword(s):  
Candidate Gene ◽  
Germ Line ◽  
Lymphoblastic Leukemia ◽  
Genomic Research ◽  
Childhood All ◽  
Genomic Variations ◽  
Vincristine Neuropathy ◽  
Genomic Basis ◽  
Resistance To Chemotherapy

s3 Childhood ALL is a model for drug-responsive cancer: it is successfully cured with medications in 85%–90% of patients, but relapse remains unacceptably high for some subgroups, and therapy is complicated by the occurrence of adverse effects. Human germ-line genomic variability is common, with ∼1 in every 300 nucleotides (at least 10 million polymorphisms among humans) differing among individuals. Identifying the important genomic variants for purposes of optimizing anticancer therapy is the current challenge in cancer pharmacogenomics. Our research has been focused on elucidating the germ-line and acquired genomic variations that influence the effectiveness of and toxicity to chemotherapy regimens, with the long-term goal of individualizing therapy based on genetics to maximize cure and minimize toxicity. We and our many collaborators are pursuing candidate gene and whole genome approaches to this end, studying children enrolled on front-line ALL protocols at St. Jude and through the Children's Oncology Group. Based on these studies, candidate gene genotyping has been already incorporated into the treatment of childhood ALL and integrated with electronic medical records at St. Jude to optimize use of a few medications. This includes genetic testing for TPMT to adjust thiopurine doses and CYP2D6 to optimize use of codeine for vincristine neuropathy. Additional genotyping is conducted on a research basis and has identified SLCO1B1 as important for methotrexate disposition, IL15 as related to antileukemic drug response, ITPA as important for thiopurine toxicity, and a genomic basis to race-related differences in relapse risk. Gene expression analyses of ALL cells show expression signatures associated with resistance to chemotherapy and relapse. The principles and techniques of pharmacogenomics also have implications for adult malignancies. Because prognostic factors (including genomic variations) depend upon the details of therapy, collection of blood (for germ-line DNA) should be part of every cancer clinical trial to advance genomic research.

scholarly journals Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Xu ◽  
Di Wu ◽  
Tianquan Yang ◽  
Chao Sun ◽  
Zaiqing Wang ◽  
...  
Keyword(s):  
Castor Bean ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Agronomic Traits ◽  
Ricinus Communis ◽  
Oilseed Crop ◽  
A Genome ◽  
Trait Locus ◽  
Wild Progenitors

Abstract Background Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. Results Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. Conclusions This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.

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