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1. Reference flow: reducing reference bias using multiple population genomes

Author:
Chen, Nae-Chyun; Solomon, Brad; Mun, Taher; Iyer, Sheila; Langmead, Ben
Source:
Genome biology 2021 v.22 no.1 pp. 8
ISSN:
1474-760X
Subject:
genetic variation,   etc   ; genome; memory;     Show all 3 Subjects
Abstract:
... Most sequencing data analyses start by aligning sequencing reads to a linear reference genome, but failure to account for genetic variation leads to reference bias and confounding of results downstream. Other approaches replace the linear reference with structures like graphs that can include genetic variation, incurring major computational overhead. We propose the reference flow alignment method ...
DOI:
10.1186/s13059-020-02229-3

2. Changes in Allele Frequencies When Different Genomic Coancestry Matrices Are Used for Maintaining Genetic Diversity

Author:
Morales-González, Elisabeth; Fernández, Jesús; Pong-Wong, Ricardo; Toro, Miguel Ángel; Villanueva, Beatriz
Source:
Genes 2021 v.12 no.5
ISSN:
2073-4425
Subject:
genetic variation,   etc   ; alleles; genomics;     Show all 3 Subjects
Abstract:
... A main objective in conservation programs is to maintain genetic variability. This can be achieved using the Optimal Contributions (OC) method that optimizes the contributions of candidates to the next generation by minimizing the global coancestry. However, it has been argued that maintaining allele frequencies is also important. Different genomic coancestry matrices can be used on OC and the cho ...
DOI:
10.3390/genes12050673

3. Plastome analysis unveils Inverted Repeat (IR) expansion and positive selection in Sea Lavenders (Limonium, Plumbaginaceae, Limonioideae, Limonieae)

Author:
Darshetkar, Ashwini M.; Maurya, Satish; Lee, Changyoung; Bazarragchaa, Badamtsetseg; Batdelger, Gantuya; Janchiv, Agiimaa; Jeong, Eun Ju; Choi, Sangho; Choudhary, Ritesh Kumar; Kim, Soo-Yong
Source:
PhytoKeys 2021 v.175 pp. 89-107
ISSN:
1314-2003
Subject:
genetic variation,   etc   ; Limonium; barcoding; introns;     Show all 4 Subjects
Abstract:
... The genus Limonium, commonly known as Sea Lavenders, is one of the most species-rich genera of the family Plumbaginaceae. In this study, two new plastomes for the genus Limonium, viz. L. tetragonum and L. bicolor, were sequenced and compared to available Limonium plastomes, viz. L. aureum and L. tenellum, to understand the gene content and structural variations within the family. The loss of the r ...
DOI:
10.3897/phytokeys.175.61054

4. The impact of genetic diversity statistics on model selection between coalescents

Author:
Freund, Fabian; Siri-Jégousse, Arno
Source:
Computational statistics & data analysis 2021 v.156 pp. 107055
ISSN:
0167-9473
Subject:
genetic variation,   etc   ; Bayesian theory; models;     Show all 3 Subjects
Abstract:
... Modeling genetic diversity needs an underlying genealogy model. To choose a fitting model based on genetic data, one can perform model selection between classes of genealogical trees, e.g. Kingman’s coalescent with exponential growth or multiple merger coalescents. Such selection can be based on many different statistics measuring genetic diversity. A random forest based Approximate Bayesian Compu ...
DOI:
10.1016/j.csda.2020.107055

5. The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors

Author:
Martel, Alexandre; Ruiz-Bedoya, Tatiana; Breit-McNally, Clare; Laflamme, Bradley; Desveaux, Darrell; Guttman, David S
Source:
Current opinion in plant biology 2021 v.62 pp. 102011
ISSN:
1369-5266
Subject:
genetic variation,   etc   ; conspecificity; immunity; pathogens; plant biology;     Show all 5 Subjects
Abstract:
... The natural diversity of pathogen effectors and host immune components represents a snapshot of the underlying evolutionary processes driving the host-pathogen arms race. In plants, this arms race is manifested by an ongoing cycle of disease and resistance driven by pathogenic effectors that promote disease (effector-triggered susceptibility; ETS) and plant resistance proteins that recognize effec ...
DOI:
10.1016/j.pbi.2021.102011

6. Accelerated discovery of functional genomic variation in pigs

Author:
Derks, Martijn F.L.; Gross, Christian; Lopes, Marcos S.; Reinders, Marcel J.T.; Bosse, Mirte; Gjuvsland, Arne B.; de Ridder, Dick; Megens, Hendrik-Jan; Groenen, Martien A.M.
Source:
Genomics 2021 v.113 no.4 pp. 2229-2239
ISSN:
0888-7543
Subject:
genetic variation,   etc   ; genomics; genotype-phenotype correlation; phenotype;     Show all 4 Subjects
Abstract:
... The genotype-phenotype link is a major research topic in the life sciences but remains highly complex to disentangle. Part of the complexity arises from the number of genes contributing to the observed phenotype. Despite the vast increase of molecular data, pinpointing the causal variant underlying a phenotype of interest is still challenging. In this study, we present an approach to map causal va ...
DOI:
10.1016/j.ygeno.2021.05.017

7. Human origins in Southern African palaeo-wetlands? Strong claims from weak evidence

Author:
Schlebusch, Carina M.; Loog, Liisa; Groucutt, Huw S.; King, Turi; Rutherford, Adam; Barbieri, Chiara; Barbujani, Guido; Chikhi, Lounes; Stringer, Chris; Jakobsson, Mattias; Eriksson, Anders; Manica, Andrea; Tishkoff, Sarah A.; Scerri, Eleanor ML.; Scally, Aylwyn; Brierley, Chris; Thomas, Mark G.
Source:
Journal of archaeological science 2021 v.130 pp. 105374
ISSN:
0305-4403
Subject:
genetic variation,   etc   ; archaeology; humans; provenance; Africa;     Show all 5 Subjects
Abstract:
... Attempts to identify a ‘homeland’ for our species from genetic data are widespread in the academic literature. However, even when putting aside the question of whether a ‘homeland’ is a useful concept, there are a number of inferential pitfalls in attempting to identify the geographic origin of a species from contemporary patterns of genetic variation. These include making strong claims from weakl ...
DOI:
10.1016/j.jas.2021.105374

8. Molecular Genetic Diversity of Plectranthus edulis (Vatke) Agnew as Revealed by Inter Simple Sequence Repeat Markers

Author:
Shiferaw, Ijara; Feyissa, Tileye; Petros, Yohannes
Source:
Proceedings of the National Academy of Sciences, India, Section B: biological sciences 2021 v.91 no.2 pp. 361-371
ISSN:
0369-8211
Subject:
genetic variation,   etc   ; Plectranthus; microsatellite repeats; India;     Show all 4 Subjects
Abstract:
... Plectranthus edulis (Vatke) Agnew is an underutilized and neglected ancient Ethiopian indigenous annual tuber crop. Very limited research has been done to improve this crop especially in the area of molecular genetic diversity. Therefore, this study was aimed to assess the genetic diversity of this crop using ISSR markers. Fourteen ISSR primers were screened, and four polymorphic and reproducible ...
DOI:
10.1007/s40011-020-01210-1

9. Oryza pan-genomics: A new foundation for future rice research and improvement

Author:
Huang, Chao; Chen, Zhuo; Liang, Chengzhi
Source:
The crop journal 2021 v.9 no.3 pp. 622-632
ISSN:
2214-5141
Subject:
genetic variation,   etc   ; genome; genomics; wild rice;     Show all 4 Subjects
Abstract:
... The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice improvement. Pan-genomics has revolutionized genomic research in plants. However, rice pan-genomic studies so far have been limited mostly to cultivated accessions, with only a few close wild relatives. Advances in sequencing technologies have permitted the assembly of high-quality r ...
DOI:
10.1016/j.cj.2021.04.003

10. Phylogenomic Framework for Taxonomic Delineation of Paracoccus spp. and Exploration of Core-Pan Genome

Author:
Puri, Akshita; Bajaj, Abhay; Lal, Sukanya; Singh, Yogendra; Lal, Rup
Source:
Indian journal of microbiology 2021 v.61 no.2 pp. 180-194
ISSN:
0046-8991
Subject:
genetic variation,   etc   ; genes; microbiology; phylogeny; topology;     Show all 5 Subjects
Abstract:
... The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Para ...
DOI:
10.1007/s12088-021-00929-3

11. Design of potentially universal SSU primers in myxomycetes using next-generation sequencing

Author:
Wang, Wan; Wang, Wei; Wei, Shuwei; Huang, Wei; Qi, Bao; Wang, Qi; Li, Yu
Source:
Journal of microbiological methods 2021 v.184 pp. 106203
ISSN:
0167-7012
Subject:
genetic variation,   etc   ; DNA barcoding; introns; protists;     Show all 4 Subjects
Abstract:
... Unlike fungi, which have a universally accepted barcode marker, universal primers still lack in myxomycetes. Typically, DNA barcode primers were designed based on comparing existing myxomycetes sequences and targeting the conserved regions. However, the extreme genetic diversity within major myxomycetes groups and the frequent occurrence of group I introns have made the development of universal DN ...
DOI:
10.1016/j.mimet.2021.106203

12. Evolutionary Potential of the Hybrid Form Pelophylax esculentus-ridibundus (Amphibia, Ranidae) within Dnieper and Desna Drainages: Its Loss Caused by the Hemiclonal Inheritance and the Compensatory Role of Parental Genomes’ Recombination

Author:
Morozov-Leonov, S. Yu.
Source:
Cytology and genetics 2021 v.55 no.3 pp. 213-226
ISSN:
0095-4527
Subject:
genetic variation,   etc   ; Pelophylax; cell biology; genome; hybrids;     Show all 5 Subjects
Abstract:
... The hemiclonal structure of the hybrid form Pelophylax esculentus-ridibundus (Amphibia: Ranidae) within the Dnieper and Desna rivers’ basins was analyzed. The presence of polyclonality in almost all populations was demonstrated. The monoclonality of the studied hybrid form was revealed in only 2 of 17 populations studied. Wide fluctuations in the level of genetic variability within P. esculentus-r ...
DOI:
10.3103/S0095452721030063

13. Comprehensive epitope mapping using polyclonally expanded human CD8 T cells and a two-step ELISpot assay for testing large peptide libraries

Author:
Michelo, Clive M.; Dalel, Jama A.; Hayes, Peter; Fernandez, Natalia; Fiore-Gartland, Andrew; Kilembe, William; Tang, Jianming; Streatfield, Claire; Gilmour, Jill; Hunter, Eric
Source:
Journal of immunological methods 2021 v.491 pp. 112970
ISSN:
0022-1759
Subject:
genetic variation,   etc   ; epitopes; humans; sequence diversity;     Show all 4 Subjects
Abstract:
... The genetic diversity of circulating HIV-1 strains poses a major barrier to the design, development and evaluation of HIV-1 vaccines. The assessment of both vaccine- and natural infection-elicited T cell responses is commonly done with multivalent peptides that are designed to maximally capture the diversity of potential T cell epitopes (PTEs) observed in natural circulating sequences. However, de ...
DOI:
10.1016/j.jim.2021.112970

14. Evaluation of genetic diversity and development of core collections of industrial brewing yeast using ISSR markers

Author:
Liu, Jun; Li, Xiaomin; Liu, Yueqin; Xing, Chengyu; Xie, Ying; Cai, Guolin; Lu, Jian
Source:
Archives of microbiology 2021 v.203 no.3 pp. 1001-1008
ISSN:
0302-8933
Subject:
genetic variation,   etc   ; alleles; germplasm; microsatellite repeats;     Show all 4 Subjects
Abstract:
... Germplasm of industrial brewing yeast of the worldwide have a richer diversity, and various successes in improving the performance of brewing yeasts. However, they are limited in that they have relatively low odds of combining desirable traits in a correct manner. To improve germplasm resource preservation, management, and utilization efficiency. In this study, the genetic diversity of 35 industri ...
DOI:
10.1007/s00203-020-02091-8

15. Genetics of canine diabetes mellitus part 1: Phenotypes of disease

Author:
Denyer, Alice L.; Catchpole, Brian; Davison, Lucy J.
Source:
The veterinary journal 2021 v.270 pp. 105611
ISSN:
1090-0233
Subject:
genetic variation,   etc   ; diabetes mellitus; dogs; risk;     Show all 4 Subjects
Abstract:
... This two-part article discusses the mechanisms by which genetic variation can influence the risk of complex diseases, with a focus on canine diabetes mellitus. In Part 1, presented here, the importance of accurate methods for classifying different types of diabetes will be discussed, since this underpins the selection of cases and controls for genetic studies. Part 2 will focus on our current unde ...
DOI:
10.1016/j.tvjl.2021.105611

16. Introgressive Hybridization of Common Wheat: Results and Prospects

Author:
Adonina, I. G.; Timonova, E. M.; Salina, E. A.
Source:
Russian journal of genetics 2021 v.57 no.4 pp. 390-407
ISSN:
1022-7954
Subject:
genetic variation,   etc   ; crops; genes; introgression; wheat;     Show all 5 Subjects
Abstract:
... This review is devoted to the introgressive hybridization of common wheat, the process of integrating the genes of other cultivated or wild species from the secondary and tertiary gene pools into its genome in order to increase the genetic diversity of this most important agricultural crop. The results achieved in the introgressive hybridization of common wheat over the past 20 years are summarize ...
DOI:
10.1134/S1022795421030029

17. Exploring Genetic Variability among and within Hail Tomato Landraces Based on Sequence-Related Amplified Polymorphism Markers

Author:
Alzahib, Reem H.; Migdadi, Hussein M.; Ghamdi, Abdullah A. Al; Alwahibi, Mona S.; Afzal, Muhammad; Elharty, Ehab H.; Alghamdi, Salem S.
Source:
Diversity 2021 v.13 no.3
ISSN:
1424-2818
Subject:
genetic variation,   etc   ; landraces; multidimensional scaling; tomatoes;     Show all 4 Subjects
Abstract:
... Landraces are valuable sources of genetic characteristics, which are of plant breeders’ interest to include in breeding programs for crop improvement. We assess the inter- and intra-genetic variability among 96 accessions representing three Hail tomato landrace using DNA-based marker sequence-related amplified polymorphism (SRAP). Seven SRAP primer combinations generated 55 alleles with a polymorp ...
DOI:
10.3390/d13030135

18. Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil

Author:
Tinker, Rory J.; da Costa, Antonio Charlys; Tahmasebi, Roozbeh; Milagres, Flavio Augusto de Pádua; dos Santos Morais, Vanessa; Pandey, Ramendra Pati; José-Abrego, Alexis; Brustulin, Rafael; Rodrigues Teles, Maria da Aparecida; Cunha, Mariana Sequetin; Araújo, Emerson Luiz Lima; Gómez, Mariela Martínez; Deng, Xutao; Delwart, Eric; Sabino, Ester Cerdeira; Leal, Elcio; Luchs, Adriana
Source:
Archives of virology 2021 v.166 no.3 pp. 905-913
ISSN:
0304-8608
Subject:
genetic variation,   etc   ; Norovirus; gastroenteritis; phylogeny; virology; Brazil;     Show all 6 Subjects
Abstract:
... From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GI ...
DOI:
10.1007/s00705-020-04944-5

19. Genetic divergence of the Sunda ratsnake (Coelognathus subradiatus) across the Lesser Sunda Islands (Squamata: Colubridae)

Author:
Reilly, Sean B.; Stubbs, Alexander L.; Karin, Benjamin R.; Arifin, Umilaela; Arida, Evy; Iskandar, Djoko T.; McGuire, Jimmy A.
ISSN:
0173-5373
Subject:
genetic variation,   etc   ; Colubridae; mitochondrial DNA; phylogeny; Timor;     Show all 5 Subjects
Abstract:
... The Lesser Sunda Archipelago consists of hundreds of oceanic islands located in southern Wallacea. The Sunda ratsnake, Coelognathus subradiatus, is endemic to the Lesser Sundas and is found on most of the major islands. Mitochondrial DNA was sequenced from snakes representing five of the major islands revealing that levels of sequence divergence between islands range from 2-7%. Phylogenetic analys ...
DOI:
10.1163/15685381-bja10048

20. A new species of the genus Pareas (Squamata, Pareidae) from Yunnan, China

Author:
Liu, Shuo; Rao, Dingqi
Source:
ZooKeys 2021 v.1011 pp. 121-138
ISSN:
1313-2970
Subject:
genetic variation,   etc   ; Squamata; genes; new species; China;     Show all 5 Subjects
Abstract:
... A new species of Pareas is described from Yunnan Province, China, based on morphological comparisons and molecular data. Genetically, the new species is most closely related to the recently-described Pareas geminatus, for which we present new topotypic findings. The genetic divergence (uncorrected p-distance) of the cytb gene between the new species and congeners ranged from 6.14% to 24.68%. Morph ...
DOI:
10.3897/zookeys.1011.59029