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1. Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error

Author:
Adams, Richard H.; Castoe, Todd A.
Source:
Molecular phylogenetics and evolution 2019 v.134 pp. 164-171
ISSN:
1055-7903
Subject:
loci,   etc   ; birds; data collection; genome; models; phylogeny;     Show all 6 Subjects
Abstract:
... Fundamental to all phylogenomic studies is the notion that increasing the amount of data – to entire genomes when possible – will increase the accuracy of phylogenetic inference. Simply adding more data does not, however, guarantee phylogenomic inferences will be more accurate. Even genome-scale reconstructions of species histories can suffer the effects of both incomplete lineage sorting (ILS) an ...
DOI:
10.1016/j.ympev.2019.02.012

2. Gene space completeness in complex plant genomes

Author:
Van Bel, Michiel; Bucchini, François; Vandepoele, Klaas
Source:
Current opinion in plant biology 2019 v.48 pp. 9-17
ISSN:
1369-5266
Subject:
quantitative trait loci,   etc   ; genes; genomics; models;     Show all 4 Subjects
Abstract:
... Genome annotations offer ample opportunities to study gene functions, biochemical and regulatory pathways, or quantitative trait loci in plants. Determining the quality and completeness of a genome annotation, and maintaining the balance between them, are major challenges, even for genomes of well-studied model organisms. In this review, we present a historical overview of the complexity in differ ...
DOI:
10.1016/j.pbi.2019.01.001

3. The Genetic Basis of Metabolic Disease

Author:
Barroso, Inês; McCarthy, Mark I.
Source:
Cell 2019 v.177 no.1 pp. 146-161
ISSN:
0092-8674
Subject:
loci,   etc   ; genome; genomics; metabolic diseases; phenotype;     Show all 5 Subjects
Abstract:
... Recent developments in genetics and genomics are providing a detailed and systematic characterization of the genetic underpinnings of common metabolic diseases and traits, highlighting the inherent complexity within systems for homeostatic control and the many ways in which that control can fail. The genetic architecture underlying these common metabolic phenotypes is complex, with each trait infl ...
DOI:
10.1016/j.cell.2019.02.024

4. Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

Author:
Van Dam, Matthew H.; Trautwein, Michelle; Spicer, Greg S.; Esposito, Lauren
Source:
Molecular ecology resources 2019 v.19 no.2 pp. 465-475
ISSN:
1755-098X
Subject:
loci,   etc   ; Opiliones; Parasitiformes; genome; genomics; mites; paraphyly;     Show all 7 Subjects
Abstract:
... Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resol ...
DOI:
10.1111/1755-0998.12962

5. The role of αβ T-cells in spontaneous regression of melanoma tumors in swine

Author:
Cizkova, Jana; Sinkorova, Zuzana; Strnadova, Kristyna; Cervinkova, Monika; Horak, Vratislav; Sinkora, Jiri; Stepanova, Katerina; Sinkora, Marek
Source:
Developmental and comparative immunology 2019 v.92 pp. 60-68
ISSN:
0145-305X
Subject:
loci,   etc   ; T-lymphocytes; melanoma; models; phenotype; swine;     Show all 6 Subjects
Abstract:
... Using a porcine model, we describe Melanoma-Associated CD4+CD8hi T-lymphocytes (MATL) in peripheral blood that increase during melanoma regression. These MATL possess the CD4+CD8hi phenotype and they have their direct counterparts in Tumor Infiltrating Lymphocytes (TIL) isolated from melanoma loci. Both MATL and CD4+CD8hi TIL have a similar expression of selected markers indicating that they repre ...
DOI:
10.1016/j.dci.2018.10.001

6. A B-Cell-Specific Enhancer Orchestrates Nuclear Architecture to Generate a Diverse Antigen Receptor Repertoire

Author:
Barajas-Mora, E. Mauricio; Kleiman, Eden; Xu, Jeffrey; Carrico, Nancy C.; Lu, Hanbin; Oltz, Eugene M.; Murre, Cornelis; Feeney, Ann J.
Source:
Molecular cell 2019 v.73 no.1 pp. 48-60.e5
ISSN:
1097-2765
Subject:
loci,   etc   ; antibodies; antigens; chromatin; genes; immunoglobulins;     Show all 6 Subjects
Abstract:
... The genome is organized into topologically associated domains (TADs) that enclose smaller subTADs. Here, we identify and characterize an enhancer that is located in the middle of the V gene region of the immunoglobulin kappa light chain (Igκ) locus that becomes active preceding the stage at which this locus undergoes V(D)J recombination. This enhancer is a hub of long-range chromatin interactions ...
DOI:
10.1016/j.molcel.2018.10.013

7. Novel loci fsd6.1 and Csgl3 regulate ultra-high fruit spine density in cucumber

Author:
Bo, Kailiang; Miao, Han; Wang, Min; Xie, Xiaoxiao; Song, Zichao; Xie, Qing; Shi, Lixue; Wang, Weiping; Wei, Shuang; Zhang, Shengping; Gu, Xingfang
Source:
Theoretical and applied genetics 2019 v.132 no.1 pp. 27-40
ISSN:
0040-5752
Subject:
loci; quantitative trait loci,   etc   ; cucumbers; domestication; fruits; genes; genetic variation; geographical distribution; phylogeny; China;     Show all 10 Subjects
Abstract:
... KEY MESSAGE: Quantitative Trait Loci (QTL) analysis of multiple populations in multiple environments revealed that the fsd6.2 locus, which includes the candidate gene Csgl3, controls high fruit spine density in natural cucumbers. GWAS identified a novel locus fsd6.1, which regulates ultra-high fruit spine density in combination with Csgl3, and evolved during cucumber domestication. Fruit spine den ...
DOI:
10.1007/s00122-018-3191-6

8. Correction to: Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions

Author:
Fraslin, Clémence; Dechamp, Nicolas; Bernard, Maria; Krieg, Francine; Hervet, Caroline; Guyomard, René; Esquerré, Diane; Barbieri, Johanna; Kuchly, Claire; Duchaud, Eric; Boudinot, Pierre; Rochat, Tatiana; Bernardet, Jean-François; Quillet, Edwige
Source:
Genetics, selection, evolution 2019 v.51 no.1 pp. 11
ISSN:
1297-9686
Subject:
quantitative trait loci,   etc   ; Flavobacterium psychrophilum; Oncorhynchus mykiss; epistasis;     Show all 4 Subjects
Abstract:
... After publication of this work [1], we noted that there was an error in Table 3 Line 4. ...
DOI:
10.1186/s12711-019-0451-0

9. A species-level phylogeny of Trachylepis (Scincidae: Mabuyinae) provides insight into their reproductive mode evolution

Author:
Weinell, Jeffrey L.; Branch, William R.; Colston, Timothy J.; Jackman, Todd R.; Kuhn, Arianna; Conradie, Werner; Bauer, Aaron M.
Source:
Molecular phylogenetics and evolution 2019 v.136 pp. 183-195
ISSN:
1055-7903
Subject:
loci,   etc   ; Trachylepis; ancestry; biogeography; mitochondria; models; ovipary; phylogeny; Africa; Madagascar;     Show all 10 Subjects
Abstract:
... Trachylepis (Mabuyinae) includes ∼80 species of fully-limbed skinks found primarily in Africa and Madagascar, but a robust species-level phylogeny for this genus is lacking and this impedes studies on a wide-range of topics from biogeography to character evolution. Trachylepis and its close relatives (which together form the Mabuya group or Mabuyinae) are notable in that they have undergone multip ...
DOI:
10.1016/j.ympev.2019.04.002

10. Phylogenomic analyses of brachyuran crabs support early divergence of primary freshwater crabs

Author:
Ma, Ka Yan; Qin, Jing; Lin, Chia-Wei; Chan, Tin-Yam; Ng, Peter K.L.; Chu, Ka Hou; Tsang, Ling Ming
Source:
Molecular phylogenetics and evolution 2019 v.135 pp. 62-66
ISSN:
1055-7903
Subject:
loci,   etc   ; Cretaceous period; crabs; data collection; fossils; internodes; phylogeny; transcriptome;     Show all 8 Subjects
Abstract:
... Recent fossil calibrated molecular phylogenies have revealed that the Brachyura underwent rapid radiation during the Cretaceous and Early Tertiary, resulting in many early diverging lineages separated by short internodes that remain difficult to resolve. Here we present the first phylogenomic analyses of Brachyura using transcriptome data from 30 brachyuran species and 22 families. Analyses were c ...
DOI:
10.1016/j.ympev.2019.02.001

11. Curation and bioinformatic analysis of strabismus genes supports functional heterogeneity and proposes candidate genes with connections to RASopathies

Author:
Ye, Xin (Cynthia); van der Lee, Robin; Wasserman, Wyeth W.
Source:
Gene 2019 v.697 pp. 213-226
ISSN:
0378-1119
Subject:
loci,   etc   ; bioinformatics; cerebellum; gene ontology; genes; retina; tumor suppressor proteins;     Show all 7 Subjects
Abstract:
... Strabismus refers to the misalignment of the eyes and occurs in 2–4% of individuals. The low-resolution label “strabismus” covers a range of heterogeneous defects, which makes it challenging to unravel this condition. Consequently a coherent understanding of the causes is lacking. Here, we attempt to gain a better understanding of the underlying genetics by combining gene curation, diverse bioinfo ...
DOI:
10.1016/j.gene.2019.02.020

12. Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

Author:
Jacobson, Elsie C.; Grand, Ralph S.; Perry, Jo K.; Vickers, Mark H.; Olins, Ada L.; Olins, Donald E.; O'Sullivan, Justin M.
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
loci,   etc   ; cell lines; karyotyping; myeloid leukemia; neoplasm cells; sequence analysis;     Show all 6 Subjects
Abstract:
... Cancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used ...
DOI:
10.1016/j.ygeno.2019.05.009

13. Per-Nucleus Crossover Covariation and Implications for Evolution

Author:
Wang, Shunxin; Veller, Carl; Sun, Fei; Ruiz-Herrera, Aurora; Shang, Yongliang; Liu, Hongbin; Zickler, Denise; Chen, Zijiang; Kleckner, Nancy; Zhang, Liangran
Source:
Cell 2019 v.177 no.2 pp. 326-338.e16
ISSN:
0092-8674
Subject:
loci,   etc   ; evolutionary adaptation; genetic models; germ cells; meiosis; sexual reproduction;     Show all 6 Subjects
Abstract:
... Crossing over is a nearly universal feature of sexual reproduction. Here, analysis of crossover numbers on a per-chromosome and per-nucleus basis reveals a fundamental, evolutionarily conserved feature of meiosis: within individual nuclei, crossover frequencies covary across different chromosomes. This effect results from per-nucleus covariation of chromosome axis lengths. Crossovers can promote e ...
DOI:
10.1016/j.cell.2019.02.021

14. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2

Author:
Beck, Christine R.; Carvalho, Claudia M.B.; Akdemir, Zeynep C.; Sedlazeck, Fritz J.; Song, Xiaofei; Meng, Qingchang; Hu, Jianhong; Doddapaneni, Harsha; Chong, Zechen; Chen, Edward S.; Thornton, Philip C.; Liu, Pengfei; Yuan, Bo; Withers, Marjorie; Jhangiani, Shalini N.; Kalra, Divya; Walker, Kimberly; English, Adam C.; Han, Yi; Chen, Ken; Muzny, Donna M.; Ira, Grzegorz; Shaw, Chad A.; Gibbs, Richard A.; Hastings, P.J.; Lupski, James R.
Source:
Cell 2019 v.176 no.6 pp. 1310-1324.e10
ISSN:
0092-8674
Subject:
loci,   etc   ; gene rearrangement; genes; humans; mutation; single-stranded DNA;     Show all 6 Subjects
Abstract:
... DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant ( ...
DOI:
10.1016/j.cell.2019.01.045

15. CONSTANS delays Arabidopsis flowering under short days

Author:
Luccioni, Laura; Krzymuski, Martín; Sánchez‐Lamas, Maximiliano; Karayekov, Elizabeth; Cerdán, Pablo D.; Casal, Jorge J.
Source:
Theplant journal 2019 v.97 no.5 pp. 923-932
ISSN:
0960-7412
Subject:
loci,   etc   ; Arabidopsis thaliana; epistasis; flowering; leaves; models; mutation; rice; sucrose;     Show all 9 Subjects
Abstract:
... Long days (LD) promote flowering of Arabidopsis thaliana compared with short days (SD) by activating the photoperiodic pathway. Here we show that growth under very‐SD (3 h) or darkness (on sucrose) also accelerates flowering on a biological scale, indicating that SD actively repress flowering compared with very‐SD. CONSTANS (CO) repressed flowering under SD, and the early flowering of co under SD ...
DOI:
10.1111/tpj.14171

16. Parentage assignment with genotyping‐by‐sequencing data

Author:
Whalen, Andrew; Gorjanc, Gregor; Hickey, John M.
Source:
Journal of animal breeding and genetics 2019 v.136 no.2 pp. 102-112
ISSN:
0931-2668
Subject:
loci,   etc   ; ecology; genotyping by sequencing; homozygosity; parentage; parents;     Show all 6 Subjects
Abstract:
... In this paper, we evaluate using genotype‐by‐sequencing (GBS) data to perform parentage assignment in lieu of traditional array data. The use of GBS data raises two issues: First, for low‐coverage (e.g., <2×) GBS data, it may not be possible to call the genotype at many loci, a critical first step for detecting opposing homozygous markers. Second, the amount of sequencing coverage may vary across ...
DOI:
10.1111/jbg.12370

17. Ribosomal DNA-connecting ribosome biogenesis and chromosome biology

Author:
Porokhovnik, Lev; Gerton, Jennifer L.
Source:
Chromosome research 2019 v.27 no.1-2 pp. 1-3
ISSN:
0967-3849
Subject:
loci,   etc   ; biogenesis; genome; ribosomal DNA; ribosomal RNA; ribosomes; translation (genetics);     Show all 7 Subjects
Abstract:
... Ribosomal DNA, the topic of this special issue, has long fascinated biologists. The RNA products of the ribosomal DNA are the ribosomal RNAs that are part of the ribosome. In this special issue, we focus on the sequence, molecular organization, repair, stability, copy number, and peculiar genetics of this region of the genome. The locus can impact not only the translational capability of cells, bu ...
DOI:
10.1007/s10577-018-9601-4

18. The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance

Author:
Bughio, Farah; Maggert, Keith A.
Source:
Chromosome research 2019 v.27 no.1-2 pp. 19-30
ISSN:
0967-3849
Subject:
loci,   etc   ; epigenetics; inheritance (genetics); phenotype; ribosomal DNA; transcription (genetics);     Show all 6 Subjects
Abstract:
... Our goal is to draw a line—hypothetical in its totality but experimentally supported at each individual step—connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for g ...
DOI:
10.1007/s10577-018-9591-2

19. Donuts and Spin Vortices at the Fermi Surfaces of Hybrid Lead-Iodide CH₃NH₃PbI₃ Perovskites

Author:
Filippetti, A.; Caddeo, C.; Bosin, A.; Delugas, P.; Mattoni, A.
Source:
Journal of physical chemistry 2019 v.123 no.11 pp. 6753-6762
ISSN:
1932-7455
Subject:
loci,   etc   ; apples; electrons; lead; photoluminescence; physical chemistry; texture;     Show all 7 Subjects
Abstract:
... We show that spin–orbit coupling in methylammonium lead-iodide perovskite generates Fermi surfaces of peculiar topology: for the low charge-injection regime of interest for photovoltaic applications, the Fermi surfaces are donuts (ring tori), which evolve into apples (spindle tori) as the band population is raised, with a vortex spin texture that indicates the dominance of the Rashba effect. This ...
DOI:
10.1021/acs.jpcc.9b00140

20. Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements

Author:
Roxo, Fábio F.; Ochoa, Luz E.; Sabaj, Mark H.; Lujan, Nathan K.; Covain, Raphaël; Silva, Gabriel S.C.; Melo, Bruno F.; Albert, James S.; Chang, Jonathan; Foresti, Fausto; Alfaro, Michael E.; Oliveira, Claudio
Source:
Molecular phylogenetics and evolution 2019
ISSN:
1055-7903
Subject:
loci,   etc   ; Loricariidae; catfish; data collection; habitats; monophyly; statistical analysis; topology;     Show all 8 Subjects
Abstract:
... Neotropical freshwaters host more than 6,000 fish species, of which 983 are suckermouth armored catfishes of the family Loricariidae – the most-diverse catfish family and fifth most species-rich vertebrate family on Earth. Given their diversity and ubiquitous distribution across many habitat types, loricariids are an excellent system in which to investigate factors that create and maintain Neotrop ...
DOI:
10.1016/j.ympev.2019.02.017