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1. TT-Mars: structural variants assessment based on haplotype-resolved assemblies

Author:
Jianzhi Yang; Mark J.P. Chaisson
Source:
Genome biology 2022 v.23 no.1 pp. 110
ISSN:
1474-760X
Subject:
genome; genome assembly,   etc   ; testing;     Show all 3 Subject
Abstract:
... Variant benchmarking is often performed by comparing a test callset to a gold standard set of variants. In repetitive regions of the genome, it may be difficult to establish what is the truth for a call, for example, when different alignment scoring metrics provide equally supported but different variant calls on the same data. Here, we provide an alternative approach, TT-Mars, that takes advantag ...
DOI:
10.1186/s13059-022-02666-2

2. Draft genome assembly and sequencing dataset of the marine diatom Skeletonema cf. costatum RCC75

Author:
Maria Sorokina; Emanuel Barth; Mahnoor Zulfiqar; Michiel Kwantes; Georg Pohnert; Christoph Steinbeck
Source:
Data in Brief 2022 v.41 pp. 107931
ISSN:
2352-3409
Subject:
genome; genome assembly,   etc   ; Bacillariophyceae; Skeletonema costatum; data collection; phytoplankton;     Show all 6 Subjects
Abstract:
... Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and ...
DOI:
10.1016/j.dib.2022.107931

3. Effects of geographic isolation on the Bulbophyllum chloroplast genomes

Author:
Jiapeng Yang; Fuwei Zhang; Yajie Ge; Wenhui Yu; Qiqian Xue; Mengting Wang; Hongman Wang; Qingyun Xue; Wei Liu; Zhitao Niu; Xiaoyu Ding
Source:
BMC plant biology 2022 v.22 no.1 pp. 201
ISSN:
1471-2229
Subject:
chloroplast genome; mitochondrial genome; nuclear genome,   etc   ; Bulbophyllum; Crassulacean acid metabolism; Oligocene epoch; chloroplasts; phylogeny; plant biology; Asia; Australia; South America;     Show all 12 Subjects
Abstract:
... BACKGROUND: Because chloroplast (cp) genome has more conserved structures than nuclear genome and mitochondrial genome, it is a useful tool in estimating the phylogenetic relationships of plants. With a series of researches for cp genomes, there have been comprehensive understandings about the cp genome features. The genus Bulbophyllum widely distributed in Asia, South America, Australia and other ...
DOI:
10.1186/s12870-022-03592-y

4. Disentangle genus microdiversity within a complex microbial community by using a multi‐distance long‐read binning method: example of Candidatus Accumulibacter

Author:
Aline Adler; Simon Poirier; Marco Pagni; Julien Maillard; Christof Holliger
Source:
Environmental microbiology 2022 v.24 no.4 pp. 2136-2156
ISSN:
1462-2912
Subject:
genome; genome assembly,   etc   ; DNA; bioreactors; lifestyle; metagenomics; microbial communities; sludge; wastewater treatment;     Show all 9 Subjects
Abstract:
... Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulib ...
DOI:
10.1111/1462-2920.15947

5. Optical mapping of the Fusarium oxysporum f. sp. melongenae genome

Author:
Duygu Ates; Hacer H. Altinok; Muhammed Bahattin Tanyolac
Source:
Journal of basic microbiology 2022 v.62 no.5 pp. 604-610
ISSN:
0233-111X
Subject:
genome; genome assembly,   etc   ; Fusarium oxysporum; National Center for Biotechnology Information; genomics; microbiology;     Show all 6 Subjects
Abstract:
... Optical mapping approaches are widely preferred and applied in different branches of genomic studies because of their accuracy, low cost, and high efficiency. In the current study, a sequence orientation of the Fusarium oxysporum f. sp. melongenae (FOMG) genome that is deposited in GenBank National Center for Biotechnology Information under accession number MPIL00000000 was used as the reference g ...
DOI:
10.1002/jobm.202100627

6. Mapping the long road to cancer

Author:
David M. Cheek; Kamila Naxerova
Source:
Cell 2022 v.185 no.6 pp. 939-940
ISSN:
0092-8674
Subject:
genome,   etc   ; blood; evolution;     Show all 3 Subjects
Abstract:
... Every cell in our body accumulates mutations throughout life, and sometimes an unfortunate combination of mutations drives the initiation of cancer. A new study infers extraordinarily detailed timelines of pre-cancerous evolution by sequencing single-cell genomes in patients with blood malignancies—finding that key mutations can arrive decades before diagnosis. ...
DOI:
10.1016/j.cell.2022.02.020

7. mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis

Author:
Yanyan Zeng; Jing Li; Chaochun Wei; Hongyu Zhao; Wang Tao
Source:
Genome biology 2022 v.23 no.1 pp. 94
ISSN:
1474-760X
Subject:
genome,   etc   ; microbiome; models;     Show all 3 Subjects
Abstract:
... The analysis of microbiome data has several technical challenges. In particular, count matrices contain a large proportion of zeros, some of which are biological, whereas others are technical. Furthermore, the measurements suffer from unequal sequencing depth, overdispersion, and data redundancy. These nuisance factors introduce substantial noise. We propose an accurate and robust method, mbDenois ...
DOI:
10.1186/s13059-022-02657-3

8. Mitochodrial Genome of Phylloscopus examinandus and Hypothesis of Its Origin

Author:
L. N. Spiridonova; O. P. Valchuk
Source:
Russian journal of genetics 2022 v.58 no.3 pp. 365-368
ISSN:
1022-7954
Subject:
mitochondrial genome; nuclear genome,   etc   ; Phylloscopus examinandus; Russia; genetic variation; haplotypes; mitochondria; mitochondrial DNA;     Show all 8 Subjects
Abstract:
... The complete mitochondrial genome sequencing of three nesting warblers Phylloscopus examinandus (Stresemann, 1913) (Passeriformes, Phylloscopidae) from Sakhalin Island was carried out for the first time. The mitochondrial genome structure was typical of the genus Phylloscopus with two control regions: functional CRI and partial (pseudo-) CRII. The genetic divergence between Ph. examinandus and Ph. ...
DOI:
10.1134/S1022795422030140

9. Plant pan-genomics: recent advances, new challenges, and roads ahead

Author:
Wei Li; Jianan Liu; Hongyu Zhang; Ze Liu; Yu Wang; Longsheng Xing; Qiang He; Huilong Du
Source:
Journal of genetics and genomics 2022 pp. -
ISSN:
1673-8527
Subject:
genome; genome assembly,   etc   ; domestication; evolution; genetic variation; genomics; multiomics; phenotypic variation; plant improvement;     Show all 9 Subjects
Abstract:
... Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pa ...
DOI:
10.1016/j.jgg.2022.06.004

10. Dynamic development of AT‐rich heterochromatin has followed diversification and genome expansion of psammophilous Mycetophylax (Formicidae: Attini: Attina)

Author:
Danon Clemes Cardoso; Mariana Neves Moura; Maykon Passos Cristiano
Source:
Insect molecular biology 2022 v.31 no.3 pp. 297-307
ISSN:
0962-1075
Subject:
genome; genome expansion,   etc   ; DNA; Formicidae; adenine; cytotypes; heterochromatin; insects; karyotyping; molecular biology; phylogeny; thymine;     Show all 12 Subjects
Abstract:
... Heterochromatin is an important genome constituent comprised by a high density of repetitive DNA sequences that mediate chromosome structure and function. The species Mycetophylax morschi currently harbours three cytotypes: 2n = 26, 2n = 28 and 2n = 30 chromosomes. However, Mycetophylax conformis and Mycetophylax simplex harbour 2n = 30 and 2n = 36 chromosomes, respectively. None of the cytotypes ...
DOI:
10.1111/imb.12759

11. Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference

Author:
Aparna Prasad; Eline D. Lorenzen; Michael V. Westbury
Source:
Molecular ecology resources 2022 v.22 no.1 pp. 45-55
ISSN:
1755-098X
Subject:
genome; genome assembly,   etc   ; Delphinapterus leucas; birds; conspecificity; genetic distance; genetic variation; heterozygosity; homozygosity; mammals;     Show all 10 Subjects
Abstract:
... When a high‐quality genome assembly of a target species is unavailable, an option to avoid the costly de novo assembly process is a mapping‐based assembly. However, mapping shotgun data to a distant relative may lead to biased or erroneous evolutionary inference. Here, we used short‐read data from a mammal (beluga whale) and a bird species (rowi kiwi) to evaluate whether reference genome phylogene ...
DOI:
10.1111/1755-0998.13457

12. Identification of sex-specific molecular markers and development of PCR-based sex detection techniques in tropical sea cucumber (Stichopus monotuberculatus)

Author:
Feifei Wu; Chuhang Cheng; Xiaomin Li; Chunhua Ren; Peng Luo; Xiao Jiang; Zixuan E; Xin Zhang; Chaoqun Hu; Ting Chen
Source:
Aquaculture 2022 v.547 pp. 737458
ISSN:
0044-8486
Subject:
genome; genome assembly,   etc   ; Stichopus; aquaculture; females; fledglings; males; polymerase chain reaction; sex determination; China;     Show all 10 Subjects
Abstract:
... Sex-specific markers are essential for understanding sex determination mechanism and developing sex detection techniques in aquatic animals. The tropical sea cucumber Stichopus monotuberculatus is a fledgling aquaculture species in southern China. In this study, a total of 399 candidate male-specific and 179 candidate female-specific sequences were obtained after genome assembly, read mapping, and ...
DOI:
10.1016/j.aquaculture.2021.737458

13. Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data

Author:
Hongyu Duan; Ashley W. Jones; Tim Hewitt; Amy Mackenzie; Yiheng Hu; Anna Sharp; David Lewis; Rohit Mago; Narayana M. Upadhyaya; John P. Rathjen; Eric A. Stone; Benjamin Schwessinger; Melania Figueroa; Peter N. Dodds; Sambasivam Periyannan; Jana Sperschneider
Source:
Genome biology 2022 v.23 no.1 pp. 84
ISSN:
1474-760X
Subject:
genome; genome assembly,   etc   ; Puccinia recondita; chromatin; diploidy; genomics; haploidy; haplotypes; heterozygosity; leaf rust; nanopores;     Show all 11 Subjects
Abstract:
... BACKGROUND: Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in dipl ...
DOI:
10.1186/s13059-022-02658-2

14. A walk through the SMC cycle: From catching DNAs to shaping the genome

Author:
Roel Oldenkamp; Benjamin D. Rowland
Source:
Molecular cell 2022 v.82 no.9 pp. 1616-1630
ISSN:
1097-2765
Subject:
genome,   etc   ; DNA; chromatids; mitosis;     Show all 4 Subjects
Abstract:
... SMC protein complexes are molecular machines that provide structure to chromosomes. These complexes bridge DNA elements and by doing so build DNA loops in cis and hold together the sister chromatids in trans. We discuss how drastic conformational changes allow SMC complexes to build such intricate DNA structures. The tight regulation of these complexes controls fundamental chromosomal processes su ...
DOI:
10.1016/j.molcel.2022.04.006

15. Genome chromatinization in giant double-stranded DNA viruses

Author:
Ying Liu; Mart Krupovic
Source:
Trends in biochemical sciences 2022 v.47 no.1 pp. 3-5
ISSN:
0968-0004
Subject:
genome,   etc   ; DNA; histones; nucleosomes;     Show all 4 Subjects
Abstract:
... Giant viruses have extravagantly large double-stranded (ds)DNA genomes that are packaged into exceedingly complex virions. In two recent papers, Liu et al. and Valencia-Sánchez, Abini-Agbomson et al. show that some giant viruses encode unique histone doublets, which form nucleosomes remarkably similar to those found across the eukaryotic domain of life. ...
DOI:
10.1016/j.tibs.2021.10.002

16. HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Author:
Yuxuan Du; Fengzhu Sun
Source:
Genome biology 2022 v.23 no.1 pp. 63
ISSN:
1474-760X
Subject:
genome,   etc   ; algorithms; chromosomes; metagenomics;     Show all 4 Subjects
Abstract:
... Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the Hi ...
DOI:
10.1186/s13059-022-02626-w

17. Importing genetically altered animals: ensuring quality

Author:
M.-C. Birling; M. D. Fray; P. Kasparek; J. Kopkanova; M. Massimi; R. Matteoni; L. Montoliu; L. M. J. Nutter; M. Raspa; J. Rozman; E. J. Ryder; F. Scavizzi; V. Voikar; S. Wells; G. Pavlovic; L. Teboul
Source:
Mammalian genome 2022 v.33 no.1 pp. 100-107
ISSN:
0938-8990
Subject:
genome,   etc   ; laboratory animals; rodents;     Show all 3 Subjects
Abstract:
... The reproducibility of research using laboratory animals requires reliable management of their quality, in particular of their genetics, health and environment, all of which contribute to their phenotypes. The point at which these biological materials are transferred between researchers is particularly sensitive, as it may result in a loss of integrity of the animals and/or their documentation. He ...
DOI:
10.1007/s00335-021-09908-x

18. Deletion in KRT75L4 linked to frizzle feather in Xiushui Yellow Chickens

Author:
B. Chen; S. Xi; H. K. El‐Senousey; M. Zhou; D. Cheng; K. Chen; L. Wan; T. Xiong; M. Liao; S. Liu; H. Mao
Source:
Animal genetics 2022 v.53 no.1 pp. 101-107
ISSN:
0268-9146
Subject:
genome; genome-wide association study,   etc   ; animal genetics; artificial selection; chickens; genotyping; missense mutation; phenotype; China;     Show all 9 Subjects
Abstract:
... Bird feathers are the product of interactions between natural and artificial selection. Feather‐related traits are important for chicken selection and breeding. Frizzle feather is characterized by the abnormally development of feathers in chickens. In the current study, frizzle feather characteristics were observed in a local breed called Xiushui Yellow Chicken in Jiangxi, China. To determine the ...
DOI:
10.1111/age.13158

19. Diverse and mobile: eccDNA‐based identification of carrot low‐copy‐number LTR retrotransposons active in callus cultures

Author:
Kornelia Kwolek; Patrycja Kędzierska; Magdalena Hankiewicz; Marie Mirouze; Olivier Panaud; Dariusz Grzebelus; Alicja Macko‐Podgórni
Source:
plant journal 2022 v.110 no.6 pp. 1811-1828
ISSN:
0960-7412
Subject:
genome; genome assembly,   etc   ; DNA; Daucus carota; RNA; adverse effects; callus; carrots; retrotransposons; terminal repeat sequences;     Show all 10 Subjects
Abstract:
... Long terminal repeat retrotransposons (LTR‐RTs) are mobilized via an RNA intermediate using a ‘copy and paste’ mechanism, and account for the majority of repetitive DNA in plant genomes. As a side effect of mobilization, the formation of LTR‐RT‐derived extrachromosomal circular DNAs (eccDNAs) occurs. Thus, high‐throughput sequencing of eccDNA can be used to identify active LTR‐RTs in plant genomes ...
DOI:
10.1111/tpj.15773

20. Genome Resource: Draft Genome of Fusarium avenaceum, Strain F156N33, Isolated from the Atmosphere Above Virginia and Annotated Based on RNA Sequencing Data

Author:
Shu Yang; Jeffrey J. Coleman; Boris A. Vinatzer
Source:
Plant disease 2022 v.106 no.2 pp. 720-722
ISSN:
0191-2917
Subject:
genome; genome assembly,   etc   ; Fusarium avenaceum; Fusarium head blight; RNA; corn; fungi; ice; ice nucleation; soil; Virginia;     Show all 11 Subjects
Abstract:
... Fusarium avenaceum is a filamentous fungus commonly associated with plants and soil. It is a causal agent of Fusarium head blight (FHB) on maize and small-grain cereals and blights on other plant species, and is one of the very few fungal species known to have ice nucleation activity (i.e., it catalyzes ice formation). Here, we report the draft genome of the ice-nucleation-active F. avenaceum stra ...
DOI:
10.1094/PDIS-04-21-0787-A