Featured
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| Open AccessThe 3D architecture of the pepper genome and its relationship to function and evolution
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.
- Yi Liao
- , Juntao Wang
- & Changming Chen
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Article
| Open AccessStructural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies
Pangenomes have a number of advantages over linear reference assemblies. Here the authors use bovine haplotype-resolved assemblies to show that structural variant-based pangenomes are consistent regardless of sequence platform, assembler, or coverage, suggesting that rigid protocols may not be required.
- Alexander S. Leonard
- , Danang Crysnanto
- & Hubert Pausch
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Article
| Open AccessLong-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer
The molecular mechanisms underlying cervical carcinogenesis following integration of HPV DNA into the human genome remain elusive. Here, the authors perform long-read sequencing in 16 HPV16-positive cervical tumors and identify distinct integration types, structural variations and potential driver genes.
- Liyuan Zhou
- , Qiongzi Qiu
- & Yan Lu
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Article
| Open AccessGenome and transcriptome mechanisms driving cephalopod evolution
“Cephalopods are known for their large nervous systems, complex behaviors, and morphological innovations. Here, the authors find that soft-bodied cephalopod genomes are more rearranged than other extant molluscs and that mRNA editing patterns are associated with the nervous system and repetitive elements”.
- Caroline B. Albertin
- , Sofia Medina-Ruiz
- & Daniel S. Rokhsar
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| Open AccessHigh-quality genome and methylomes illustrate features underlying evolutionary success of oaks
The genus Quercus (oaks) has diversified into over 450 species which often play dominant roles in the ecosystems in which they occur. Here the authors present a genome and methylome for a California endemic oak, Quercus lobata, and describe features relevant to its evolutionary success.
- Victoria L. Sork
- , Shawn J. Cokus
- & Steven L. Salzberg
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| Open AccessUsing deep learning to predict abdominal age from liver and pancreas magnetic resonance images
Approaches to both determine abdominal age and identify risk factors for accelerated abdominal age will help delay the onset of several diseases. Here, the authors build an abdominal age predictor by training convolutional neural networks to predict abdominal age from liver and pancreas MRIs.
- Alan Le Goallec
- , Samuel Diai
- & Chirag J. Patel
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Article
| Open AccessWhole-genome sequencing of 1,171 elderly admixed individuals from Brazil
Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.
- Michel S. Naslavsky
- , Marilia O. Scliar
- & Mayana Zatz
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| Open AccessNuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium
The snail Bulinus truncatus is an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium. Here the authors report the genome of Bu. truncatus, explore protein groups inferred to play a role in its interaction with the schistosome parasite, and identify expansions in gene families linked to immune response regulation.
- Neil D. Young
- , Andreas J. Stroehlein
- & Robin B. Gasser
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Article
| Open AccessIn vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue
Mutations in mitochondrial DNA can lead to clinically heterogeneous disease. Here the authors demonstrate in vivo base editing of mouse mitochondrial DNA in a post-mitotic tissue by AAV delivery of DddA-derived cytosine base editor (DdCBE).
- Pedro Silva-Pinheiro
- , Pavel A. Nash
- & Michal Minczuk
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Article
| Open AccessGraph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
Increasing studies have suggested that single reference genome is insufficient to capture all variations in the genome. Here, the authors report a graph-based cucumber pan-genome by analyzing 12 chromosome-scale assemblies and reveal variations associated with agronomic traits and domestication.
- Hongbo Li
- , Shenhao Wang
- & Zhonghua Zhang
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Article
| Open AccessSignatures of selection in recently domesticated macadamia
Macadamia is a recently domesticated nut crop. Here, the authors report the genome assembly of Hawaiian cultivar ‘Kau’ and conduct population genomic analyses to reveal the origin of Hawaiian cultivars and the genomic basis for one-step operation for the clonal crop domestication.
- Jishan Lin
- , Wenping Zhang
- & Ray Ming
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Article
| Open AccessThe Chloranthus sessilifolius genome provides insight into early diversification of angiosperms
Chloranthales remain the last lineage of core angiosperms that lacks a nuclear genome assembly. Here, the authors report the genome assembly of Chloranthus sesilifolius and show that both hybridization and incomplete lineage sorting may have contributed to the phylogenetic incongruities in the literature.
- Jianxiang Ma
- , Pengchuan Sun
- & Yongzhi Yang
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Article
| Open AccessChromatin network retards nucleoli coalescence
Nuclear bodies are membraneless condensates that may form via liquid-liquid phase separation; however, they defy theoretical predictions where the equilibrium state should consist of a single droplet. Here the authors use a diploid human genome model parameterized with Hi-C data to simulate nucleoli formation. Their model suggests the chromatin network allows for existence of multiple droplets.
- Yifeng Qi
- & Bin Zhang
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Article
| Open AccessThe genetic architecture of DNA replication timing in human pluripotent stem cells
The genetic basis of how cells replicate their DNA is not well understood. Here, the authors identify >1000 genetic elements that control human replication and reveal a complex epigenetic system that regulates replication origin activities.
- Qiliang Ding
- , Matthew M. Edwards
- & Amnon Koren
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Article
| Open AccessStructural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation
Although many studies have characterized genetic variation in human populations, few have investigated structural variation and few have been in non-European populations. Here, the authors have performed long read sequencing on 405 Chinese individuals to identify structural variants and link them to phenotypes.
- Zhikun Wu
- , Zehang Jiang
- & Zhi Xie
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| Open AccessUnderwater CAM photosynthesis elucidated by Isoetes genome
Despite extensive characterization of crassulacean acid metabolism (CAM) in terrestrial angiosperms, little attention has been given to aquatics and early diverging land plants. Here, the authors assemble the genome of Isoetes taiwanensis and investigate the genetic factors driving CAM in this aquatic lycophyte.
- David Wickell
- , Li-Yaung Kuo
- & Fay-Wei Li
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Article
| Open AccessHuman cell based directed evolution of adenine base editors with improved efficiency
Application of adenine base editors (ABE) has been precluded by low activity. Here the authors show the generation of a human cell based ABE directional screening system and identification of ABE variant (NG-ABEmax-KR) exhibiting a significant increase in activity for human and mouse genome manipulation.
- Junhao Fu
- , Qing Li
- & Feng Gu
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| Open AccessCalibrated rare variant genetic risk scores for complex disease prediction using large exome sequence repositories
Identifying associations of rare variants with disease is challenging due to small effect sizes, technical artefacts and population structure heterogeneity. Here, the authors present RV-EXCALIBER, a method that uses large summary-level exome data to robustly calibrate rare variant burden.
- Ricky Lali
- , Michael Chong
- & Guillaume Paré
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Article
| Open AccessIncipient diploidization of the medicinal plant Perilla within 10,000 years
Perilla is a young allotetraploid species within the mint family Lamiaceae. Here, the authors assemble the genomes of a tetraploid species and its diploid progenitor, characterize the incipient diploidization of the tetraploid, conduct population genetics analyses, and identify loci associate with pigmentation and oil content.
- Yujun Zhang
- , Qi Shen
- & Shilin Chen
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| Open AccessFunctional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Identifying causal variants at GWAS loci is important to understand disease mechanisms. Here the authors use massively parallel reporter assays to identify type 2 diabetes-associated variants that alter cis-regulatory activity, narrowing in on the causal variants and genetic mechanisms behind the disease.
- Shubham Khetan
- , Susan Kales
- & Michael L. Stitzel
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| Open AccessFour chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding
Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.
- John T. Lovell
- , Nolan B. Bentley
- & Jennifer J. Randall
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Article
| Open AccessIdentification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton
Blue light penetrates deeper than red light in ocean, thus blue light sensing is critical for adaptation to marine environments. Here, the authors report the genome of Pyconococcus provasolii and identify a chimeric dual orange/far-red and blue light receptor composed of a phytochrome and a cryptochrome by analyzing the marine metagenomes.
- Yuko Makita
- , Shigekatsu Suzuki
- & Minami Matsui
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| Open AccessThe impact of chromosomal fusions on 3D genome folding and recombination in the germ line
How mammalian genomes are packaged and the heritability of structural variations in genome folding is incomplete. Here, the authors investigate the impact of chromosomal fusions on three-dimensional genome topology and meiotic recombination, highlighting the implications of large-scale genome reorganizations on genome function, evolution, and fertility.
- Covadonga Vara
- , Andreu Paytuví-Gallart
- & Aurora Ruiz-Herrera
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| Open AccessThe tepary bean genome provides insight into evolution and domestication under heat stress
In contrast to common bean, tepary bean is highly adapted to heat and drought. Here, the authors assemble the genomes of tepary bean landrace and wild accession, discuss the possible mechanism for resilience to heat stress, and reveal a reduced disease resistance gene repertoire.
- Samira Mafi Moghaddam
- , Atena Oladzad
- & Phillip E. McClean
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Article
| Open AccessIntegrative reconstruction of cancer genome karyotypes using InfoGenomeR
Karyotyping of cancer genomes at the base-level is technically challenging. Here, the authors introduce InfoGenomeR, an algorithm that can infer cancer genome karyotypes from whole-genome sequencing data, and test their model on breast, ovarian and brain cancer samples; and identify private and shared mutations between primary and metastatic cancer samples.
- Yeonghun Lee
- & Hyunju Lee
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Article
| Open AccessIdentifying therapeutic drug targets using bidirectional effect genes
Prioritising genes as potential drug targets is challenging and often unsuccessful once testing efficacy in humans. Here, the authors propose an approach to identifying drug targets that uses evidence from gain- or loss-of-function mutations associated with bidirectional effects on phenotypes.
- Karol Estrada
- , Steven Froelich
- & Lon R. Cardon
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Article
| Open AccessPopDel identifies medium-size deletions simultaneously in tens of thousands of genomes
Identifying structural variants (SVs) from whole genome sequence data has been a significant bioinformatic challenge. Here, the authors describe PopDel, which uses a joint SV detection approach to reliably and efficiently identify 500-10,000 bp deletions across large population cohorts.
- Sebastian Niehus
- , Hákon Jónsson
- & Birte Kehr
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| Open AccessComplete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation
Sequencing and mapping of long repetitive regions can be challenging due to technical difficulties in sequencing and assembly of the sequence data. Here authors report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe to reveal highly polymorphic and hot spots for genome variation features.
- Yusuke Oizumi
- , Takuto Kaji
- & Junko Kanoh
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Article
| Open AccessAlt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24
Many alternative ORFs are co-encoded with characterized proteins, but their function is often not understood. Here, the authors discover that ribosomal protein L36 is co-encoded with alternative protein, which they identify as an upstream regulator of PI3K-AKT-mTOR signaling.
- Xiongwen Cao
- , Alexandra Khitun
- & Sarah A. Slavoff
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Article
| Open AccessCohesin depleted cells rebuild functional nuclear compartments after endomitosis
The role of cohesin in organizing a functional nuclear architecture remains poorly understood. Here the authors show that cohesin depleted cells pass through endomitosis forming a multilobulated nucleus able to proceed through S-phase with typical features of active and inactive nuclear compartments and spatio-temporal patterns of replication domains.
- Marion Cremer
- , Katharina Brandstetter
- & Thomas Cremer
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Article
| Open AccessPopulation-scale study of eRNA transcription reveals bipartite functional enhancer architecture
Enhancer RNAs are transcribed bidirectionally from core transcription initiation regions. Here, by employing nascent RNA sequencing, the authors identify quantitative trait loci (QTLs) associated with enhancer RNA level and directionality, revealing the bipartite architecture of enhancers.
- Katla Kristjánsdóttir
- , Alexis Dziubek
- & Hojoong Kwak
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| Open AccessDominant subtype switch in avian influenza viruses during 2016–2019 in China
In this study, the authors present a genomic surveillance of avian influenza genomes sampled from live poultry markets in China. They report that a number of variants have emerged since 2016 that pose an increased risk to humans. They highlight the importance of continuous genome surveillance of circulating influenza strains.
- Yuhai Bi
- , Juan Li
- & Weifeng Shi
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Article
| Open AccessGenome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
Solanum pimpinellifolium (SP) is the progenitor of cultivated tomato and an important germplasm. Here, the authors assemble SP genome, identify structural variants (SVs) by comparing with modern cultivar, reveal SVs associated with important breeding traits, and detect SVs harboring master regulators of fruit quality traits.
- Xin Wang
- , Lei Gao
- & Zhangjun Fei
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| Open AccessGenome biology of the paleotetraploid perennial biomass crop Miscanthus
The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.
- Therese Mitros
- , Adam M. Session
- & Daniel S. Rokhsar
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| Open AccessDiversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints
Genebanks hold comprehensive collections of wild species, wild relatives, and landraces that are useful for genetic improvement. Here, the authors report the genotype of nearly 80,000 wheat accessions using DArTseq technology to show the less explored genetic diversity.
- Carolina Sansaloni
- , Jorge Franco
- & Kevin Pixley
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| Open AccessFonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate
Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.
- Michael Abrouk
- , Hanin Ibrahim Ahmed
- & Simon G. Krattinger
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Article
| Open AccessFastClone is a probabilistic tool for deconvoluting tumor heterogeneity in bulk-sequencing samples
Multiple algorithms exist for predicting heterogeneity and clonal architecture from the bulk sequencing of tumor tissue. Here, the authors report on an algorithm, FastClone, which was developed from a DREAM challenge and show that FastClone can accurately predict clonality in simulated data and data from colon cancer.
- Yao Xiao
- , Xueqing Wang
- & Yuanfang Guan
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Article
| Open AccessThe impact of transposable elements on tomato diversity
Transposable element insertion polymorphisms (TIPs) are a potential source of large effect alleles. Here, the authors use genome resequencing data for 602 tomato accessions together with transcriptomic and extensive phenotypic information to investigate the contribution of TIPs to tomato diversity.
- Marisol Domínguez
- , Elise Dugas
- & Leandro Quadrana
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Article
| Open AccessGenome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties
Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.
- Weiyi Zhang
- , Youjun Zhang
- & Weiwei Wen
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Article
| Open AccessEndogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia
Transposable elements are a potential source of transcriptional regulators, but how these sequences contribute to oncogenesis remains poorly understood. Here, the authors identify endogenous retroviruses (ERVs) with acute myeloid leukemia (AML)-associated enhancer chromatin signatures, and provide evidence that ERV activation provides an additional layer of gene regulation in AML.
- Özgen Deniz
- , Mamataz Ahmed
- & Miguel R. Branco
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Article
| Open AccessDiscovery and population genomics of structural variation in a songbird genus
Structural genomic variation can fuel evolution. Here, authors present genome data from seven Corvus species and unearth structural variants that vary between incipient crow species in Europe, with implications for premating isolation involving plumage patterning.
- Matthias H. Weissensteiner
- , Ignas Bunikis
- & Jochen B. W. Wolf
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Article
| Open AccessThe Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms
Available genomics studies have mostly focused on planktonic centric diatom. Here, the authors report the genome assembly of the marine biofilm-forming diatom Seminavis robusta and the resequencing data of a panel of accessions to reveal their evolutionary adaptations.
- Cristina Maria Osuna-Cruz
- , Gust Bilcke
- & Klaas Vandepoele
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Article
| Open AccessFunctional annotation of rare structural variation in the human brain
Structural variants (SVs) contribute to the genetic architecture of many brain-related disorders. Here, the authors integrate SV calls from genome sequencing (n = 755) with RNA-seq data (n = 629) from post-mortem dorsal lateral prefrontal cortex to annotate the gene regulatory effects of SVs in the human brain and their potential to contribute to disease.
- Lide Han
- , Xuefang Zhao
- & Douglas M. Ruderfer
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Article
| Open AccessLandscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes
Multi-nucleotide variants (MNV) are genetic variants in close proximity of each other on the same haplotype whose functional impact is difficult to predict if they reside in the same codon. Here, Wang et al. use the gnomAD dataset to assemble a catalogue of MNVs and estimate their global mutation rate.
- Qingbo Wang
- , Emma Pierce-Hoffman
- & Daniel G. MacArthur
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Article
| Open AccessChromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution
Horseshoe crabs have been morphologically stable across evolutionary time. Here, the authors generate a chromosome-level assembly for the mangrove horseshoe crab, with implications for innate immunity, and challenging assumptions about the role of genome duplication in adaptive radiation.
- Prashant Shingate
- , Vydianathan Ravi
- & Byrappa Venkatesh
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| Open AccessThe impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC
The genome of the malaria parasite Plasmodium falciparum contains a record of past evolutionary forces. Here, using 2537 parasite sequences from the Democratic Republic of the Congo, the authors demonstrate how drug pressure and human movement have shaped the present-day parasite population.
- Robert Verity
- , Ozkan Aydemir
- & Jonathan J. Juliano
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Article
| Open AccessHaplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
Taurine and indicine cattle have different desirable traits making them better adapted to different climates across the world. Here, Low et al. describe a pipeline to produce haplotype-resolved, chromosome-level genomes of Angus and Brahman cattle breeds from a crossbred individual and report on comparisons of the two genomes.
- Wai Yee Low
- , Rick Tearle
- & John L. Williams
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Article
| Open AccessSex chromosome evolution in parasitic nematodes of humans
Many nematode worms, including Caenorhabditis elegans have XX/XO sex determination, while other species have XY. The authors use a new genome assembly of the filarial parasite Brugia malayi and published data to show that nematode sex chromosome evolution is highly plastic.
- Jeremy M. Foster
- , Alexandra Grote
- & Elodie Ghedin
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Article
| Open AccessNuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans
Recent evidence has questioned the dogma of strict maternal transmission of mitochondrial DNA (mtDNA) in humans. Wei et al. saw no evidence of paternal transmission of mtDNA in 11,035 human trios, and show that nuclear-mitochondrial segments (NUMTs) can give the impression of paternal mtDNA transmission, but are actually inherited through the nuclear genome.
- Wei Wei
- , Alistair T. Pagnamenta
- & Patrick F. Chinnery