Featured
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| Open AccessAdaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events
Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.
- Guangji Chen
- , Dan Yu
- & Shaohong Feng
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Article
| Open AccessAllopolyploid origin and diversification of the Hawaiian endemic mints
Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage
- Crystal M. Tomlin
- , Sitaram Rajaraman
- & Charlotte Lindqvist
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Article
| Open AccessA chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution
Modern sugarcane cultivars have complicated genome due to interspecific crosses and multiple backcrossing. Here, the authors report the haplotype-resolved, chromosome-level genome assembly of a modern hybrid sugarcane cultivar and reveal the expansion of genes related to sugar accumulation and smut resistance.
- Yixue Bao
- , Qing Zhang
- & Muqing Zhang
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Article
| Open AccessA sequence-aware merger of genomic structural variations at population scale
Existing tools for structural variations (SVs) calling and merging often lead to fragmented SVs and the potential of introducing unnecessary errors. Here, the authors report the PanPop pipeline to address these issues by implementing sequence-aware SV merging algorithm to efficiently merge SVs of various types.
- Zeyu Zheng
- , Mingjia Zhu
- & Yongzhi Yang
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Article
| Open AccessMultiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family
Hyoscyamine and scopolamine (HS) are two tropane alkaloids with medicinal significance produced by distantly related lineages in the Solanaceae family. Here, the authors assemble the genome of three HS-producing and one non-HS-producing species within Solanaceae, and reveal the evolution of the biosynthetic pathway.
- Jiao Yang
- , Ying Wu
- & Jianquan Liu
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Article
| Open AccessMaternal dominance contributes to subgenome differentiation in allopolyploid fishes
Cyprinids fish species contain multiple subgenomes as a result of past duplications. Here, Xu et al. report new genomes of 21 cyprinid fish and conclude that observed subgenome dominance patterns are likely due to both maternal dominance and transposable element densities in each polyploid.
- Min-Rui-Xuan Xu
- , Zhen-Yang Liao
- & Hua-Hao Zhang
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Article
| Open AccessPolyethyleneimine-coated MXene quantum dots improve cotton tolerance to Verticillium dahliae by maintaining ROS homeostasis
Verticillum wilt is an important cotton disease caused by fungal pathogen Verticillium dahiae. Here, the authors assemble the genomes of defoliating and non-defoliating isolates of the pathogen, identify virulence gene SP3, and develop a disease control strategy using polyethyleneimine-coated MXene quantum dots.
- Ping Qiu
- , Jiayue Li
- & Longfu Zhu
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Article
| Open AccessDiagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms
Staphylococcus pseudintermedius has a wide host-range in domesticated and wild animals, yet it has also been isolated as an opportunistic pathogen in human wounds. In this work, the authors genotypically analyse S. pseudintermedius isolates from veterinary diagnostic laboratories and medical care centres, alongside household surfaces and inhabitants.
- Sanjam S. Sawhney
- , Rhiannon C. Vargas
- & Gautam Dantas
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Article
| Open AccessThe admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes
The brushtail possum is a treasured Australian marsupial, but also a harmful pest introduced into New Zealand. Here, using functional genomics and a new chromosome-level genome assembly of New Zealand possums, Bond et al. quantify their genome admixture and identify unique parent-specific and weaning associated gene expression.
- Donna M. Bond
- , Oscar Ortega-Recalde
- & Timothy A. Hore
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Article
| Open AccessDynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi
In the absence of recombination, the number of transposable elements (TEs) increases, but their accumulation dynamics are not well characterized. This study shows that TEs rapidly accumulated in non-recombining fungal mating-type chromosomes before reaching a plateau, possibly forming a TE reservoir.
- Marine Duhamel
- , Michael E. Hood
- & Tatiana Giraud
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Article
| Open AccessComparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus
Yellow-seed trait is preferred in rapeseed breeding as it can greatly improve seed oil yield and quality. Here, the authors assemble the genome of two rapeseed lines with yellow-seed and black-seed phenotypes, and clone an R2R3-MYB-type transcription factor encoding gene as a key regulator of seed color.
- Cunmin Qu
- , Meichen Zhu
- & Jiana Li
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Article
| Open AccessSubtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica
Resistance to herbicide glyphosate can be evolved trough copy number variation (CNV) of its target gene EPSPS in goosegrass. Here, the authors assemble the genomes of glyphosate susceptible and resistance lines and provide evidence of sub-telomeric-repeat driven CNV of EPSPS could lead to glyphosate resistance.
- Chun Zhang
- , Nicholas A. Johnson
- & Eric L. Patterson
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Article
| Open AccessEvolutionary genomics of camouflage innovation in the orchid mantis
Camouflage is a widespread phenomenon in nature, and the orchid mantis is a particularly striking example. Here the authors use evolutionary genomics to uncover the genetic mechanisms behind the colour and morphology that produce innovative camouflage in the orchid mantis and dead leaf mantis.
- Guangping Huang
- , Lingyun Song
- & Fuwen Wei
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Article
| Open AccessEpistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence
The virulence of extra-intestinal pathogenic Escherichia coli is associated with multiple different genes in different lineages. Here, Royer et al. show that the emergence of virulence is associated with acquisition of the siderophore-encoding high-pathogenicity island (HPI), and full virulence is associated with the additional presence of the aer or sit operons.
- Guilhem Royer
- , Olivier Clermont
- & Erick Denamur
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Article
| Open AccessGenomics of cold adaptations in the Antarctic notothenioid fish radiation
The notothenioid radiation is a remarkable group of fish adapted to life in the icy waters of the Southern Ocean. This study investigates the evolutionary history of this group and the basis of their adaption to cold environments through genomic analysis of 24 new genome assemblies.
- Iliana Bista
- , Jonathan M. D. Wood
- & Richard Durbin
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Article
| Open AccessOrigin of minicircular mitochondrial genomes in red algae
While the organelle genome is commonly considered to be a single circular DNA molecule, extensive variation exists. Here, the authors report multipartite minicircular genomes in red algae and indicate an origin driven by recombination due to loss of DNA replication, recombination, and repair genes.
- Yongsung Lee
- , Chung Hyun Cho
- & Hwan Su Yoon
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Article
| Open AccessDistinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms
Annelid worms have colonised extreme ecological niches, such as hydrothermal vents and whale falls thanks to symbiotic bacteria. This study finds that Osedax worms and the related Vestimentifera have evolved different genomic adaptations to sustain their bacterial symbioses and exploit different resources, such as decaying bone.
- Giacomo Moggioli
- , Balig Panossian
- & José M. Martín-Durán
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Article
| Open AccessThe in vivo measurement of replication fork velocity and pausing by lag-time analysis
Lag-time analysis was developed to measure in vivo replisome dynamics. Observed dynamics are both locus and cell-cycle dependent: Pauses of seconds are observed at wild-type ribosomal DNA loci, as well as temporal fork velocity oscillations.
- Dean Huang
- , Anna E. Johnson
- & Paul A. Wiggins
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Article
| Open AccessPan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Pan-genomes provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Here, the authors report a new rice pan-genome including 73 Asian rice and two wild relatives (Oryza rufipogon and O. punctata), and reveal the prevalence and scale of large inversions across the pan-genome.
- Yong Zhou
- , Zhichao Yu
- & Rod A. Wing
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Article
| Open AccessKey innovations and the diversification of Hymenoptera
Hymenoptera is an incredibly diverse order, with numerous behavioral and morphological innovations. Here, the authors compile a time-calibrated Hymenoptera phylogeny and find that secondary transitions to phytophagy, plant feeding, are associated with significant increases in diversification rate in this group.
- Bonnie B. Blaimer
- , Bernardo F. Santos
- & Matthew L. Buffington
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Article
| Open AccessGenomic attributes of Vibrio cholerae O1 responsible for 2022 massive cholera outbreak in Bangladesh
Vibrio cholerae has undergone continuous evolution, and differing strains have caused numerous outbreaks. Here, the authors present a genomic study of Vibrio cholerae O1 responsible for a 2022 outbreak in Dhaka.
- Md Mamun Monir
- , Mohammad Tarequl Islam
- & Munirul Alam
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Article
| Open AccessMicro and macroevolution of sea anemone venom phenotype
Venom is a complex trait with unresolved underlying toxin expression dynamics. Here, the authors compare expression across sea anemone species, revealing variation in dominant toxin diploid copy number across populations which generates distinct haplotypes.
- Edward G. Smith
- , Joachim M. Surm
- & Yehu Moran
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Article
| Open AccessGenome-wide signatures of adaptation to extreme environments in red algae
Extremophilic red algae have thrived in hot springs for more than a billion years. Here, the authors analyze chromosome-level assemblies from three red algal species, finding that horizontal gene transfer, subtelomeric gene duplication, and loss of genes or reduction in gene family size have supported key extremophilic adaptations.
- Chung Hyun Cho
- , Seung In Park
- & Hwan Su Yoon
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Article
| Open AccessBiosynthesis of mushroom-derived type II ganoderic acids by engineered yeast
The biosynthetic pathway of type II ganoderic acids (GAs) in Ganoderma lucidum, a traditional medicinal mushroom, is unknown. Here, the authors assemble the genome of type II GAs accumulating accession, identify CYPs involving in type II GAs biosynthesis, and achieve their production in engineered baker’s yeast.
- Wei Yuan
- , Chenjian Jiang
- & Han Xiao
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Article
| Open AccessHigh-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation
Tong et al. describe a super pangenome assembled from long-read sequences of 545 wild and domesticated silkworms. Naturally selected (diapause, aposemantic coloration) or artificially selected (silk yield and fineness) sets of genes are delineated.
- Xiaoling Tong
- , Min-Jin Han
- & Fangyin Dai
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Article
| Open AccessGenomic insights into rapid speciation within the world’s largest tree genus Syzygium
The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium.
- Yee Wen Low
- , Sitaram Rajaraman
- & Victor A. Albert
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Article
| Open AccessDelineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing
Mycobacterium abscessus is an emerging infection of increasing public health concern due to outbreaks and intrinsic multidrug-resistance. Here, the authors develop and evaluate a core-genome multilocus sequence typing scheme for this pathogen to facilitate standardised molecular surveillance.
- Margo Diricks
- , Matthias Merker
- & Florian P. Maurer
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Article
| Open AccessCombined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection
Patient variables, such as comorbidities, partially explain which patients will progress to Klebsiella infection, with colonization of the gut acting as a reservoir. Little is known, however, regarding Klebsiella genes that may increase risk of disease in colonized individuals. Here, authors conduct a comparative genomics study to identify genes associated with progression from colonisation to infection.
- Jay Vornhagen
- , Emily K. Roberts
- & Michael A. Bachman
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Article
| Open AccessMyriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes
Myriapods play an important ecological role in soil and forest ecosystems. Here the authors analyse nine myriapod genomes, showing rapid evolution of distinct genomic pathways in centipede and millipede lineages, shaped by differing ecological pressures.
- Wai Lok So
- , Wenyan Nong
- & Jerome H. L. Hui
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Article
| Open AccessLarge differences in carbohydrate degradation and transport potential among lichen fungal symbionts
Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. Here, Resl et al. show that, contrary to other fungal symbioses, fungal association with a phototroph in lichens does not result in loss of fungal enzymes for plant cell-wall degradation.
- Philipp Resl
- , Adina R. Bujold
- & Toby Spribille
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Article
| Open AccessPossible stochastic sex determination in Bursaphelenchus nematodes
In most species, sex is determined by genetic or environmental factors. Here, the authors present evidence that sex determination in Bursaphelenchus nematodes is instead likely to be regulated by a random, epigenetic mechanism.
- Ryoji Shinya
- , Simo Sun
- & Paul W. Sternberg
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Article
| Open AccessSystematic and quantitative view of the antiviral arsenal of prokaryotes
Bacteria and archaea have developed multiple antiviral mechanisms. Here, Tesson et al. present a tool that automatically detects known antiviral systems in prokaryotic genomes, and show that variations in antiviral strategies correlate with genome size, viral threat, and lifestyle traits.
- Florian Tesson
- , Alexandre Hervé
- & Aude Bernheim
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Article
| Open AccessDevelopmental mRNA m5C landscape and regulatory innovations of massive m5C modification of maternal mRNAs in animals
mRNAs are known to be decorated with m5C at a low-to-medium level. Here, the authors generate atlases of mRNA m5C during animal development in 6 species and identify convergent and unexpected massive methylation of maternal mRNAs by NSUN2 and NSUN6.
- Jianheng Liu
- , Tao Huang
- & Rui Zhang
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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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Article
| Open AccessChromosome evolution and the genetic basis of agronomically important traits in greater yam
While greater yam provides food and income security for millions of people around the world, there are limited genomic resources available. Here, the authors report a chromosome-scale assembly of the greater yam genome as well as quantitative trait loci associated with anthracnose resistance and tuber traits.
- Jessen V. Bredeson
- , Jessica B. Lyons
- & Daniel S. Rokhsar
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Article
| Open AccessAnopheles mosquitoes reveal new principles of 3D genome organization in insects
Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehensively characterize chromatin architecture and its evolutionary dynamics in five Anopheles species.
- Varvara Lukyanchikova
- , Miroslav Nuriddinov
- & Veniamin Fishman
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Article
| Open AccessReshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax
The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
- Zhen-Hui Wang
- , Xin-Feng Wang
- & Lin-Feng Li
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Article
| Open AccessRecurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots
Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes.
- Zhen Huang
- , Ivanete De O. Furo
- & Luohao Xu
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Comment
| Open AccessAusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic
The COVID-19 pandemic has accelerated the demand for near real-time analysis and dissemination of pathogen genomic data. In this comment, the authors describe how Australia has developed and rolled out its SARS-CoV-2 genomics platform, AusTrakka, and used it to support public health action.
- Tuyet Hoang
- , Anders Gonçalves da Silva
- & Torsten Seemann
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Article
| Open AccessGenomic insights into the evolution of Echinochloa species as weed and orphan crop
Echinochloa is an important genus in the grass family as many of them are either problematic weeds or domesticated millets. Here, the authors assemble three polyploidy genomes in this genus using the diploid-assisted scaffolding method DipHic and provide genomic insights into the dual roles of some species as weeds and orphan crops.
- Dongya Wu
- , Enhui Shen
- & Chu-Yu Ye
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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 AccessOptimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings
Vancomycin-resistant Enterococcus faecium is an important healthcare-associated pathogen and genomic analyses could inform targeted interventions. Here, the authors optimise an analysis pipeline for identification of putative transmission events using core genome multilocus sequence type clustering and split kmer analysis.
- Charlie Higgs
- , Norelle L. Sherry
- & Benjamin P. Howden
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Article
| Open AccessPolygenic contribution to the relationship of loneliness and social isolation with schizophrenia
Loneliness and social isolation (LNL-ISO) are associated with schizophrenia. Here the authors demonstrate the role of shared heritability, bidirectional causal relationships and significant differences by sex, illustrating the genomic footprint of social isolation on schizophrenia.
- Álvaro Andreu-Bernabeu
- , Covadonga M. Díaz-Caneja
- & Javier González-Peñas
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Article
| Open AccessMolecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer
Muntjac deer underwent rapid species radiation and dramatic chromosome fusions within a short period of time. Here the authors reveal that repeat sequences likely mediated illegitimate recombination to result in chromosome fusions and that 3D chromatin architecture around fusion sites have no significant change, while significant interactions across fusion sites were gradually established after speciation.
- Yuan Yin
- , Huizhong Fan
- & Fuwen Wei
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Article
| Open AccessThree chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway
Papaver species P. setigerum, P. rhoeas, and P. somniferum accumulates different levels of morphine and noscapine. Here, the authors report the improved genome assembly of P. somniferum and de novo assembly of the other two species, and reveal the evolution of the benzylisoquinoline alkaloids biosynthetic pathway.
- Xiaofei Yang
- , Shenghan Gao
- & Kai Ye
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Article
| Open AccessDNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans
Transposons are accepted as evolutionary catalysts but how they do so remains less clear. Analyzing 100 animal genomes finds that terminal inverted repeat-type transposable elements catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.
- Shengjun Tan
- , Huijing Ma
- & Yong E. Zhang
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Article
| Open AccessProfiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
Variable number tandem repeats (VNTRs) are difficult to analyze by short-read sequencing in disease studies. Here, the authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph. This method will help elucidate the contribution of VNTRs to diversity and disease.
- Tsung-Yu Lu
- , Katherine M. Munson
- & Mark J. P. Chaisson
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Article
| Open AccessA chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis
Camptothecin is a monoterpene indole alkaloid with anti-tumor activity. Here, the authors assemble the genome of the camptothecin producing plant Camptotheca acuminata and provide insights into the evolutionary origin of camptothecin biosynthesis by comparing to the vinblastine and vincristine biosynthetic pathway in Catharanthus roseus.
- Minghui Kang
- , Rao Fu
- & Jianquan Liu
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Article
| 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