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Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oraminense strains. DNA Res. (IF 4.1) Pub Date : 2023-11-11 Amanda Christine Ramdass,Sephra Nalini Rampersad
For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved
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Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome. DNA Res. (IF 4.1) Pub Date : 2023-10-01 Fernando Cruz,Jèssica Gómez-Garrido,Marta Gut,Tyler S Alioto,Joan Pons,Josep Alós,Margarida Barcelo-Serra
The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for
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Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes. DNA Res. (IF 4.1) Pub Date : 2023-10-01 Xianwei Yang,Yue Song,Rui Zhang,Mengjun Yu,Xinyu Guo,Haobing Guo,Xiao Du,Shuai Sun,Chunhua Li,Xuebin Mao,Guangyi Fan,Xin Liu
Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies
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Evolution of the viral genomes of SARS-CoV-2 in association with the changes in local condition: a genomic epidemiological study of a suburban city of Japan. DNA Res. (IF 4.1) Pub Date : 2023-10-01 Yukie Kashima,Taketoshi Mizutani,Yuki Okimoto,Minami Maeda,Kaoru Musashino,Ryo-Ichi Nishide,Akira Matsukura,Jison Nagase,Yutaka Suzuki
Understanding the factors driving the spread and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the local, regional, national, and international levels is important in protecting against future pandemics. By exploring their viral genomes, we attempted to analyse the spread of SARS-CoV-2 and its evolutionary convergence in Kashiwa City, as an example of a representative
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Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits. DNA Res. (IF 4.1) Pub Date : 2023-10-01 Suyu Zhang,Yue Song,Meiru Liu,Zengbao Yuan,Mengqi Zhang,He Zhang,Inge Seim,Guangyi Fan,Shanshan Liu,Xin Liu
Chaetodontidae, known as butterflyfishes, are typical fish in coral ecosystems, exhibiting remarkable interspecific differences including body colour patterns and feeding ecology. In this study, we report genomes of three butterflyfish species (Chelmon rostratus, Chaetodon trifasciatus and Chaetodon auriga) and a closely related species from the Pomacanthidae family, Centropyge bicolour, with an average
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GINGER: an integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level. DNA Res. (IF 4.1) Pub Date : 2023-08-01 Takeaki Taniguchi,Miki Okuno,Takahiro Shinoda,Fumiya Kobayashi,Kazuki Takahashi,Hideaki Yuasa,Yuta Nakamura,Hiroyuki Tanaka,Rei Kajitani,Takehiko Itoh
The prediction of gene structure within the genome sequence is the starting point of genome analysis, and its accuracy has a significant impact on the quality of subsequent analyses. Gene structure prediction is roughly divided into RNA-Seq-based methods, ab initio-based methods, homology-based methods, and the integration of individual prediction methods. Integrated methods are mainstream in recent
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Self-grafting-induced epigenetic changes leading to drought stress tolerance in tomato plants. DNA Res. (IF 4.1) Pub Date : 2023-08-01 Maria Isabel Fuentes-Merlos,Masaru Bamba,Shusei Sato,Atsushi Higashitani
Grafting is widely used as a method to increase stress tolerance in good fruiting lines of Solanaceae plants. However, little is known about how grafting, affects epigenetic modifications and leads to stress tolerance, especially within the same line. Here, we studied the effects of self-grafting in tomato plants on histone and DNA modifications and changes in gene expression related to drought stress
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Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma. DNA Res. (IF 4.1) Pub Date : 2023-08-01 Taiga Uchida,Yuki Yoshioka,Yu Yoshida,Manabu Fujie,Ayuta Yamaki,Akira Sasaki,Koji Inoue,Chuya Shinzato
Vestimentiferan tubeworms are representative members of deep-sea chemosynthetic ecosystems. In this study, we developed a draft genome and gene models and performed genomic and transcriptomic analyses of Lamellibrachia satsuma, the only vestimentiferan reported from the euphotic zone. The quality of the genome assembly and gene models is comparable to or higher than those of previously reported vestimentiferan
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Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community. DNA Res. (IF 4.1) Pub Date : 2023-06-01 Hiroshi Mori,Tamotsu Kato,Hiroaki Ozawa,Mitsuo Sakamoto,Takumi Murakami,Todd D Taylor,Atsushi Toyoda,Moriya Ohkuma,Ken Kurokawa,Hiroshi Ohno
To quantify the biases introduced during human gut microbiome studies, analyzing an artificial mock community as the reference microbiome is indispensable. However, there are still limited resources for a mock community which well represents the human gut microbiome. Here, we constructed a novel mock community comprising the type strains of 18 major bacterial species in the human gut and assessed the
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Genome assembly of the pioneer species Plantago major L. (Plantaginaceae) provides insight into its global distribution and adaptation to metal-contaminated soil. DNA Res. (IF 4.1) Pub Date : 2023-08-01 Shanwu Lyu,Qiming Mei,Hui Liu,Baosheng Wang,Jun Wang,Hans Lambers,Zhengfeng Wang,Bin Dong,Zhanfeng Liu,Shulin Deng
Plantago is a major genus belonging to the Plantaginaceae family and is used in herbal medicine, functional food, and pastures. Several Plantago species are also characterized by their global distribution, but the mechanism underpinning this is not known. Here, we present a high-quality, chromosome-level genome assembly of Plantago major L., a species of Plantago, by incorporating Oxford Nanopore sequencing
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Chromosome-level genome assembly of an endangered plant Prunus mongolica using PacBio and Hi-C technologies. DNA Res. (IF 4.1) Pub Date : 2023-08-01 Qiang Zhu,Yali Wang,Ning Yao,Xilu Ni,Cuiping Wang,Meng Wang,Lei Zhang,Wenyu Liang
Prunus mongolica is an ecologically and economically important xerophytic tree native to Northwest China. Here, we report a high-quality, chromosome-level P. mongolica genome assembly integrating PacBio high-fidelity sequencing and Hi-C technology. The assembled genome was 233.17 Mb in size, with 98.89% assigned to eight pseudochromosomes. The genome had contig and scaffold N50s of 24.33 Mb and 26
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Genome sequence and salinity adaptation of the desert shrub Nitraria sibirica (Nitrariaceae, Sapindales). DNA Res. (IF 4.1) Pub Date : 2023-05-11 Xiaohui Ma,Dafu Ru,Diego F Morales-Briones,Fengyuan Mei,Jingjing Wu,Jianquan Liu,Shengdan Wu
The genetic bases of halophytes for salinity tolerance are crucial for genetically breeding salt-tolerant crops. All natural Nitrariaceae species that exclusively occur in arid environments are highly tolerant to salt stress, but the underlying genomic bases to this adaptation remain unknown. Here we present a high-quality, chromosome-level genome sequence of Nitraria sibirica, with an assembled size
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Base-excision restriction enzymes: expanding the world of epigenetic immune systems. DNA Res. (IF 4.1) Pub Date : 2023-08-01 Kenji K Kojima,Ichizo Kobayashi
The restriction enzymes examined so far are phosphodiesterases, which cleave DNA strands by hydrolysing phosphodiester bonds. Based on the mobility of restriction-modification systems, recent studies have identified a family of restriction enzymes that excise a base in their recognition sequence to generate an abasic (AP) site unless the base is properly methylated. These restriction glycosylases also
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Detection of tandem repeats in the Capsicum annuum genome. DNA Res. (IF 4.1) Pub Date : 2023-04-25 Valentina Rudenko,Eugene Korotkov
In this study, we modified the multiple alignment method based on the generation of random position weight matrices (RPWM) and used it to search for tandem repeats (TRs) in the Capsicum annuum genome. The application of the modified (m)RPWM method, which considers the correlation of adjusting nucleotides, resulted in the identification of 908,072 TR regions with repeat lengths from 2 to 200 bp in the
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The genome sequence and demographic history of Przewalskia tangutica (Solanaceae), an endangered alpine plant on the Qinghai-Tibet Plateau. DNA Res. (IF 4.1) Pub Date : 2023-04-01 Ying Wu,Jiao Yang,Yongzhi Yang,Jianquan Liu
To adapt to high-altitude habitats, many alpine plants develop self-compatible breeding systems from outcrossing. The genetic bases for this shift and the resulting demographic consequences remain largely unexplored. Here, we present a high-quality, chromosome-level genome assembly of the monotypic and endangered alpine perennial Przewalskia tangutica (Solanaceae) occurring on the Qinghai-Tibet Plateau
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Chromosome-level genome assembly of the endangered plant Tetraena mongolica. DNA Res. (IF 4.1) Pub Date : 2023-04-01 Bingru Liu,Xiaoyu Zhao,Ziyin Wang,Huili Liu,Xueshuang Huang,Peng Yang
Tetraena mongolica is an endangered xerophytic shrub with high ecological value for the restoration of desert vegetation because of its high tolerance to drought and heat stress. Here, we generated a high-quality chromosome-level reference genome of T. mongolica by combining PacBio HiFi data and Hi-C sequencing technologies, which was approximately 1.12 Gb (contig N50 of 25.5 Mb) in size and contained
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Chromosome-level genome assembly of Phrynocephalus forsythii using third-generation DNA sequencing and Hi-C analysis. DNA Res. (IF 4.1) Pub Date : 2023-04-01 Yue Qi,Wei Zhao,Yangyang Zhao,Chenkai Niu,Shuhui Cao,Yingmei Zhang
Phrynocephalus forsythii is a viviparous sand lizard that is endemic to the Tarim Basin with a broad altitudinal range of 872-3,100 m. Such variation in altitude and ecological variables can offer an opportunity to uncover genetic mechanisms of ectothermic adaptation to extreme environments at high- and low-altitude. Furthermore, the evolutionary relationship of karyotype with two different chromosome
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A chromosome-level genome assembly of the Henosepilachna vigintioctomaculata provides insights into the evolution of ladybird beetles. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Wenbo Zhu,Shengqi Chi,Yanchun Wang,Haorong Li,Zhongkai Wang,Songdong Gu,Ting Sun,Hui Xiang,Ping You,Yandong Ren
The ladybird beetle Henosepilachna vigintioctomaculata is an economically significant oligophagous pest that induces damage to many Solanaceae crops. An increasing number of studies have examined the population and phenotype diversity of ladybird beetles. However, few comparative genome analyses of ladybird beetle species have been conducted. Here, we obtained a high-quality chromosome-level genome
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The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Yuuki Kobayashi,Tomoko F Shibata,Hideki Hirakawa,Tomoaki Nishiyama,Akiyoshi Yamada,Mitsuyasu Hasebe,Shuji Shigenobu,Masayoshi Kawaguchi
Mycorrhizae are one of the most fundamental symbioses between plants and fungi, with ectomycorrhizae being the most widespread in boreal forest ecosystems. Ectomycorrhizal fungi are hypothesized to have evolved convergently from saprotrophic ancestors in several fungal clades, especially members of the subdivision Agaricomycotina. Studies on fungal genomes have identified several typical characteristics
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Characterization of proteogenomic signatures of differentiation of CD4+ T cell subsets. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Toshio Kanno,Ryo Konno,Keisuke Miyako,Takahiro Nakajima,Satoru Yokoyama,Shigemi Sasamoto,Hikari K Asou,Junichiro Ohzeki,Yusuke Kawashima,Yoshinori Hasegawa,Osamu Ohara,Yusuke Endo
Functionally distinct CD4+ helper T (Th) cell subsets, including Th1, Th2, Th17, and regulatory T cells (Treg), play a pivotal role in the regulation of acquired immunity. Although the key proteins involved in the regulation of Th cell differentiation have already been identified how the proteogenomic landscape changes during the Th cell activation remains unclear. To address this issue, we characterized
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Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Congcong Dong,Shang Wang,Han Zhang,Jianquan Liu,Minjie Li
Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available
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Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Yoshinori Hasegawa,Takashi Watanabe,Reo Otsuka,Shigenobu Toné,Shin Kubota,Hideki Hirakawa
Only two hydromedusan species, Turritopsis dohrnii and T. sp., have exhibited experimental multiple-repeat life cycle reversion in the laboratory, which can be artificially induced by various means such as incubation with CsCl, heat shock, and mechanical damage with needles. In the present study, we constructed a genome assembly of T. dohrnii using Pacific Biosciences long-reads and Illumina short-reads
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The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Yu Ning,Yang Li,Shu Bin Dong,Hong Guo Yang,Chun Yi Li,Biao Xiong,Jun Yang,Yu Kun Hu,Xian Yun Mu,Xiao Fei Xia
Kobresia species are common in meadows on the Qinghai-Tibet Plateau. They are important food resources for local livestock, and serve a critical foundation for ecosystem integration. Genetic resources of Kobresia species are scarce. Here, we generated a chromosome-level genome assembly for K. myosuroides (Cyperaceae), using PacBio long-reads, Illumina short-reads, and Hi-C technology. The final assembly
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Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Hengchao Wang,Dong Xu,Sen Wang,Anqi Wang,Lihong Lei,Fan Jiang,Boyuan Yang,Lihua Yuan,Rong Chen,Yan Zhang,Wei Fan
Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first reference genome for the subgenus Albersia, combining PacBio HiFi, Nanopore ultra-long and Hi-C data. The
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The methanogen core and pangenome: conservation and variability across biology's growth temperature extremes. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Paula Prondzinsky,Sakae Toyoda,Shawn Erin McGlynn
Temperature is a key variable in biological processes. However, a complete understanding of biological temperature adaptation is lacking, in part because of the unique constraints among different evolutionary lineages and physiological groups. Here we compared the genomes of cultivated psychrotolerant and thermotolerant methanogens, which are physiologically related and span growth temperatures from
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Correction to: The genome of Prunus humilis provides new insights to drought adaption and population diversity. DNA Res. (IF 4.1) Pub Date : 2022-12-01
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Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Amit Rai,Hideki Hirakawa,Megha Rai,Yohei Shimizu,Kenta Shirasawa,Shinji Kikuchi,Hikaru Seki,Mami Yamazaki,Atsushi Toyoda,Sachiko Isobe,Toshiya Muranaka,Kazuki Saito
A high-quality genome assembly is imperative to explore the evolutionary basis of characteristic attributes that define chemotype and provide essential resources for a molecular breeding strategy for enhanced production of medicinal metabolites. Here, using single-molecule high-fidelity (HiFi) sequencing reads, we report chromosome-scale genome assembly for Chinese licorice (Glycyrrhiza uralensis)
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A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Takeshi Takeuchi,Yoshihiko Suzuki,Shugo Watabe,Kiyohito Nagai,Tetsuji Masaoka,Manabu Fujie,Mayumi Kawamitsu,Noriyuki Satoh,Eugene W Myers
Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes
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A chromosomal-scale reference genome of the New World Screwworm, Cochliomyia hominivorax. DNA Res. (IF 4.1) Pub Date : 2023-02-01 Sophie Tandonnet,Flavia Krsticevic,Tatiana Basika,Philippos A Papathanos,Tatiana T Torres,Maxwell J Scott
The New World Screwworm, Cochliomyia hominivorax (Calliphoridae), is the most important myiasis-causing species in America. Screwworm myiasis is a zoonosis that can cause severe lesions in livestock, domesticated and wild animals, and occasionally in people. Beyond the sanitary problems associated with this species, these infestations negatively impact economic sectors, such as the cattle industry
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Improved assembly and annotation of the sesame genome. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Mingcheng Wang,Jianwei Huang,Song Liu,Xiaofeng Liu,Rui Li,Junjia Luo,Zhixi Fu
Sesame (Sesamum indicum L.) is an important oilseed crop that produces abundant seed oil and has a pleasant flavor and high nutritional value. To date, several Illumina-based genome assemblies corresponding to different sesame genotypes have been published and widely used in genetic and genomic studies of sesame. However, these assemblies consistently showed low continuity with numerous gaps. Here
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De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Kenta Shirasawa,Hideki Hirakawa,Akifumi Azuma,Fumiya Taniguchi,Toshiya Yamamoto,Akihiko Sato,Andrea Ghelfi,Sachiko N Isobe
The first genome sequence of an interspecific grape hybrid (Vitis labruscana × Vitis vinifera), 'Shine Muscat', an elite table grape cultivar bred in Japan, is presented. The resultant genome assemblies included two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a 'pseudo-haploid' genome. The unphased sequences, assembled to
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Assembly-free discovery of human novel sequences using long reads. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Qiuhui Li,Bin Yan,Tak-Wah Lam,Ruibang Luo
DNA sequences that are absent in the human reference genome are classified as novel sequences. The discovery of these missed sequences is crucial for exploring the genomic diversity of populations and understanding the genetic basis of human diseases. However, various DNA lengths of reads generated from different sequencing technologies can significantly affect the results of novel sequences. In this
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Rapid transcriptomic and physiological changes in the freshwater pennate diatom Mayamaea pseudoterrestris in response to copper exposure. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Shigekatsu Suzuki,Shuhei Ota,Takahiro Yamagishi,Akihiro Tuji,Haruyo Yamaguchi,Masanobu Kawachi
Diatoms function as major primary producers, accumulating large amounts of biomass in most aquatic environments. Given their rapid responses to changes in environmental conditions, diatoms are used for the biological monitoring of water quality and for performing ecotoxicological tests in aquatic ecosystems. However, the molecular basis for their toxicity to chemical compounds remains largely unknown
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De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Tao Zhou,Guoqing Bai,Yiheng Hu,Markus Ruhsam,Yanci Yang,Yuemei Zhao
Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was ~1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes
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Chromosome-level genome of a leaf vegetable Glebionis coronaria provides insights into the biosynthesis of monoterpenoids contributing to its special aroma. DNA Res. (IF 4.1) Pub Date : 2022-12-01 Sen Wang,Anqi Wang,Hengchao Wang,Fan Jiang,Dong Xu,Wei Fan
Glebionis coronaria is a popular vegetable with special aroma and a medical plant in East Asia and Mediterranean, but its biological studies and breeding have been hindered by the lack of reference genome. Here, we present a chromosome-level reference genome of G. coronaria, with assembled genome size of 6.8 Gb, which is the largest among all the published genomes of diploid Asteraceae species. The
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Comprehensive analysis of 124 transcriptomes from 31 tissues in developing, juvenile, and adult Japanese Black cattle. DNA Res. (IF 4.1) Pub Date : 2022-08-23 Taichi Arishima,Hiroyuki Wakaguri,Ryotaro Nakashima,Seigo Sakakihara,Keisuke Kawashima,Yoshikazu Sugimoto,Yutaka Suzuki,Shinji Sasaki
Omic analyses of economically important animals, including Japanese Black cattle, are currently underway worldwide. In particular, tissue and developmental stage-specific transcriptome characterization is essential for understanding the molecular mechanisms underlying the phenotypic expression of genetic disorders and economic traits. Here, we conducted a comprehensive analysis of 124 transcriptomes
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Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea. DNA Res. (IF 4.1) Pub Date : 2022-08-23 Wanapinun Nawae,Chutima Sonthirod,Thippawan Yoocha,Pitchaporn Waiyamitra,Pipat Soisook,Sithichoke Tangphatsornruang,Wirulda Pootakham
Bats (Chiroptera) constitute the second largest order of mammals and have several distinctive features, such as true self-powered flight and strong immunity. The Pendlebury's roundleaf bat, Hipposideros pendleburyi, is endemic to Thailand and listed as a vulnerable species. We employed the 10× Genomics linked-read technology to obtain a genome assembly of H. pendleburyi. The assembly size was 2.17 Gb
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Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping. DNA Res. (IF 4.1) Pub Date : 2022-08-23 Daisuke Sekine,Satoshi Oku,Tsukasa Nunome,Hideki Hirakawa,Mai Tsujimura,Toru Terachi,Atsushi Toyoda,Masayoshi Shigyo,Shusei Sato,Hikaru Tsukazaki
Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping
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Chromosomal-level genome of velvet bean (Mucuna pruriens) provides resources for L-DOPA synthetic research and development. DNA Res. (IF 4.1) Pub Date : 2022-08-23 Shijie Hao,Qijin Ge,Yunchang Shao,Benqin Tang,Guangyi Fan,Canyu Qiu,Xue Wu,Liangwei Li,Xiaochuan Liu,Chengcheng Shi,Simon Ming-Yuen Lee
Mucuna pruriens, commonly called velvet bean, is the main natural source of levodopa (L-DOPA), which has been marketed as a psychoactive drug for the clinical management of Parkinson's disease and dopamine-responsive dystonia. Although velvet bean is a very important plant species for food and pharmaceutical manufacturing, the lack of genetic and genomic information about this species severely hinders
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Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana. DNA Res. (IF 4.1) Pub Date : 2022-08-23 Changjuan Mo,Zhengdan Wu,Xiaohong Shang,Pingli Shi,Minghua Wei,Haiyan Wang,Liang Xiao,Sheng Cao,Liuying Lu,Wendan Zeng,Huabing Yan,Qiusheng Kong
Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana
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Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Ruksana Aziz,Piyali Sen,Pratyush Kumar Beura,Saurav Das,Debapriya Tula,Madhusmita Dash,Nima Dondu Namsa,Ramesh Chandra Deka,Edward J Feil,Siddhartha Sankar Satapathy,Suvendra Kumar Ray
A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates
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Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Andi Madihah Manggabarani,Takuyu Hashiguchi,Masatsugu Hashiguchi,Atsushi Hayashi,Masataka Kikuchi,Yusdar Mustamin,Masaru Bamba,Kunihiro Kodama,Takanari Tanabata,Sachiko Isobe,Hidenori Tanaka,Ryo Akashi,Akihiro Nakaya,Shusei Sato
As soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (G×E). To achieve this goal, we conducted the field experiments
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BLSSpeller to discover novel regulatory motifs in maize. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Razgar Seyed Rahmani,Dries Decap,Jan Fostier,Kathleen Marchal
With the decreasing cost of sequencing and availability of larger numbers of sequenced genomes, comparative genomics is becoming increasingly attractive to complement experimental techniques for the task of transcription factor (TF) binding site identification. In this study, we redesigned BLSSpeller, a motif discovery algorithm, to cope with larger sequence datasets. BLSSpeller was used to identify
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High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Curtis R Carlson,Anneliek M Ter Horst,J Spencer Johnston,Elizabeth Henry,Bryce W Falk,Yen-Wen Kuo
The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Presently, few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high-quality, chromosome-scale genome assemblies of
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Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Chuankun Zhu,Haiyang Liu,Zhengjun Pan,Lei Cheng,Yanhong Sun,Hui Wang,Guoliang Chang,Nan Wu,Huaiyu Ding,Haitao Zhao,Lei Zhang,Xiangsheng Yu
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54%
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Chromosome-level genome of Tibetan naked carp (Gymnocypris przewalskii) provides insights into Tibetan highland adaptation. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Fei Tian,Sijia Liu,Bingzheng Zhou,Yongtao Tang,Yu Zhang,Cunfang Zhang,Kai Zhao
Gymnocypris przewalskii, a cyprinid fish endemic to the Qinghai-Tibetan Plateau, has evolved unique morphological, physiological and genetic characteristics to adapt to the highland environment. Herein, we assembled a high-quality G. przewalskii tetraploid genome with a size of 2.03 Gb and scaffold N50 of 44.93 Mb, which was anchored onto 46 chromosomes. The comparative analysis suggested that gene
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Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Jing-Shan Yang,Zhi-Hao Qian,Tao Shi,Zhi-Zhong Li,Jin-Ming Chen
Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of ∼ 520 Mb. More than half of the N. indica genome
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The genome of Prunus humilis provides new insights to drought adaption and population diversity. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Yi Wang,Jun Xie,Hongna Zhang,Weidong Li,Zhanjun Wang,Huayang Li,Qian Tong,Gaixia Qiao,Yujuan Liu,Ying Tian,Yongzan Wei,Ping Li,Rong Wang,Weiping Chen,Zhengchang Liang,Meilong Xu
Prunus humilis (2n = 2x = 16) is a dwarf shrub fruit tree native to China and distributed widely in the cold and arid northern region. In this study, we obtained the whole genome sequences of P. humilis by combining Illumina, PacBio and HiC sequencing technologies. This genome was 254.38 Mb long and encodes 28,301 putative proteins. Phylogenetic analysis indicated that P. humilis shares the same ancestor
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Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica. DNA Res. (IF 4.1) Pub Date : 2022-06-25 Takumi Kamiyama,Yuko Shimada-Niwa,Hiroyuki Tanaka,Minami Katayama,Takayoshi Kuwabara,Hitoha Mori,Akari Kunihisa,Takehiko Itoh,Atsushi Toyoda,Ryusuke Niwa
Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic
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Environmental DNA analysis for macro-organisms: species distribution and more. DNA Res. (IF 4.1) Pub Date : 2022-05-27 Toshifumi Minamoto
In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive
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Universal Surface Biotinylation: a simple, versatile and cost-effective sample multiplexing method for single-cell RNA-seq analysis. DNA Res. (IF 4.1) Pub Date : 2022-05-27 Michihiko Sugimoto,Yuhki Tada,Shigeyuki Shichino,Saeko Koyamatsu,Noriyuki Tsumaki,Kuniya Abe
Recent advances in single-cell analysis technology have made it possible to analyse tens of thousands of cells at a time. In addition, sample multiplexing techniques, which allow the analysis of several types of samples in a single run, are very useful for reducing experimental costs and improving experimental accuracy. However, a problem with this technique is that antigens and antibodies for universal
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Inventory of ATP-binding cassette proteins in Lithospermum erythrorhizon as a model plant producing divergent secondary metabolites. DNA Res. (IF 4.1) Pub Date : 2022-05-27 Hao Li,Hinako Matsuda,Ai Tsuboyama,Ryosuke Munakata,Akifumi Sugiyama,Kazufumi Yazaki
ATP-binding cassette (ABC) proteins are the largest membrane transporter family in plants. In addition to transporting organic substances, these proteins function as ion channels and molecular switches. The development of multiple genes encoding ABC proteins has been associated with their various biological roles. Plants utilize many secondary metabolites to adapt to environmental stresses and to communicate
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Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production. DNA Res. (IF 4.1) Pub Date : 2022-05-27 Junya Yamamoto,Onuma Chumsakul,Yoshihiro Toya,Takuya Morimoto,Shenghao Liu,Kenta Masuda,Yasushi Kageyama,Takashi Hirasawa,Fumio Matsuda,Naotake Ogasawara,Hiroshi Shimizu,Ken-Ichi Yoshida,Taku Oshima,Shu Ishikawa
Partial bacterial genome reduction by genome engineering can improve the productivity of various metabolites, possibly via deletion of non-essential genome regions involved in undesirable metabolic pathways competing with pathways for the desired end products. However, such reduction may cause growth defects. Genome reduction of Bacillus subtilis MGB874 increases the productivity of cellulases and
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A chromosome-level genome assembly of the pollinating fig wasp Valisia javana. DNA Res. (IF 4.1) Pub Date : 2022-05-27 Lianfu Chen,Chao Feng,Rong Wang,Xiaojue Nong,Xiaoxia Deng,Xiaoyong Chen,Hui Yu
Fig wasp has always been thought the species-specific pollinator for their host fig (Moraceae, Ficus) and constitute a model system with its host to study co-evolution and co-speciation. The availability of a high-quality genome will help to further reveal the mechanisms underlying these characteristics. Here, we present a high-quality chromosome-level genome for Valisa javana developed by a combination
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Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad. DNA Res. (IF 4.1) Pub Date : 2022-05-27 Hans Christoph Liedtke,Fernando Cruz,Jèssica Gómez-Garrido,Diego Fuentes Palacios,Marina Marcet-Houben,Marta Gut,Tyler Alioto,Toni Gabaldón,Ivan Gomez-Mestre
Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened group of vertebrates, present a vast diversity in reproductive modes, are extremely diverse in morphology, occupy most ecoregions of the world, and present the widest range in genome
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Chromosome-level genome assembly and characterization of Sophora Japonica. DNA Res. (IF 4.1) Pub Date : 2022-05-27 Weixiao Lei,Zefu Wang,Man Cao,Hui Zhu,Min Wang,Yi Zou,Yunchun Han,Dandan Wang,Zeyu Zheng,Ying Li,Bingbing Liu,Dafu Ru
Sophora japonica is a medium-size deciduous tree belonging to Leguminosae family and famous for its high ecological, economic and medicinal value. Here, we reveal a draft genome of S. japonica, which was ∼511.49 Mb long (contig N50 size of 17.34 Mb) based on Illumina, Nanopore and Hi-C data. We reliably assembled 110 contigs into 14 chromosomes, representing 91.62% of the total genome, with an improved
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Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex. DNA Res. (IF 4.1) Pub Date : 2022-02-27 Verónica Mixão,Valentina Del Olmo,Eva Hegedűsová,Ester Saus,Leszek Pryszcz,Andrea Cillingová,Jozef Nosek,Toni Gabaldón
Candida parapsilosis species complex comprises three important pathogenic species: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis. The majority of C. orthopsilosis and all C. metapsilosis isolates sequenced thus far are hybrids, and most of the parental lineages remain unidentified. This led to the hypothesis that hybrids with pathogenic potential were formed by
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Chromosomal-level genome assembly of the orchid tree Bauhinia variegata (Leguminosae; Cercidoideae) supports the allotetraploid origin hypothesis of Bauhinia. DNA Res. (IF 4.1) Pub Date : 2022-02-27 Yan Zhong,Yong Chen,Danjing Zheng,Jingyi Pang,Ying Liu,Shukai Luo,Shiyuan Meng,Lei Qian,Dan Wei,Seping Dai,Renchao Zhou
Cercidoideae, one of the six subfamilies of Leguminosae, contains one genus Cercis with its chromosome number 2n = 14 and all other genera with 2n = 28. An allotetraploid origin hypothesis for the common ancestor of non-Cercis genera in this subfamily has been proposed; however, no chromosome-level genomes from Cercidoideae have been available to test this hypothesis. Here, we conducted a chromosome-level
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MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.). DNA Res. (IF 4.1) Pub Date : 2022-02-27 Kazusa Nishimura,Ko Motoki,Akira Yamazaki,Rihito Takisawa,Yasuo Yasui,Takashi Kawai,Koichiro Ushijima,Ryohei Nakano,Tetsuya Nakazaki
MIG-seq (Multiplexed inter-simple sequence repeats genotyping by sequencing) has been developed as a low cost genotyping technology, although the number of polymorphisms obtained is assumed to be minimal, resulting in the low application of this technique to analyses of agricultural plants. We applied MIG-seq to 12 plant species that include various crops and investigated the relationship between genome
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The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis. DNA Res. (IF 4.1) Pub Date : 2022-02-27 Ting Li,Xi Yu,Yumeng Ren,Minghui Kang,Wenjie Yang,Landi Feng,Quanjun Hu
Gentiana dahurica Fisch. is a perennial herb of the family Gentianaceae. This species is used as a traditional Tibetan medicine because of its rich gentiopicroside constituents. Here, we generate a high-quality, chromosome-level genome of G. dahurica with a total length of 1,416.54 Mb. Comparative genomic analyses showed that G. dahurica shared one whole-genome duplication (WGD) event with Gelsemium