DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes最新文献_第2页

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake) 松茸(口蘑)端粒-端粒基因组组装的研究

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-07-25 DOI: 10.1101/2022.07.25.501483

Hiroyuki Kurokochi, Naoyuki Tajima, Mitsuhiko P. Sato, K. Yoshitake, S. Asakawa, S. Isobe, K. Shirasawa

{"title":"Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)","authors":"Hiroyuki Kurokochi, Naoyuki Tajima, Mitsuhiko P. Sato, K. Yoshitake, S. Asakawa, S. Isobe, K. Shirasawa","doi":"10.1101/2022.07.25.501483","DOIUrl":"https://doi.org/10.1101/2022.07.25.501483","url":null,"abstract":"Here, we report the first telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake), which consists of 13 chromosomes (spanning 160.7 Mb) and a 76 kb circular mitochondrial genome. The chromosome sequences were supported with telomeric repeats at the ends. GC-rich regions are located at the middle of the chromosomes and are enriched with long interspersed nuclear elements (LINEs). Repetitive sequences including long-terminal repeats (LTRs) and LINEs occupy 71.7% of the genome. A total of 28,322 potential protein-coding genes and 324 tRNA genes were predicted. Sequence and structure variant analysis revealed 2,322,349 single nucleotide polymorphisms and 102,831 insertions and deletions, 0.6% of which disrupted gene structure and function and were therefore classified as deleterious mutations. As many as 683 copies of the LTR retrotransposon MarY1 were detected in the matsutake genome, 91 of which were inserted in gene sequences. In addition, 187 sequence variations were found in the mitochondrial genome. The genomic data reported in this study would serve as a great reference for exploring the genetics and genomics of matsutake in the future, and the information gained would ultimately facilitate the conservation of this vulnerable genetic resource.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73031896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

BLSSpeller to discover novel regulatory motifs in maize. BLSSpeller发现玉米中新的调控基序。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-25 DOI: 10.1093/dnares/dsac029

Razgar Seyed Rahmani, Dries Decap, Jan Fostier, Kathleen Marchal

{"title":"BLSSpeller to discover novel regulatory motifs in maize.","authors":"Razgar Seyed Rahmani, Dries Decap, Jan Fostier, Kathleen Marchal","doi":"10.1093/dnares/dsac029","DOIUrl":"https://doi.org/10.1093/dnares/dsac029","url":null,"abstract":"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 novel motifs in Zea mays in a comparative genomics setting with 16 monocot lineages. We discovered 61 motifs of which 20 matched previously described motif models in Arabidopsis. In addition, novel, yet uncharacterized motifs were detected, several of which are supported by available sequence-based and/or functional data. Instances of the predicted motifs were enriched around transcription start sites and contained signatures of selection. Moreover, the enrichment of the predicted motif instances in open chromatin and TF binding sites indicates their functionality, supported by the fact that genes carrying instances of these motifs were often found to be co-expressed and/or enriched in similar GO functions. Overall, our study unveiled several novel candidate motifs that might help our understanding of the genotype to phenotype association in crops.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/25/74/dsac029.PMC9358016.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40667064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome of Tibetan naked carp (Gymnocypris przewalskii) provides insights into Tibetan highland adaptation. 青藏裸鱼(gymnocyis przewalskii)染色体水平基因组为青藏高原适应性研究提供了新的思路。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-25 DOI: 10.1093/dnares/dsac025

Fei Tian, Sijia Liu, Bingzheng Zhou, Yongtao Tang, Yu Zhang, Cunfang Zhang, Kai Zhao

{"title":"Chromosome-level genome of Tibetan naked carp (Gymnocypris przewalskii) provides insights into Tibetan highland adaptation.","authors":"Fei Tian, Sijia Liu, Bingzheng Zhou, Yongtao Tang, Yu Zhang, Cunfang Zhang, Kai Zhao","doi":"10.1093/dnares/dsac025","DOIUrl":"https://doi.org/10.1093/dnares/dsac025","url":null,"abstract":"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 families related to highland adaptation were significantly expanded in G. przewalskii. According to the G. przewalskii genome, we evaluated the phylogenetic relationship of 13 schizothoracine fishes, and inferred that the demographic history of G. przewalskii was strongly associated with geographic and eco-environmental alterations. We noticed that G. przewalskii experienced whole-genome duplication, and genes preserved post duplication were functionally associated with adaptation to high salinity and alkalinity. In conclusion, a chromosome-scale G. przewalskii genome provides an important genomic resource for teleost fish, and will particularly promote our understanding of the molecular evolution and speciation of fish in the highland environment.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40622595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations. 高质量，染色体规模基因组组装:三个柑橘木虱(亚洲柑橘木虱)地理种群的比较。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-25 DOI: 10.1093/dnares/dsac027

Curtis R Carlson, Anneliek M Ter Horst, J Spencer Johnston, Elizabeth Henry, Bryce W Falk, Yen-Wen Kuo

{"title":"High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations.","authors":"Curtis R Carlson, Anneliek M Ter Horst, J Spencer Johnston, Elizabeth Henry, Bryce W Falk, Yen-Wen Kuo","doi":"10.1093/dnares/dsac027","DOIUrl":"https://doi.org/10.1093/dnares/dsac027","url":null,"abstract":"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 D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules-a reduction in assembly size of 41-45% compared with previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and annotated each assembly for repetitive elements, protein-coding genes, transfer RNAs, ribosomal RNAs, piwi-interacting RNA clusters, and endogenous viral elements. Between 19,083 and 20,357 protein-coding genes were predicted. Repetitive DNA accounts for 36.87-38.26% of each assembly. Comparative analyses and mitochondrial haplotype networks suggest that Taiwan and Uruguay D. citri are more closely related, while California D. citri are closely related to Florida D. citri. These high-quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/64/0c/dsac027.PMC9338690.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40528933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons. 结合过渡到翻转比和无义突变，改进了密码子中同义和非同义位点数量的估计。

IF 4.1

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-25 DOI: 10.1093/dnares/dsac023

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

{"title":"Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons.","authors":"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","doi":"10.1093/dnares/dsac023","DOIUrl":"https://doi.org/10.1093/dnares/dsac023","url":null,"abstract":"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 and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2022-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9358017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40688407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica 拟内寄生蜂Asobara japonica全基因组测序分析及RNA干扰方案

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-10 DOI: 10.1093/dnares/dsac019

Takumi Kamiyama, Yuko Shimada-Niwa, Hiroyuki Tanaka, M. Katayama, Takayoshi Kuwabara, Hitoha Mori, A. Kunihisa, T. Itoh, A. Toyoda, R. Niwa

{"title":"Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica","authors":"Takumi Kamiyama, Yuko Shimada-Niwa, Hiroyuki Tanaka, M. Katayama, Takayoshi Kuwabara, Hitoha Mori, A. Kunihisa, T. Itoh, A. Toyoda, R. Niwa","doi":"10.1093/dnares/dsac019","DOIUrl":"https://doi.org/10.1093/dnares/dsac019","url":null,"abstract":"Abstract 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 lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75317345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Environmental DNA analysis for macro-organisms: species distribution and more 大型生物的环境DNA分析:物种分布等

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-06-01 DOI: 10.1093/dnares/dsac018

T. Minamoto

{"title":"Environmental DNA analysis for macro-organisms: species distribution and more","authors":"T. Minamoto","doi":"10.1093/dnares/dsac018","DOIUrl":"https://doi.org/10.1093/dnares/dsac018","url":null,"abstract":"Abstract 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 and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81986643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production 全球调节因子AbrB的组成性表达恢复了基因组减少的枯草芽孢杆菌菌株的生长缺陷，并提高了其代谢物的产量

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-05-24 DOI: 10.1093/dnares/dsac015

Junya Yamamoto, O. Chumsakul, Yoshihiro Toya, T. Morimoto, Shenghao Liu, K. Masuda, Y. Kageyama, T. Hirasawa, Fumio Matsuda, N. Ogasawara, H. Shimizu, Ken-Ichi Yoshida, T. Oshima, S. Ishikawa

{"title":"Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production","authors":"Junya Yamamoto, O. Chumsakul, Yoshihiro Toya, T. Morimoto, Shenghao Liu, K. Masuda, Y. Kageyama, T. Hirasawa, Fumio Matsuda, N. Ogasawara, H. Shimizu, Ken-Ichi Yoshida, T. Oshima, S. Ishikawa","doi":"10.1093/dnares/dsac015","DOIUrl":"https://doi.org/10.1093/dnares/dsac015","url":null,"abstract":"Abstract 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 proteases but reduces their growth rate. Here, we show that this growth defect could be restored by silencing redundant or less important genes affecting exponential growth by manipulating the global transcription factor AbrB. Comparative transcriptome analysis revealed that AbrB-regulated genes were upregulated and those involved in central metabolic pathway and synthetic pathways of amino acids and purine/pyrimidine nucleotides were downregulated in MGB874 compared with the wild-type strain, which we speculated were the cause of the growth defects. By constitutively expressing high levels of AbrB, AbrB regulon genes were repressed, while glycolytic flux increased, thereby restoring the growth rate to wild-type levels. This manipulation also enhanced the productivity of metabolites including γ-polyglutamic acid. This study provides the first evidence that undesired features induced by genome reduction can be relieved, at least partly, by manipulating a global transcription regulation system. A similar strategy could be applied to other genome engineering-based challenges aiming toward efficient material production in bacteria.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83222699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad 西部掌足蟾蜍的染色体水平组装、注释和分类

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-05-18 DOI: 10.1093/dnares/dsac013

H. C. Liedtke, F. Cruz, J. Gómez-Garrido, Diego Fuentes Palacios, M. Marcet-Houben, M. Gut, T. Alioto, T. Gabaldón, I. Gomez‐Mestre

{"title":"Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad","authors":"H. C. Liedtke, F. Cruz, J. Gómez-Garrido, Diego Fuentes Palacios, M. Marcet-Houben, M. Gut, T. Alioto, T. Gabaldón, I. Gomez‐Mestre","doi":"10.1093/dnares/dsac013","DOIUrl":"https://doi.org/10.1093/dnares/dsac013","url":null,"abstract":"Abstract 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 sizes of any major group of vertebrates. We combined Illumina, Nanopore and Hi-C sequencing technologies to assemble a chromosome-level genome sequence for an anuran with a moderate genome size (assembly span 3.09 Gb); Pelobates cultripes, the western spadefoot toad. The genome has an N50 length of 330 Mb with 98.6% of the total sequence length assembled into 14 super scaffolds, and 87.7% complete BUSCO genes. We use published transcriptomic data to provide annotations, identifying 32,684 protein-coding genes. We also reconstruct the P. cultripes phylome and identify 2,527 gene expansions. We contribute the first draft of the genome of the western spadefoot toad, P. cultripes. This species represents a relatively basal lineage in the anuran tree with an interesting ecology and a high degree of developmental plasticity, and thus is an important resource for amphibian genomic research.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75127546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.) MIG-seq是小麦(Triticum spp.)高通量基因分型的有效方法。

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Pub Date : 2022-04-01 DOI: 10.1093/dnares/dsac011

Kazusa Nishimura, Koichi Motoki, Akira Yamazaki, Rihito Takisawa, Y. Yasui, T. Kawai, K. Ushijima, R. Nakano, T. Nakazaki

{"title":"MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.)","authors":"Kazusa Nishimura, Koichi Motoki, Akira Yamazaki, Rihito Takisawa, Y. Yasui, T. Kawai, K. Ushijima, R. Nakano, T. Nakazaki","doi":"10.1093/dnares/dsac011","DOIUrl":"https://doi.org/10.1093/dnares/dsac011","url":null,"abstract":"Abstract 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 size and the number of bases that can be stably sequenced. The genome size and the number of loci, which can be sequenced by MIG-seq, are positively correlated. This is due to the linkage between genome size and the number of simple sequence repeats (SSRs) through the genome. The applicability of MIG-seq to population structure analysis, linkage mapping, and quantitative trait loci (QTL) analysis in wheat, which has a relatively large genome, was further evaluated. The results of population structure analysis for tetraploid wheat showed the differences among collection sites and subspecies, which agreed with previous findings. Additionally, in wheat biparental mapping populations, over 3,000 SNPs/indels with low deficiency were detected using MIG-seq, and the QTL analysis was able to detect recognized flowering-related genes. These results revealed the effectiveness of MIG-seq for genomic analysis of agricultural plants with large genomes, including wheat.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83159232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2