GENOME 是一份月刊，成立于 1959 年，发表原创研究文章、评论、小型评论、当前观点和评论。感兴趣的领域包括一般遗传学和基因组学、细胞遗传学、分子和进化遗传学、发育遗传学、种群遗传学、系统基因组学、分子鉴定，以及生态、比较和功能基因组学等新兴领域。

Genome is a monthly journal established in 1959, publishing original research articles, reviews, mini-reviews, current perspectives, and commentaries. The journal covers a wide range of topics including general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, systems genomics, molecular identification, as well as emerging fields such as ecological, comparative, and functional genomics.

《Genome》是一本成立于1959年的月刊，主要发表原创研究文章、评论、小型评论、当前观点和综述。期刊关注的领域包括一般遗传学和基因组学、细胞遗传学、分子与进化遗传学、发育遗传学、种群遗传学、系统基因组学、分子鉴定，以及生态、比较和功能基因组学等新兴领域。

Genome

The three quantitative trait loci (qSH1, qSH3, and qSH4) causing reduction of seed shattering were investigated to examine their relative importance during rice domestication. The qSH1 and qSH4 loci showed a distinct effect on the reduction of shattering, compared with the qSH3 locus. Fine mapping and sequence analysis strongly suggested that the qSH1 and qSH4 loci are the same as the recently reported genes. A non-shattering allele at qSH1 drastically changed the shattering phenotype to a non-shattering phenotype even in the presence of shattering alleles at the qSH3 and qSH4 loci, showing that qSH1 is genetically epistatic to the other loci. The level of the reduction in sequence diversity was compared between the qSH1 and qSH4 regions. The sequence diversity was severely reduced in the qSH1 region of Oryza sativa subsp. japonica compared with that of O. sativa subsp. indica, despite that the level of diversity was similarly reduced at the qSH4 region in the 2 subspecies. Phylogenetic reconstruction based on the combined sequences of the flanking sites showed different patterns in the 2 subspecies. The 2 subspecies formed a single clade with respect to qSH4, whereas they were separated into different lineages with respect to qSH1, suggesting that these loci had different histories during rice domestication.

Kazumitsu Onishi

Kyoko Takagi

Manabu Kontani

Takumi Tanaka

Yoshio Sano

Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication

Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved. Here, we developed 16 oligonucleotide probes for rapid and accurate identification of chromosomes in Gossypium hirsutum: 9 probes, of which each is able to distinguish individually one pair of chromosomes, and seven probes, of which each distinguishes multiple pairs of chromosomes. Besides the identification of Chrs. A09 and D09, we first find Chr. D08, which carries both 45S and 5S rDNA sequences. Interestingly, we also find Chr. A07 has a small 45S rDNA size, suggesting that the size of this site on Chr. A07 may have reduced during evolution. By the combination of 45S and 5S rDNA sequences and oligonucleotide probes developed, 10 chromosomes (Chrs. 3–7, and 9–13) in A subgenome and 7 (Chrs. 1–2, 4–5, and 7–9) in D subgenome of cotton are able to be recognized. This study establishes cotton oligonucleotide fluorescence in situ hybridization technology for discrimination of chromosomes, which supports and guides for sequence assembling, particularly, for tandem repeat sequences in cotton.

Min Xu

Haiyue Guo

Yingying Wang

Baoliang Zhou

Identification of chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes

通过开发寡核苷酸探针在Gossypium hirsutum中通过荧光原位杂交鉴定染色体

Precision medicine is an emerging approach to clinical research and patient care that focuses on understanding and treating disease by integrating multi-modal or multi-omics data from an individual to make patient-tailored decisions. With the large and complex datasets generated using precision medicine diagnostic approaches, novel techniques to process and understand these complex data were needed. At the same time, computer science has progressed rapidly to develop techniques that enable the storage, processing, and analysis of these complex datasets, a feat that traditional statistics and early computing technologies could not accomplish. Machine learning, a branch of artificial intelligence, is a computer science methodology that aims to identify complex patterns in data that can be used to make predictions or classifications on new unseen data or for advanced exploratory data analysis. Machine learning analysis of precision medicine’s multi-modal data allows for broad analysis of large datasets and ultimately a greater understanding of human health and disease. This review focuses on machine learning utilization for precision medicine’s “big data”, in the context of genetics, genomics, and beyond.

Sarah J. MacEachern

Nils D. Forkert

Machine learning for precision medicine

Nothapodytes nimmoniana is a medicinally important plant producing anticancer monoterpene indole alkaloid (MIA), camptothecin (CPT). The CPT is synthesised through the strictosidine intermediate following the MIA pathway; however, transcriptional regulation of CPT pathway is still elusive in N. nimmoniana. Biosynthesis of MIA is regulated by various transcription factors (TFs) belonging to AP2/ERF, bHLH, MYB, and WRKY families. The present study identified transcriptionally active full-length 105 AP2/ERF and 68 bHLH family TFs from the N. nimmoniana. AP2/ERF TFs were divided into three subfamilies along with a soloist, while bHLH TFs were divided into 10 subfamilies according to their phylogenetic similarities. Three group IXa ERFs, Nn-ERF22, Nn-ERF29, and Nn-ERF41, one subfamily IVa TF Nn-bHLH7, and three subfamilies IIIe Nn-bHLH33, Nn-bHLH51, and Nn-bHLH52 clustered with the TFs regulating alkaloid biosynthesis in Catharanthus roseus, tomato, tobacco, and Artemisia annua. Expression of these TFs in N. nimmoniana was higher in roots, which is a primary CPT accumulating tissue. Moreover, genome skimming approach was used to reconstruct the promoter regions of candidate ERF genes to identify the cis-regulatory elements. The presence of G-boxes and other jasmonic acid-responsive elements in the promoter suggests the regulation of ERFs by bHLHs. The present study effectively generated and used genomics resource for characterisation of regulatory TFs from non-model medicinal plant.

Rucha C. Godbole

Swapnil B. Kadam

Anupama A. Pable

Sudhir Singh

Vitthal T. Barvkar

Phylogenomics of transcriptionally active AP2/ERF and bHLH transcription factors and study of their promoter regions in Nothapodytes nimmoniana (J.Graham) Mabb

转录活跃的AP2/ERF和bHLH转录因子的系统基因组学及其在Nothapodytes nimmoniana (J.Graham) Mabb中的启动子区域研究

WD40 repeat proteins are largely distributed across the plant kingdom and play an important role in diverse biological activities. In this work, we performed genome-wide identification, characterization, and expression level analysis of WD40 genes in cotton. A total of 579, 318, and 313 WD40 genes were found in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. Based on phylogenetic tree analyses, WD40 genes were divided into 11 groups with high similarities in exon/intron features and protein domains within the group. Expression analysis of WD40 genes showed differential expression at different stages of cotton fiber development (0 and 8 DPA) and cotton stem. A number of miRNAs were identified to target WD40 genes that are significantly involved in cotton fiber development during the initiation and elongation stages. These include miR156, miR160, miR162, miR164, miR166, miR167, miR169, miR171, miR172, miR393, miR396, miR398, miR2950, and miR7505. The findings provide a stronger indication of WD40 gene function and their involvement in the regulation of cotton fiber development during the initiation and elongation stages.

Haron Salih

Wenfang Gong

Mtawa Mkulama

Xiongming Du

Genome-wide characterization, identification, and expression analysis of the WD40 protein family in cotton

棉花中WD40蛋白家族的全基因组特征、鉴定及表达分析

Chromosomes, as carriers of genes, are the fundamental units of heredity, with the eukaryotic genome divided into multiple chromosomes. Each species typically has a consistent number of chromosomes within its lineage. Ants, however, display remarkable diversity in chromosome numbers, and previous studies have shown that this variation may correlate with ant diversity. As ants evolved, various karyotypes emerged, primarily through chromosomal fissions, leading to an increase in chromosome number and a decrease in chromosome size. In this study, we investigate chromosome evolution in ants from a phylogenetic perspective using ancestral reconstruction. Our analysis indicates that the most recent common ancestor of ants had an ancestral haploid chromosome number of eleven, likely composed of biarmed chromosomes. The bimodal distribution of karyotypes and the trend toward increased chromosome numbers align with previous assumptions. Although both dysploidy and ploidy changes have been indicated as likely mechanisms of chromosome number evolution. Descending dysploidy occurs consistently throughout the phylogeny, while changes in ploidy are believed to occur occasionally within the subfamilies during genus diversification. We propose, based on our results and previous evidence (e.g., genome size in ants), that both fusions and fissions contribute equally to karyotype changes in Formicidae. Additionally, changes in ploidy should not be fully ignored, as they can occur across specific lineages.

Danon Clemes Cardoso

Maykon Passos Cristiano

A phylogenetic perspective of chromosome evolution in Formicidae

蚁科染色体进化的系统发育视角

Autism spectrum disorder (ASD) is an increasingly recognized childhood developmental disorder. Despite extensive study, causal variants and molecular diagnosis remain elusive. There is both heterogeneity of the phenotype, as well as the genetic landscape associated with phenotype, which includes both inherited and de-novo mutations. Currently, diagnosis is complex and behaviourally based, oftentimes occurring years after the ideal 1-2 years age. Structural variants (SVs) are large and sometimes complex genomic variants that are likely underrepresented contributors to ASD due to the limitations of short-read DNA sequencing, such as alignment in repetitive regions and regions with GC bias. Here, we performed long read sequencing (LRS) on four individuals with autism spectrum disorder to delineate SV complexity and determine precise breakpoints for SVs, which was not possible with short read sequencing (SRS). We use LRS to interrogate the methylation pattern associated with the SVs and phase the SV haplotypes to further clarify their contribution to disorder. LRS allows insight into the genome and methylome that allow us to uncover variant complexity and contribution that was previously unseen with SRS. Ultimately, this furthers precision diagnosis and contributes to individualized treatment for affected individuals and their families within the clinic.

Sarah Dada

Katherine Dixon

Vahid Akbari

Cameron J. Grisdale

Kristina Calli

Sally Martell

Caralyn Reisle

Amanda Lillico-Ouachour

M. E. Suzanne Lewis

Steven J.M. Jones

Uncovering the complexity of structural variants in four individuals with Autism Spectrum Disorder

揭示四名自闭症谱系障碍患者结构变异的复杂性

The domestication of Emu (Dromaius novaehollandiae) began in the 1970s, but their productive characteristics have not undergone significant genetic enhancement. This study investigated the inbreeding and genetic diversity of 50 emus from various farms in Japan using Double digest restriction-site associated DNA sequencing (ddRAD-seq) markers. Single nucleotide polymorphism (SNP) calling revealed 1,71,975 high-quality SNPs while runs of homozygosity (ROH) analysis identified 1,843 homozygous segments, with an average of 36.86 ROH per individual and a mean genome length of 27 Mb under ROH. The majority (86%) of ROH were short (0.5-1 Mb), indicating ancient or remote inbreeding. The average genomic inbreeding coefficient (FROH) was 0.0228, suggesting nearly no inbreeding. Overlapping ROH regions were identified, with top consensus regions found on chromosomes 8 and Z. Seven candidate genes related to egg production, feather development, and energy metabolism were annotated in these regions. The findings highlight the prevalence of genetic diversity and low inbreeding levels in the studied emu population. This research highlights the potentiality of random mating in genetic management and conservation of emus. Further studies should focus on enhancing productive traits through selective breeding while preserving genetic diversity to ensure the sustainable growth of the emu farming.

Rangasai Chandra Goli

Karan Mahar

Kiyevi G Chishi

Sonu Choudhary

Pallavi Rathi

Chandana C Sree

Pala Haritha

Nidhi Sukhija

KK Kanaka

Runs of Homozygosity assessment using Reduced Representation Sequencing highlight the evidence of random mating in Emu (Dromaius novaehollandiae)

使用简化代表性测序评估同型配对区域的分析揭示了鸸鹋（Dromaius novaehollandiae）中随机交配的证据

Brassica napus, commonly known as rapeseed or canola, is an economically valuable oilseed crop grown throughout Canada that currently faces several challenges due to industrial farming practices as well as a changing climate. Calcium-dependent protein kinases (CDPKs) are key regulators of stress signaling in multiple plant species. CDPKs sense changes in cellular calcium levels via a calmodulin-like domain and are able to respond to these changes via their protein kinase domain. In this mini-review, we provide a quick guide to BnaCDPKs. We present an updated phylogeny of the BnaCDPK family in relation to CDPKs from Arabidopsis thaliana and Oryza sativa and we provide a standardized nomenclature for the large BnaCDPK family that contains many co-orthologs. We analyze expression patterns of BnaCDPKs across tissue types and in response to abiotic and biotic stresses, and we summarize known functions of BnaCDPKs. We hope this guide is useful to anyone interested in exploring the prospect of harnessing the potential of BnaCDPKs in the generation of elite cultivars of B. napus.

Virginia N Miguel

Jacqueline Monaghan

A quick guide to the calcium-dependent protein kinase family in Brassica napus

油菜中依赖钙蛋白激酶家族的快速指南

Successful resistance to disease-causing pathogens is underpinned by properly regulated immune signalling and defence responses in plants. The plant immune system is controlled at multiple levels of gene and protein regulation—from chromatin-associated epigenetic processes to protein post-translational modifications. Optimal fine-tuning of plant immune signalling and responses is important to prevent plant disease development, which is being exacerbated by a globally changing climate. In this review, we focus on how changing climatic factors mechanistically intercept plant immunity at different levels of regulation (chromatin, transcriptional, post-transcriptional, translational and post-translational). We specifically highlight recent studies that have provided molecular insights into critically important climate-sensitive nodes and mechanisms of the plant immune system. We then propose several potential future directions to build climate-resilient plant disease resistance using cutting-edge biotechnology. Overall, this conceptual understanding and promising biotechnological advances provide a foundational platform towards novel approaches to engineer plant immune resilience.

Christian Danve M Castroverde

Chi Kuan

Jong Hum Kim

Plant immune resilience to a changing climate: Molecular insights and biotechnological roadmaps

植物对气候变化的免疫韧性：分子洞察与生物技术路线图

Abbreviation
Journal Impact	2.38
Quartiles(Global)	GENETICS & HEREDITY(Q3)

ISSN	0831-2796, 1480-3321
h-index	108

Publication Information	Publisher: National Research Council of Canada，Publishing cycle: Bimonthly，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 1987，Proportion of original research papers: 100.00%，Self Citation Rate:4.30%， Gold OA Rate: 16.67%
Average review cycle	网友分享经验：较慢,6-12周
Average recruitment ratio	网友分享经验：较易

Genome

Journal Citation Format

A journal article with 1 author

A journal article with 2 authors

A journal article with 3 authors

A journal article with 5 or more authors

Books Citation Format

Thesis Citation Format

Web sites Citation Format

Patent Citation Format

Staying up late manually editing references? ivySCI automatically matches journals and helps you generate references with a single click.

Share Submission Experience