BMC GENOMICS 是一本开放获取、同行评议的期刊，考虑关于基因组规模分析、功能基因组学和蛋白质组学各个方面的文章。BMC GENOMICS 是 BMC 系列的一部分，该系列出版专注于个人研究需求的特定主题期刊生物学和医学所有领域的社区。我们提供高效、公平和友好的同行评审服务，并致力于出版所有可靠的科学，前提是工作提供的知识有所进步。

BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genomic-scale analysis, functional genomics, and proteomics. As part of the BMC series, it focuses on specific topics that cater to the research needs of the biological and medical communities. We provide efficient, fair, and friendly peer review services and are committed to publishing all reliable science, provided that the work contributes to the advancement of knowledge.

BMC Genomics 是一本开放获取、同行评审的期刊，接受关于基因组规模分析、功能基因组学和蛋白质组学各个方面的研究文章。作为 BMC 系列的一部分，该系列专注于满足生物学和医学领域研究者的特定需求。我们提供高效、公平和友好的同行评审服务，致力于出版所有可靠的科学研究，前提是这些研究能够推动知识的进步。

BMC Genomics

Abstract Background Jasmonate (JA) is the important phytohormone to regulate plant growth and adaption to stress signals. MYC2, an bHLH transcription factor, is the master regulator of JA signaling. Although MYC2 in maize has been identified, its function remains to be clarified. Results To understand the function and regulatory mechanism of MYC2 in maize, the joint analysis of DAP-seq and RNA-seq is conducted to identify the binding sites and target genes of ZmMYC2. A total of 3183 genes are detected both in DAP-seq and RNA-seq data, potentially as the directly regulating genes of ZmMYC2. These genes are involved in various biological processes including plant growth and stress response. Besides the classic cis -elements like the G-box and E-box that are bound by MYC2, some new motifs are also revealed to be recognized by ZmMYC2, such as nGCATGCAnn, AAAAAAAA, CACGTGCGTGCG. The binding sites of many ZmMYC2 regulating genes are identified by IGV-sRNA. Conclusions All together, abundant target genes of ZmMYC2 are characterized with their binding sites, providing the basis to construct the regulatory network of ZmMYC2 and better understanding for JA signaling in maize.

Lijun Liu

Yuhan Zhang

Chen Tang

Jine Wu

Jingye Fu

Qiang Wang

Genome-wide identification of ZmMYC2 binding sites and target genes in maize

玉米中ZmMYC2结合位点和靶基因的全基因组鉴定

BackgroundPhylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data.ResultsWe developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline.ConclusionsUsing SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

Tae-Ho Lee

Hui Guo

Xiyin Wang

Changsoo Kim

Andrew H Paterson

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

SNPhylo：从大量SNP数据构建系统发育树的流程

The AP2/ERF transcription factor is widely distributed across the plant kingdom and plays a crucial role in various abiotic stress responses in plants. Tritipyrum, an octoploid resulting from an intergeneric cross between Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), is a valuable source of germplasm for incorporating superior traits of Th. elongatum into T. aestivum. With the recent availability of whole -genome sequences for T. aestivum and Th. elongatum, we explored the organization and expression profiling of Tritipyrum AP2/ERF genes across the entire genome. Our investigation identified 543 Tritipyrum AP2/ERF genes, which evolutionary analysis categorized into four major groups (AP2, DREB, ERF, and RAV), whose members share a conserved motif composition. These 543 TtAP2/ERF genes were distributed throughout 28 chromosomes, with 132 duplications. Synteny analysis suggests that the AP2/ERF gene family may have a common ancestor. Transcriptome data and Real-Time PCR expression profiles revealed 43 TtAP2/ERF genes with high expression levels in response to various salt stressors and recovery regimens. Tel2E01T236300 (TtERF_B2-50) was particularly salt stress-sensitive and evolutionarily related to the salt-tolerant gene AtERF7 in A. thaliana. Pearson correlation analysis identified 689 genes positively correlated (R > 0.9) with TtERF_B2-50 expression, enriched in metabolic activities, cellular processes, stimulus response, and biological regulation. Real-time PCR showed that TtERF_B2-50 was highly expressed in roots, stems, and leaves under salt stress. These findings suggest that TtERF_B2-50 may be associated with salt stress tolerance and may serve as a valuable foreign gene for enhancing salt tolerance in wheat.

Xiaojuan Liu

Guangyi Zhou

Songshu Chen

Zhenzhen Jia

Suqin Zhang

Mingjian Ren

Fang He

Genome-wide analysis of the AP2/ERF gene family in Tritipyrum and the response of TtERF_B2-50 in salt-tolerance

拟南芥基因家族在Tritipyrum中的全基因组分析及TtERF_B2-50在耐盐性中的响应

Transcription factor lark has been demonstrated to play multiple functions in Drosophila, but the function of this gene in embryonic development remains to be elucidated. In this study, the CRISPR/Cas9 gene-editing method was used to construct a Bmlark mutant strain of Bombyx mori to investigate the roles of this gene. The results showed that the homozygous mutant Bmlark−/− was lethal. The Bmlark−/− embryos showed obvious developmental defects, such as defective sclerotization and melanization of the exoskeleton. A transcriptomic comparison of Bmlark−/− and wild-type embryos showed that the differentially expressed genes were mainly enriched in the structure and metabolic processes of chitin and cuticles. While the expression levels of chitin metabolism-related enzyme genes did not significantly change, in the mutant embryos compared to the wild-type embryos, the expression levels of 63 putative cuticle protein genes showed significant differences. Among which, 35 genes were downregulated and 28 genes were upregulated. The expression levels of the transcription factor BmPOUM2 and eight wing disc cuticle protein genes (WCP) also changed. BmPOUM2, WCP5, WCP9, WCP10, WCP11 were downregulated and WCP1, WCP2, WCP3, WCP6 were upregulated in Bmlark−/− embryos. While the expression level of TH in the tyrosine-mediated pigmentation pathway was upregulated in the mutant embryos, the expression levels of the four key pigment synthesis genes DDC, aaNAT, Laccase2A, and yellow-f2 were significantly downregulated. The expression levels of 63 putative cuticle protein genes, eight WCP genes, and five pigment synthesis genes significantly changed in Bmlark mutant B. mori compared to those of the wildtype. These results suggest that Bmlark is essential for normal development of cuticle and tyrosine-mediated melanization in silkworm embryos.

Yuling Peng

Jin Li

Kangkang Niu

Man Wang

Yanfei Chen

Chunmei Tong

Qili Feng

Bmlark is essential for embryonic development

Bmlark 对胚胎发育至关重要

Abstract Background As an economically important crop, tea is strongly nitrogen (N)-dependent. However, the physiological and molecular mechanisms underlying the response of N deficiency in tea are not fully understood. Tea cultivar “Chunlv2” [ Camellia sinensis (L.) O. Kuntze] were cultured with a nutrient solution with 0 mM [N-deficiency] or 3 mM (Control) NH 4 NO 3 in 6 L pottery pots containing clean river sands. Results N deficiency significantly decreased N content, dry weight, chlorophyll (Chl) content, L-theanine and the activities of N metabolism-related enzymes, but increased the content of total flavonoids and polyphenols in tea leaves. N deficiency delayed the sprouting time of tea buds. By using the RNA-seq technique and subsequent bioinformatics analysis, 3050 up-regulated and 2688 down-regulated differentially expressed genes (DEGs) were isolated in tea leaves in response to N deficiency. However, only 1025 genes were up-regulated and 744 down-regulated in roots. Gene ontology (GO) term enrichment analysis showed that 205 DEGs in tea leaves were enriched in seven GO terms and 152 DEGs in tea roots were enriched in 11 GO items based on P &lt; 0.05. In tea leaves, most GO-enriched DEGs were involved in chlorophyll a/b binding activities, photosynthetic performance, and transport activities. But most of the DEGs in tea roots were involved in the metabolism of carbohydrates and plant hormones with regard to the GO terms of biological processes. N deficiency significantly increased the expression level of phosphate transporter genes, which indicated that N deficiency might impair phosphorus metabolism in tea leaves. Furthermore, some DEGs, such as probable anion transporter 3 and high-affinity nitrate transporter 2.7, might be of great potential in improving the tolerance of N deficiency in tea plants and further study could work on this area in the future. Conclusions Our results indicated N deficiency inhibited the growth of tea plant, which might be due to altered N metabolism and expression levels of DEGs involved in the photosynthetic performance, transport activity and oxidation–reduction processes.

Zheng-He Lin

Chang-Song Chen

Shui-Qing Zhao

Yuan Liu

Qiu-Sheng Zhong

Qi-Chun Ruan

Zhi-Hui Chen

Xiao-Mei You

Rui-Yang Shan

Xin-Lei Li

Ya-Zhen Zhang

Molecular and physiological mechanisms of tea (Camellia sinensis (L.) O. Kuntze) leaf and root in response to nitrogen deficiency

茶（Camellia sinensis (L.) O. Kuntze）叶片和根系响应氮缺乏的分子和生理机制

Abstract Background Quinoa, as a new food crop, has attracted extensive attention at home and abroad. However, the natural disaster of spike germination seriously threatens the quality and yield of quinoa. Currently, there are limited reports on the molecular mechanisms associated with spike germination in quinoa. Results In this study, we utilized transcriptome sequencing technology and successfully obtained 154.51 Gb of high-quality data with a comparison efficiency of more than 88%, which fully demonstrates the extremely high reliability of the sequencing results and lays a solid foundation for subsequent analysis. Using these data, we constructed a weighted gene co-expression network (WGCNA) related to starch, sucrose, α-amylase, and phenolic acid metabolites, and screened six co-expression modules closely related to spike germination traits. Two of the modules associated with physiological indicators were analyzed in depth, and nine core genes were finally predicted. Further functional annotation revealed four key transcription factors involved in the regulation of dormancy and germination processes: gene LOC110698065 , gene LOC110696037 , gene LOC110736224 , and gene LOC110705759 , belonging to the bHLH , NF-YA , MYB , and FAR1 gene families, respectively. Conclusions These results provide clues to identify the core genes involved in quinoa spike germination. This will ultimately provide a theoretical basis for breeding new quinoa varieties with resistance.

Liubin Huang

Lingyuan Zhang

Ping Zhang

Junna Liu

Li Li

Hanxue Li

Xuqin Wang

Yutao Bai

Guofei Jiang

Peng Qin

Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines

比较转录组学和WGCNA揭示不同藜麦品系芽发育的关键基因

Chenxi Che

Peng Yang

Kangxiang Qin

Yuntao Li

Ziwei Fan

Wenjun Li

Shan Gao

Chunlin Wang

Changkao Mu

Huan Wang

Based on metabolomics analysis: metabolic mechanism of intestinal tract of Scylla paramamosain under low-salt saline-alkali water aquaculture environment

基于代谢组学分析：低盐碱水养殖环境下拟穴青蟹肠道的代谢机制

The diversity-generating retroelements (DGRs) are a family of genetic elements that can produce mutations in target genes often related to ligand-binding functions, which possess a C-type lectin (CLec) domain that tolerates massive variations. They were first identified in viruses, then in bacteria and archaea from human-associated and environmental genomes. This DGR mechanism represents a fast adaptation of organisms to ever- changing environments. However, their existence, phylogenetic and structural diversity, and functions in a wide range of environments are largely unknown. Here we present a study of DGR systems based on metagenome-assembled genomes (MAGs) from host-associated, aquatic, terrestrial and engineered environments. In total, we identified 861 non-redundant DGR-RTs and ~ 5.7% are new. We found that microbes associated with human hosts harbor the highest number of DGRs and also exhibit a higher prevalence of DGRs. After normalizing with genome size and including more genome data, we found that DGRs occur more frequently in organisms with smaller genomes. Overall, we identified nine main clades in the phylogenetic tree of reverse transcriptases (RTs), some comprising specific phyla and cassette architectures. We identified 38 different cassette patterns and 6 of them were shown in at least 10 DGRs, showing differences in terms of the numbers, arrangements, and orientations of their components. Finally, most of the target genes were related to ligand-binding and signaling functions, but we discovered a few cases in which the VRs were situated in domains different from the CLec. Our research sheds light on the widespread prevalence of DGRs within environments and taxa, and supports the DGR phylogenetic divergence in different organisms. These variations might also occur in their structures since some cassette architectures were common in specific underrepresented phyla. In addition, we suggest that VRs could be found in domains different to the CLec, which should be further explored for organisms in scarcely studied environments.

Mariela Carrasco-Villanueva

Chaoxian Wang

Chaochun Wei

Identification of diversity-generating retroelements in host-associated and environmental genomes: prevalence, diversity, and roles

宿主相关和环境基因组中多样性生成逆转录元件的鉴定：流行性、多样性及其作用

Abstract Background Parasitic nematodes significantly undermine global human and animal health and productivity. Parasite control is reliant on anthelmintic administration however over-use of a limited number of drugs has resulted in escalating parasitic nematode resistance, threatening the sustainability of parasite control and underscoring an urgent need for the development of novel therapeutics. FMRFamide-like peptides (FLPs), the largest family of nematode neuropeptides, modulate nematode behaviours including those important for parasite survival, highlighting FLP receptors (FLP-GPCRs) as appealing putative novel anthelmintic targets. Advances in omics resources have enabled the identification of FLPs and neuropeptide-GPCRs in some parasitic nematodes, but remaining gaps in FLP-ligand libraries hinder the characterisation of receptor-ligand interactions, which are required to drive the development of novel control approaches. Results In this study we exploited recent expansions in nematode genome data to identify 2143 flp -genes in &gt; 100 nematode species across free-living, entomopathogenic, plant, and animal parasitic lifestyles and representing 7 of the 12 major nematode clades. Our data reveal that: (i) the phylum-spanning flps , flp -1, -8, -14, and − 18, may be representative of the flp profile of the last common ancestor of nematodes; (ii) the majority of parasitic nematodes have a reduced flp complement relative to free-living species; (iii) FLP prepropeptide architecture is variable within and between flp -genes and across nematode species; (iv) FLP prepropeptide signatures facilitate flp -gene discrimination; (v) FLP motifs display variable length, amino acid sequence, and conservation; (vi) CLANS analysis provides insight into the evolutionary history of flp -gene sequelogues and reveals putative flp -gene paralogues and, (vii) flp expression is upregulated in the infective larval stage of several nematode parasites. Conclusions These data provide the foundation required for phylum-spanning FLP-GPCR deorphanisation screens in nematodes to seed the discovery and development of novel parasite control approaches.

Ciaran J. McCoy

Christopher P. Wray

Laura Freeman

Bethany A. Crooks

Luca Golinelli

Nikki J. Marks

Liesbet Temmerman

Isabel Beets

Louise E. Atkinson

Angela Mousley

Exploitation of phylum-spanning omics resources reveals complexity in the nematode FLP signalling system and provides insights into flp-gene evolution

利用跨门类组学资源揭示线虫FLP信号系统的复杂性并提供对flp基因进化的见解

Trends in the development of genetic markers for the purposes of genomic and marker-assisted selection primarily focus on identifying causative polymorphisms. Using these polymorphisms as markers enables a more accurate association between genotype and phenotype. Bioinformatic analysis allows calculating the impact of missense polymorphisms on the structural and functional characteristics of proteins, which makes it promising for identifying causative polymorphisms. In this study, a bioinformatic approach is applied to evaluate and differentiate polymorphisms based on their causality in genes that affect the production traits of pigs and cows, which are two important livestock species. The influence of both known causative and candidate missense polymorphisms in the MC4R, NR6A1, PRKAG3, RYR1, and SYNGR2 genes of pigs, as well as the ABCG2, DGAT1, GHR, and MSTN genes of cows, was assessed. The study included an evaluation of the effect of polymorphisms on protein functions, considering the evolutionary and physicochemical characteristics of amino acids at polymorphic sites. Additionally, it examined the impact of polymorphisms on the stability of tertiary protein structures, including changes in folding, binding of protein monomers, and interaction with ligands. The comprehensive bioinformatic analysis used in this study enables the differentiation of polymorphisms into neutral, where both amino acids in the polymorphic site do not significantly affect the structure and function of the protein, and causative, where one of the amino acids significantly impacts the protein's properties. This approach can be employed in future research to screen extensive sets of polymorphisms in animal genomes, identifying the most promising polymorphisms for further investigation in association studies.

Mykyta Peka

Viktor Balatsky

Bioinformatic approach to identifying causative missense polymorphisms in animal genomes

生物信息学方法识别动物基因组中致病错义多态性

Abbreviation	BMC Genom.
Journal Impact	3.53
Quartiles(Global)	GENETICS & HEREDITY(Q2)

ISSN	1471-2164
h-index	199
Top Journals	Yes

Publication Information	Publisher: BioMed Central Ltd，Publishing cycle: Monthly，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 2000，Proportion of original research papers: 99.76%，Self Citation Rate:2.90%， Gold OA Rate: 99.84%
Journal Fees	$2990Details
Average review cycle	网友分享经验：平均6.0个月
Average recruitment ratio	网友分享经验：约32.5%

BMC Genomics

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