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Optical genome mapping of structural variants in Parkinson's disease-related induced pluripotent stem cells. 帕金森病相关诱导多能干细胞结构变异的光学基因组图谱。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-19 DOI: 10.1186/s12864-024-10902-1
Joanne Trinh, Susen Schaake, Carolin Gabbert, Theresa Lüth, Sally A Cowley, André Fienemann, Kristian K Ullrich, Christine Klein, Philip Seibler

Background: Certain structural variants (SVs) including large-scale genetic copy number variants, as well as copy number-neutral inversions and translocations may not all be resolved by chromosome karyotype studies. The identification of genetic risk factors for Parkinson's disease (PD) has been primarily focused on the gene-disruptive single nucleotide variants. In contrast, larger SVs, which may significantly influence human phenotypes, have been largely underexplored. Optical genomic mapping (OGM) represents a novel approach that offers greater sensitivity and resolution for detecting SVs. In this study, we used induced pluripotent stem cell (iPSC) lines of patients with PD-linked SNCA and PRKN variants as a proof of concept to (i) show the detection of pathogenic SVs in PD with OGM and (ii) provide a comprehensive screening of genetic abnormalities in iPSCs.

Results: OGM detected SNCA gene triplication and duplication in patient-derived iPSC lines, which were not identified by long-read sequencing. Additionally, various exon deletions were confirmed by OGM in the PRKN gene of iPSCs, of which exon 3-5 and exon 2 deletions were unable to phase with conventional multiplex-ligation-dependent probe amplification. In terms of chromosomal abnormalities in iPSCs, no gene fusions, no aneuploidy but two balanced inter-chromosomal translocations were detected in one line that were absent in the parental fibroblasts and not identified by routine single nucleotide variant karyotyping.

Conclusions: In summary, OGM can detect pathogenic SVs in PD-linked genes as well as reveal genomic abnormalities for iPSCs that were not identified by other techniques, which is supportive for OGM's future use in gene discovery and iPSC line screening.

背景:某些结构变异(SV),包括大规模遗传拷贝数变异以及拷贝数中性倒位和易位,可能无法通过染色体核型研究全部解决。帕金森病(PD)遗传风险因素的鉴定主要集中在基因破坏性单核苷酸变异上。与此相反,可能对人类表型产生重大影响的较大的 SVs 在很大程度上还未得到充分探索。光学基因组图谱(OGM)是一种新型方法,它能为检测 SVs 提供更高的灵敏度和分辨率。在这项研究中,我们使用与帕金森病相关的SNCA和PRKN变体患者的诱导多能干细胞(iPSC)系作为概念验证,(i) 显示了用OGM检测帕金森病致病性SV的方法,(ii) 提供了在iPSC中全面筛查基因异常的方法:结果:OGM在患者衍生的iPSC细胞系中检测到了SNCA基因的三倍和重复,而长线程测序并未识别出这些基因。此外,OGM 还在 iPSCs 的 PRKN 基因中证实了多种外显子缺失,其中第 3-5 号外显子和第 2 号外显子缺失无法通过传统的多重连接依赖性探针扩增进行分期。在 iPSCs 染色体异常方面,没有发现基因融合和非整倍体,但在一个品系中发现了两个平衡的染色体间易位,而亲代成纤维细胞中没有这种情况,常规的单核苷酸变异核型检查也没有发现:总之,OGM 可以检测与 PD 相关的基因中的致病性 SV,并揭示其他技术未发现的 iPSC 基因组异常,这为 OGM 今后用于基因发现和 iPSC 株系筛选提供了支持。
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引用次数: 0
Insights into trait-association of selection signatures and adaptive eQTL in indigenous African cattle. 对非洲本土牛的选择特征和适应性 eQTL 的性状关联的见解。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-19 DOI: 10.1186/s12864-024-10852-8
Juliane Friedrich, Shuli Liu, Lingzhao Fang, James Prendergast, Pamela Wiener

Background: African cattle represent a unique resource of genetic diversity in response to adaptation to numerous environmental challenges. Characterising the genetic landscape of indigenous African cattle and identifying genomic regions and genes of functional importance can contribute to targeted breeding and tackle the loss of genetic diversity. However, pinpointing the adaptive variant and determining underlying functional mechanisms of adaptation remains challenging.

Results: In this study, we use selection signatures from whole-genome sequence data of eight indigenous African cattle breeds in combination with gene expression and quantitative trait loci (QTL) databases to characterise genomic targets of artificial selection and environmental adaptation and to identify the underlying functional candidate genes. In general, the trait-association analyses of selection signatures suggest the innate and adaptive immune system and production traits as important selection targets. For example, a large genomic region, with selection signatures identified for all breeds except N'Dama, was located on BTA27, including multiple defensin DEFB coding-genes. Out of 22 analysed tissues, genes under putative selection were significantly enriched for those overexpressed in adipose tissue, blood, lung, testis and uterus. Our results further suggest that cis-eQTL are themselves selection targets; for most tissues, we found a positive correlation between allele frequency differences and cis-eQTL effect size, suggesting that positive selection acts directly on regulatory variants.

Conclusions: By combining selection signatures with information on gene expression and QTL, we were able to reveal compelling candidate selection targets that did not stand out from selection signature results alone (e.g. GIMAP8 for tick resistance and NDUFS3 for heat adaptation). Insights from this study will help to inform breeding and maintain diversity of locally adapted, and hence important, breeds.

背景:非洲牛是适应众多环境挑战的独特遗传多样性资源。描述非洲本土牛的遗传景观并确定具有重要功能的基因组区域和基因有助于进行有针对性的育种并解决遗传多样性丧失的问题。然而,精确定位适应性变体并确定适应性的潜在功能机制仍具有挑战性:在这项研究中,我们利用来自八个非洲本土牛种全基因组序列数据的选择特征,结合基因表达和数量性状位点(QTL)数据库,描述了人工选择和环境适应的基因组目标,并确定了潜在的功能候选基因。总体而言,选择特征的性状关联分析表明,先天性和适应性免疫系统以及生产性状是重要的选择目标。例如,在 BTA27 上发现了一个大的基因组区域,其中包括多个防御素 DEFB 编码基因,除 N'Dama 外,所有品种都发现了该区域的选择特征。在分析的 22 个组织中,脂肪组织、血液、肺、睾丸和子宫中过表达的基因明显富集。我们的研究结果进一步表明,顺式-eQTL本身就是选择目标;在大多数组织中,我们发现等位基因频率差异与顺式-eQTL效应大小之间存在正相关,这表明正选择直接作用于调控变体:结论:通过将选择特征与基因表达和 QTL 信息相结合,我们能够揭示出令人信服的候选选择目标,而这些目标并没有从单独的选择特征结果中脱颖而出(如抗蜱性的 GIMAP8 和热适应性的 NDUFS3)。这项研究的启示将有助于为育种提供信息,并保持适应当地环境的品种多样性,因此也是重要的品种。
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引用次数: 0
Genomic insights into Aspergillus tamarii TPD11: enhancing polyphyllin production and uncovering potential therapeutic applications. 对塔玛氏曲霉 TPD11 基因组的深入研究:提高多卟啉的产量并发掘潜在的治疗应用。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-18 DOI: 10.1186/s12864-024-10776-3
Qing Zhang, Hai Liu, Xiaojun Zhao, Jili Yang, Weidi Tang, Ying Yang, Sheng Chang, Bo Cai, Juan Liu, Yaoshun Zhu, Bo Zhou, Tao Liu

Background: The excavation and utilization of endophytic fungi from medicinal plants is highly important for the development of new drugs. The endophytic fungus Aspergillus tamarii TPD11, which was isolated and obtained by the authors in the previous stage, can produce a variety of polyphyllins with important potential applications in hemostasis, inflammation and antitumor activities; however, the genomic information of TPD11 is still unknown.

Results: In this study, we sequenced and assembled the whole genome of the endophytic fungus A. tamarii TPD11, resolved the genome evolutionary relationships of 24 Aspergillus strains, and phylogenetic analysis of the genomes of 16 strains revealed the evolutionary differences between Aspergillus and Penicillium and the mechanisms of genome expansion and contraction. CAZy annotation analysis revealed that TPD11 obtains nutrients mainly by ingesting starch from the host plant. TPD11 has a biosynthesis-related gene cluster for the synthesis of squalestatin S1, and the silencing of this biosynthesis-related gene cluster might increase the content of polyphyllin. Annotation of 11 UDP-glycosyltransferase genes helps to further reveal the biosynthetic pathway of polyphyllin. In addition, secondary metabolism gene cluster and CAZy analyses confirmed the potential probiotic, insecticidal and antimicrobial activities of TPD11 on host plants.

Conclusions: This study reveals the intrinsic mechanism by which endophytic fungi increase the content of polyphyllin, which provides a basis for the synthetic synthesis of the natural product polyphyllin.

背景:从药用植物中挖掘和利用内生真菌对新药开发具有重要意义。作者前一阶段分离获得的内生真菌塔马曲霉 TPD11 能产生多种多肽类物质,在止血、炎症和抗肿瘤等方面具有重要的潜在应用价值,但 TPD11 的基因组信息尚不清楚:本研究对内生真菌A. tamarii TPD11的全基因组进行了测序和组装,解析了24株曲霉的基因组进化关系,并对16株菌株的基因组进行了系统进化分析,揭示了曲霉与青霉的进化差异以及基因组扩展和收缩的机制。CAZy 注释分析表明,TPD11 主要通过摄取寄主植物的淀粉获得营养。TPD11 有一个合成角斑素 S1 的生物合成相关基因簇,沉默该生物合成相关基因簇可能会增加多角斑素的含量。11 个 UDP-糖基转移酶基因的注释有助于进一步揭示多花植物素的生物合成途径。此外,次生代谢基因簇和 CAZy 分析证实了 TPD11 对寄主植物潜在的益生、杀虫和抗菌活性:本研究揭示了内生真菌增加多浆菌素含量的内在机制,为合成天然产物多浆菌素提供了依据。
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引用次数: 0
Detection of structural variants linked to mutton flavor and odor in two closely related black goat breeds. 在两个密切相关的黑山羊品种中检测与羊肉风味和气味有关的结构变异。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-18 DOI: 10.1186/s12864-024-10874-2
Lingle Chang, Xi Niu, Shihui Huang, Derong Song, Xueqin Ran, Jiafu Wang

Background: Mutton quality is closely related to genetic variants and gene expression alterations during growth and development, resulting in differences in nutritional values, flavor, and odor.

Results: We first evaluated and compared the composition of crude protein, crude fat, cholesterol, amino acid (AA), and fatty acid (FA) in the longissimus dorsi muscle of Guizhou black goats (GZB, n = 5) and Yunshang black goats (YBG, n = 6). The contents of cholesterol and FA related to odor in GZB were significantly lower than that in YBG, while the concentrations of umami amino acids and intramuscular fat were significantly higher in GZB. Furthermore, structural variants (SVs) in the genomes of GZB (n = 30) and YBG (n = 11) were explored. It was found that some regions in Chr 10/12/18 were densely involved with a large number of SVs in the genomes of GZB and YBG. By setting FST ≥ 0.25, we got 837 stratified SVs, of which 25 SVs (involved in 12 genes, e.g., CORO1A, CLIC6, PCSK2, and TMEM9) were limited in GZB. Functional enrichment analysis of 14 protein-coding genes (e.g., ENPEP, LIPC, ABCA5, and SLC6A15) revealed multiple terms and pathways related with metabolisms of AA, FA, and cholesterol. The SVs (n = 10) obtained by the whole genome resequencing were confirmed in percentages of 36.67 to 86.67% (n = 96) by PCR method. The SVa and SVd polymorphisms indicated a moderate negative correlation with HMGCS1 activity (n = 17).

Conclusion: This study is the first to comprehensively reveal potential SVs related to mutton nutritional values, flavor, and odor based on genomic compare between two black goat breeds with closely genetic relationship. The SVs generated in this study provide a data resource for deeper studies to understand the genomic characteristics and possible evolutionary outcomes with better nutritional values, flavor and extremely light odor.

背景:羊肉的品质与生长发育过程中的遗传变异和基因表达改变密切相关,从而导致营养价值、风味和气味的差异:我们首先评估并比较了贵州黑山羊(GZB,n = 5)和云上黑山羊(YBG,n = 6)背长肌中粗蛋白、粗脂肪、胆固醇、氨基酸(AA)和脂肪酸(FA)的组成。黔东南黑山羊的胆固醇和与气味相关的脂肪酸含量明显低于云南黑山羊,而黔东南黑山羊的味氨基酸和肌内脂肪含量明显高于云南黑山羊。此外,研究人员还探讨了广州番荔枝(30 个)和云南番荔枝(11 个)基因组中的结构变异(SVs)。结果发现,在 GZB 和 YBG 的基因组中,Chr 10/12/18 中的一些区域与大量 SVs 紧密相关。通过设定FST≥0.25,我们得到了837个分层SVs,其中25个SVs(涉及12个基因,如CORO1A、CLIC6、PCSK2和TMEM9)被限制在GZB中。对 14 个蛋白编码基因(如 ENPEP、LIPC、ABCA5 和 SLC6A15)的功能富集分析表明了与 AA、FA 和胆固醇代谢相关的多个术语和通路。通过全基因组重测序获得的 SVs(n = 10)经 PCR 方法确认的比例为 36.67% 至 86.67%(n = 96)。SVa 和 SVd 多态性与 HMGCS1 活性呈中度负相关(n = 17):本研究首次基于遗传关系密切的两个黑山羊品种的基因组比较,全面揭示了与羊肉营养价值、风味和气味相关的潜在 SVs。本研究中产生的 SVs 为更深入的研究提供了数据资源,有助于了解营养价值、风味和气味更佳的基因组特征和可能的进化结果。
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引用次数: 0
Chemical composition determination and transcriptomic analyses provide insight into the differences between wild and grafted Semen Ziziphi Spinosae. 通过化学成分测定和转录组分析,可以深入了解野生和嫁接 Semen Ziziphi Spinosae 之间的差异。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-18 DOI: 10.1186/s12864-024-10837-7
Yaxing Kong, Shulei He, Donglai Ma, Xian Gu, Qian Wang, Jingqiao Zhao, Jianyun Zhang, Qian Tian, Yuguang Zheng, Yanmei Chen, Kaiyan Zheng

Semen Ziziphi Spinosae (SZS) is a traditional Chinese herbal medicine widely used to treat insomnia and anxiety in clinical practice. Currently, the demand for SZS is increasing every year, but the production of wild SZS is unstable due to environmental factors. Grafting sour jujube scions onto sour jujube or jujube tree stocks can achieve a high production rate within a short period of time. However, the effects of grafting on the quality of SZS have not been reported. This study investigated the differences between wild-type and grafted SZS from three aspects: phenotype, chemical composition, and molecular mechanism. The findings revealed that the grafted specimens were generally larger in morphology and lighter in color than the wild-type samples. The dimensions of both the grafted specimens were generally larger than those of the wild specimens. The HPLC-ELSD results revealed that the three main chemical components in the grafted SZS, namely, spinosin, jujuboside A, and jujuboside B, had higher contents than their wild-type counterparts. Comprehensive transcriptome sequencing analysis and KEGG annotation revealed that DEG enrichment between grafted and wild-type SZS occurred mainly during stress resistance and rootstock scion healing. There were 23 DEGs that may encode enzymes involved in the biosynthetic pathway of flavonoids and 21 genes encoding terpenoid saponins. Further investigation revealed that the expression of the genes C4H, CHS, CHI, and F3'5'H in the flavonoid biosynthesis pat.hway and HMGR, MVK, MVD, and FPPS in the saponin biosynthesis pathway accounted for the difference in quality between grafted and wild SZS. Furthermore, WGCNA identified 15 core genes related to medicinal ingredients between grafted and wild SZS. These results provide support for further research on the differences in the quality of medicinal ingredients between grafted and wild SZS.

酸枣仁(SZS)是一种传统中药材,在临床上被广泛用于治疗失眠和焦虑症。目前,人们对酸枣仁的需求量逐年增加,但受环境因素影响,野生酸枣仁的产量并不稳定。将酸枣接穗嫁接到酸枣或枣树种群上可在短时间内实现高产量。然而,嫁接对 SZS 质量的影响尚未见报道。本研究从表型、化学成分和分子机理三个方面研究了野生型和嫁接型 SZS 的差异。研究结果表明,与野生型样本相比,嫁接样本的形态一般较大,颜色较浅。两种嫁接样本的尺寸普遍大于野生样本。HPLC-ELSD结果显示,嫁接深圳红豆杉中的三种主要化学成分,即刺五加苷、大枣苷A和大枣苷B的含量均高于野生型。综合转录组测序分析和KEGG注释发现,嫁接深圳红豆杉与野生型深圳红豆杉之间的DEG富集主要发生在抗逆和砧木接穗愈合过程中。有 23 个 DEG 可能编码参与黄酮类化合物生物合成途径的酶,21 个基因编码萜类皂甙。进一步研究发现,黄酮类化合物生物合成途径中的基因 C4H、CHS、CHI 和 F3'5'H,以及皂苷生物合成途径中的基因 HMGR、MVK、MVD 和 FPPS 的表达是造成嫁接深圳红豆杉和野生深圳红豆杉品质差异的原因。此外,WGCNA 还发现了 15 个与嫁接和野生 SZS 的药用成分相关的核心基因。这些结果为进一步研究嫁接和野生深圳龙眼的药用成分质量差异提供了支持。
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引用次数: 0
Protective effect of fructooligosaccharide against oxidative stress and apoptosis induced by Aeromonas hydrophila in Megalobrama amblycephala. 果寡糖对姬蛙水单胞菌诱导的氧化应激和细胞凋亡的保护作用
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-17 DOI: 10.1186/s12864-024-10881-3
Chunnuan Zhang, Dongxue Jiang, Huajuan Shi, Cheng Zhang, Feng Yang, Qian Qi, Ruiyi Xu

This research aimed to investigate the effects of dietary fructooligosaccharides (FOS) on attenuating the Aeromonas hydrophila (A. hydrophila)-induced oxidative stress and apoptosis in blunt snout bream Megalobrama amblycephala. Fish were divided into three groups as follows: C1 (Control), T1 (A. hydrophila), and T2 (A. hydrophila + 4 g/kg FOS). The results showed that the activities of antioxidant enzymes increased, the liver morphology had disorderly arrangement, and extensive cell necrosis occurred because of A. hydrophila-infection. While the dietary FOS improved the above-mentioned liver damage. Additionaly, FOS elevated mRNA levels of pro-apoptotic molecules, including caspase-8 and 9, and down-regulated mRNA levels of the anti-apoptotic molecule Bcl-2, which is triggered by A. hydrophila-infection. The transcriptome analysis showed that the oxidative stress-related DEGs pathways were activated in intestine of blunt snout bream by A. hydrophila-infection. The FOS-added group led to the enrichment of more pathways to health. Further WGCNA co-expression network analysis showed that the screened single genes were clustered into 49 modules. The two modules with the highest association to the five traits (10 hub genes) were chosen to build the network by combining the physiological and biochemical characteristic. In summary, this research offers a foundation for the exploring of A. hydrophila-restoration genes in dietary FOS, and also lays a theoretical foundation for aquaculture in the future.

本研究旨在探讨膳食果寡糖(FOS)对钝吻鳊(Megalobrama amblycephala)嗜水气单胞菌(A. hydrophila)诱导的氧化应激和细胞凋亡的影响。鱼类分为以下三组:C1(对照组)、T1(蚜茧蜂)和 T2(蚜茧蜂 + 4 g/kg FOS)。结果表明,蚜茧蜂感染导致抗氧化酶活性增加,肝脏形态排列紊乱,细胞大面积坏死。而膳食纤维素能改善上述肝损伤。此外,FOS还提高了促凋亡分子(包括caspase-8和9)的mRNA水平,并下调了抗凋亡分子Bcl-2的mRNA水平。转录组分析表明,鳗鲡感染钝口鳊后,肠道中与氧化应激相关的 DEGs 通路被激活。添加 FOS 的组别富集了更多的健康通路。进一步的WGCNA共表达网络分析显示,筛选出的单个基因被聚类为49个模块。结合生理生化特征,选择与五个性状关联度最高的两个模块(10 个中枢基因)构建网络。综上所述,本研究为探索食源性 FOS 中的亲水藻类修复基因奠定了基础,也为今后的水产养殖奠定了理论基础。
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引用次数: 0
Post-transcriptional regulation of Dufour's gland reproductive signals in bumble bees. 大黄蜂杜氏腺生殖信号的转录后调控。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-17 DOI: 10.1186/s12864-024-10873-3
Nathan Derstine, Tatiana Laremore, Etya Amsalem

Pheromone communication is a key mechanism by which the reproductive division of labor is maintained within insect communities. Understanding how pheromones evolved to regulate social behavior requires knowledge of the molecular regulation of their production. However, even in cases where pheromones were identified, our understanding of their biosynthesis and molecular regulation remains limited. Bumble bees provide a unique system to explore pheromone biosynthesis since workers produce ester sterility signals in their Dufour's gland that differ from gyne-specific esters and are not produced by queens. These esters are hypothesized to be produced in the exocrine gland where they are stored, and indeed queens, gynes and workers differ significantly in the expression of Dufour's gland genes coding to enzymes involved in the biosynthesis of esters. However, a previous transcriptome analysis revealed no gene expression differences in the Dufour's gland of workers despite differences in both ester production and ovarian activation, suggesting that ester production may be regulated lower down. Proteomics of the Dufour's gland of queens, gynes, and workers recovered over 2400 proteins and broadly matched the previous RNAseq data. However, more than 100 differentially expressed proteins were found between the worker groups, including key enzymes in fatty acid biosynthesis, indicating that the regulation of reproductive signal biosynthesis in workers is done post-transcription. Overall, our data provide evidence that pheromone biosynthesis in the Dufour's gland is caste specific, that gynes and workers are likely using different enzymes to make their respective wax esters, and that the regulation on pheromone production in queens, gynes and workers is likely done at different regulatory levels, with workers signals being subjected to regulation at the protein level.

信息素交流是昆虫群落中维持生殖分工的一个关键机制。要了解信息素是如何进化来调节社会行为的,就必须了解信息素产生的分子调控。然而,即使在信息素被确定的情况下,我们对其生物合成和分子调控的了解仍然有限。熊蜂为探索信息素的生物合成提供了一个独特的系统,因为工蜂的杜富尔腺会产生酯类不育信号,这种信号不同于雌蜂特异的酯类,也不是由蜂王产生的。据推测,这些酯类是在储存这些酯类的外分泌腺中产生的,而且雌蜂、雄蜂和工蜂的杜氏腺基因在编码参与酯类生物合成的酶的表达上确实存在显著差异。然而,之前的转录组分析表明,尽管酯类生产和卵巢激活存在差异,但工蜂杜氏腺的基因表达却没有差异,这表明酯类生产可能是由下层调节的。对雌蜂、雄蜂和工蜂杜氏腺进行的蛋白质组学研究发现了 2400 多种蛋白质,与之前的 RNAseq 数据基本吻合。然而,在工蜂组之间发现了 100 多种不同表达的蛋白质,其中包括脂肪酸生物合成的关键酶,这表明工蜂的生殖信号生物合成的调控是在转录后完成的。总之,我们的数据提供了证据,证明杜氏腺中信息素的生物合成具有种姓特异性,雌虫和工虫很可能使用不同的酶来制造各自的蜡酯,而且对雌虫、雌虫和工虫信息素生产的调控很可能是在不同的调控水平上进行的,工虫信号受到蛋白质水平的调控。
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引用次数: 0
Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation. 鲤形目下五种鲤形目对虾线粒体基因组的序列比较:系统发育意义和分化时间估计。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1186/s12864-024-10775-4
Yuman Sun, Wanting Liu, Jian Chen, Jiji Li, Yingying Ye, Kaida Xu

Background: The Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.

Methods: Here, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.

Results: The mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.

Conclusions: This study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.

背景:鲤形目(Caridea)隶属于马氏目(Malacostraca)、十足目(Decapoda)和褶虾目(Pleocyemata),是最重要的虾类之一。它们广泛分布于世界各地不同的水生生境,丰富了它们的进化史。方法:本文利用第二代高通量测序技术测定了五种鲤形目物种的完整线粒体基因组(mitogenome)序列,这五种物种分别是Heterocarpus sibogae、Procletes levicarina、Macrobrachium sp.、Latreutes anoplonyx和Atya gabonensis。分析了它们有丝分裂基因组的基本结构特征、核苷酸组成、氨基酸含量和密码子使用偏向。此外,还计算了豹科、豹属和蚁属物种中蛋白质编码基因(PCGs)的选择压力值。根据来自103个鲤形目物种的13个PCGs的核苷酸和氨基酸序列构建了系统发生树,并估算了鲤形目内各科的分化时间:结果:这五个鲤形目物种的有丝分裂基因组长度从 15 782 个碱基对到 16 420 个碱基对不等,共编码 37 或 38 个基因,包括 13 个 PCGs、2 个 rRNA 基因和 22 或 23 个 tRNA 基因。具体来说,L. anoplonyx 编码一个额外的 tRNA 基因,使其基因总数达到 38 个。这五个物种的有丝分裂基因组的碱基组成中,腺嘌呤-胸腺嘧啶(AT)碱基所占比例较高。在这五个物种中发现了六个起始密码子和四个终止密码子。对氨基酸含量和密码子使用情况的分析表明这五个物种之间存在差异。对潘达尔科、帕拉伊蒙科和阿蒂科的选择压力分析表明,这三个科中 PCGs 的 Ka/Ks 值均小于 1,表明纯化选择影响了它们的进化。系统进化分析表明,鲤形目各科均为单系。基因重排和系统进化分析的结果表明了这两方面的相关性。化石记录支持的分化时间估计表明,鲤形目物种的分化发生在中生代的三叠纪,随后在侏罗纪分化为两大系:本研究探讨了鲤形目亚目有丝分裂基因组的基本特征和系统发育关系,为鲤形目分类、种间进化模式和各科的进化状况提供了有价值的见解。这些发现为鉴别虾类物种和检测鲤形目下统内的重大基因重排提供了重要参考。
{"title":"Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation.","authors":"Yuman Sun, Wanting Liu, Jian Chen, Jiji Li, Yingying Ye, Kaida Xu","doi":"10.1186/s12864-024-10775-4","DOIUrl":"https://doi.org/10.1186/s12864-024-10775-4","url":null,"abstract":"<p><strong>Background: </strong>The Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.</p><p><strong>Methods: </strong>Here, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.</p><p><strong>Results: </strong>The mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.</p><p><strong>Conclusions: </strong>This study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-wide identification of AP2/ERF gene family in Coptis Chinensis Franch reveals its role in tissue-specific accumulation of benzylisoquinoline alkaloids. 对黄连 AP2/ERF 基因家族的全基因组鉴定揭示了其在苄基异喹啉生物碱组织特异性积累中的作用。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1186/s12864-024-10883-1
Mengyu Zhang, Pingping Lu, Yating Zheng, Xue Huang, Junnan Liu, Han Yan, Huige Quan, Rui Tan, Fengming Ren, Hezhong Jiang, Jiayu Zhou, Hai Liao

Background: The Plant-specific AP2/ERF gene family encodes proteins involved in various biological and physiological processes. Although the genome of Coptis chinensis Franch, a plant producing benzylisoquinoline alkaloids (BIAs), has been sequenced at the chromosome level, studies on the AP2/ERF gene family in C. chinensis are lacking. Thus, a genome-wide identification of AP2/ERF gene family in C. chinensis was conducted to explore its role in BIAs biosynthesis.

Results: A total of 96 CcAP2/ERF genes were identified and categorized into five subfamilies, including 43 ERFs, 32 DREBs, 17 AP2s, 3 RAVs, and 1 Soloist, based on their structural domains. These CcAP2/ERF genes were unevenly distributed across nine chromosomes. Analysis of gene duplication events identified 17 CcAP2/ERF gene pairs in the genome, with 7 involved in tandem duplication events and 10 involved in segmental duplicate events, indicating that both types of duplications contributed to the expansion of the AP2/ERF gene family. The Ka/Ks ratio analysis suggested that the CcAP2/ERF gene family underwent strong purifying selection. Two phytohormones, methyl jasmonate and abscisic acid, were identified as potential key inducers of BIAs biosynthesis due to the cis-acting element prediction. Analysis of the spatial transcriptomic data revealed that 28 differentially expressed AP2/ERF genes had the highest or relatively higher expression levels in the rhizome, 17 of which positively correlated with the tissue-specific accumulation of BIAs. Further real-time PCR verification and protein-protein interaction analysis indicated that DREB1B might be one of the central regulators in a highly complex BIAs biosynthesis network.

Conclusion: These findings provide significant insight into the function of AP2/ERF genes in C. chinensis, particularly in the regulatory network of BIAs biosynthesis in C. chinensis. This study also identifies candidate genes for metabolic engineering to increase BIAs content in C. chinensis.

背景:植物特异性 AP2/ERF 基因家族编码参与各种生物和生理过程的蛋白质。尽管已对生产苄基异喹啉生物碱(BIAs)的植物 Coptis chinensis Franch 的基因组进行了染色体水平的测序,但缺乏对 C. chinensis 中 AP2/ERF 基因家族的研究。因此,本研究在全基因组范围内对盐肤木中的 AP2/ERF 基因家族进行了鉴定,以探讨其在 BIAs 生物合成中的作用:结果:共鉴定出 96 个 CcAP2/ERF 基因,并根据其结构域将其分为五个亚家族,包括 43 个 ERF、32 个 DREB、17 个 AP2、3 个 RAV 和 1 个 Soloist。这些 CcAP2/ERF 基因不均匀地分布在 9 条染色体上。对基因复制事件的分析发现,基因组中有17对CcAP2/ERF基因,其中7对涉及串联复制事件,10对涉及片段复制事件,表明这两种类型的复制都有助于AP2/ERF基因家族的扩展。Ka/Ks比值分析表明,CcAP2/ERF基因家族经历了强烈的纯化选择。由于顺式作用元件的预测,两种植物激素--茉莉酸甲酯和脱落酸--被确定为 BIAs 生物合成的潜在关键诱导因子。空间转录组数据分析显示,28 个差异表达的 AP2/ERF 基因在根茎中的表达水平最高或相对较高,其中 17 个基因与 BIAs 的组织特异性积累呈正相关。进一步的实时 PCR 验证和蛋白质相互作用分析表明,DREB1B 可能是高度复杂的 BIAs 生物合成网络中的核心调控因子之一:结论:这些研究结果为我们深入了解AP2/ERF基因在盐肤木中的功能,尤其是在盐肤木BIAs生物合成调控网络中的功能提供了重要依据。本研究还发现了可用于代谢工程以增加 BIAs 含量的候选基因。
{"title":"Genome-wide identification of AP2/ERF gene family in Coptis Chinensis Franch reveals its role in tissue-specific accumulation of benzylisoquinoline alkaloids.","authors":"Mengyu Zhang, Pingping Lu, Yating Zheng, Xue Huang, Junnan Liu, Han Yan, Huige Quan, Rui Tan, Fengming Ren, Hezhong Jiang, Jiayu Zhou, Hai Liao","doi":"10.1186/s12864-024-10883-1","DOIUrl":"https://doi.org/10.1186/s12864-024-10883-1","url":null,"abstract":"<p><strong>Background: </strong>The Plant-specific AP2/ERF gene family encodes proteins involved in various biological and physiological processes. Although the genome of Coptis chinensis Franch, a plant producing benzylisoquinoline alkaloids (BIAs), has been sequenced at the chromosome level, studies on the AP2/ERF gene family in C. chinensis are lacking. Thus, a genome-wide identification of AP2/ERF gene family in C. chinensis was conducted to explore its role in BIAs biosynthesis.</p><p><strong>Results: </strong>A total of 96 CcAP2/ERF genes were identified and categorized into five subfamilies, including 43 ERFs, 32 DREBs, 17 AP2s, 3 RAVs, and 1 Soloist, based on their structural domains. These CcAP2/ERF genes were unevenly distributed across nine chromosomes. Analysis of gene duplication events identified 17 CcAP2/ERF gene pairs in the genome, with 7 involved in tandem duplication events and 10 involved in segmental duplicate events, indicating that both types of duplications contributed to the expansion of the AP2/ERF gene family. The Ka/Ks ratio analysis suggested that the CcAP2/ERF gene family underwent strong purifying selection. Two phytohormones, methyl jasmonate and abscisic acid, were identified as potential key inducers of BIAs biosynthesis due to the cis-acting element prediction. Analysis of the spatial transcriptomic data revealed that 28 differentially expressed AP2/ERF genes had the highest or relatively higher expression levels in the rhizome, 17 of which positively correlated with the tissue-specific accumulation of BIAs. Further real-time PCR verification and protein-protein interaction analysis indicated that DREB1B might be one of the central regulators in a highly complex BIAs biosynthesis network.</p><p><strong>Conclusion: </strong>These findings provide significant insight into the function of AP2/ERF genes in C. chinensis, particularly in the regulatory network of BIAs biosynthesis in C. chinensis. This study also identifies candidate genes for metabolic engineering to increase BIAs content in C. chinensis.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11484470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Clusterin from endometrial glands plays a critical role in decidualization via Trem2. 来自子宫内膜腺体的集簇素通过 Trem2 在蜕膜化过程中发挥关键作用。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1186/s12864-024-10827-9
Sitong Yao, Yingni Chen, Rui Cao, Lin Lu, Jingsi Yang, Wei Lei, Yugu Li, Xiaohuan Liang

Background: Decidualization is a critical step in establishing pregnancy in mammals. Successful decidualization depends on intricate gland-stromal crosstalk. Clusterin (Clu) is a ubiquitously secreted protein in physiological fluids that is involved in numerous physiological functions. However, the role of Clu in decidualization is not fully understood.

Results: In this study, we examined the expression pattern of Clu during early pregnancy in mice and explored its potential function in decidualization. Our results revealed that Clu was expressed in the uterine glands on Days 1-2 of early pregnancy and on Days 5-8 during decidualization after embryo implantation, as well as in glands at the interimplantation site. Additionally, ovariectomized mice exhibited significant upregulation of Clu expression in the uterine glands 3 h after in vivo estrogen injection. Trem2, a receptor for Clu, was detected in the decidual region of mice on Days 5-8 of early pregnancy, where it mediates Clu to regulate the decidual region. Furthermore, we observed that recombinant CLU protein increased the expression of the decidualization marker molecules insulin-like growth factor binding protein 1 (IGFBP1) and prolactin (PRL) in decidual cells. However, this upregulation was not observed when Trem2 expression was inhibited with siRNA.

Conclusions: Uterine gland-derived Clu, a new paracrine modulator, may participate in early pregnancy by influencing the decidualization process mediated by Trem2 in mice.

背景:蜕膜化是哺乳动物建立妊娠的关键步骤。蜕膜化的成功取决于腺体与间质之间错综复杂的相互作用。Clusterin(Clu)是一种在生理液体中普遍分泌的蛋白质,参与多种生理功能。然而,Clu在蜕膜化过程中的作用尚未完全明了:在这项研究中,我们检测了小鼠妊娠早期 Clu 的表达模式,并探讨了其在蜕膜化过程中的潜在功能。结果:我们研究了小鼠早期妊娠过程中 Clu 的表达模式,并探讨了其在蜕膜化过程中的潜在功能。我们的结果显示,Clu 在早期妊娠第 1-2 天的子宫腺体中、胚胎植入后第 5-8 天的蜕膜化过程中以及中期植入部位的腺体中均有表达。此外,体内注射雌激素 3 小时后,卵巢切除的小鼠子宫腺体中的 Clu 表达明显上调。在妊娠早期的第5-8天,在小鼠的蜕膜区检测到了Clu的受体Trem2,它介导Clu调节蜕膜区。此外,我们还观察到重组 CLU 蛋白增加了蜕膜细胞中蜕膜化标记分子胰岛素样生长因子结合蛋白 1(IGFBP1)和催乳素(PRL)的表达。然而,当使用 siRNA 抑制 Trem2 的表达时,却观察不到这种上调:结论:子宫腺源性 Clu 是一种新的旁分泌调节因子,它可能通过影响由 Trem2 介导的小鼠蜕膜化过程而参与早孕。
{"title":"Clusterin from endometrial glands plays a critical role in decidualization via Trem2.","authors":"Sitong Yao, Yingni Chen, Rui Cao, Lin Lu, Jingsi Yang, Wei Lei, Yugu Li, Xiaohuan Liang","doi":"10.1186/s12864-024-10827-9","DOIUrl":"10.1186/s12864-024-10827-9","url":null,"abstract":"<p><strong>Background: </strong>Decidualization is a critical step in establishing pregnancy in mammals. Successful decidualization depends on intricate gland-stromal crosstalk. Clusterin (Clu) is a ubiquitously secreted protein in physiological fluids that is involved in numerous physiological functions. However, the role of Clu in decidualization is not fully understood.</p><p><strong>Results: </strong>In this study, we examined the expression pattern of Clu during early pregnancy in mice and explored its potential function in decidualization. Our results revealed that Clu was expressed in the uterine glands on Days 1-2 of early pregnancy and on Days 5-8 during decidualization after embryo implantation, as well as in glands at the interimplantation site. Additionally, ovariectomized mice exhibited significant upregulation of Clu expression in the uterine glands 3 h after in vivo estrogen injection. Trem2, a receptor for Clu, was detected in the decidual region of mice on Days 5-8 of early pregnancy, where it mediates Clu to regulate the decidual region. Furthermore, we observed that recombinant CLU protein increased the expression of the decidualization marker molecules insulin-like growth factor binding protein 1 (IGFBP1) and prolactin (PRL) in decidual cells. However, this upregulation was not observed when Trem2 expression was inhibited with siRNA.</p><p><strong>Conclusions: </strong>Uterine gland-derived Clu, a new paracrine modulator, may participate in early pregnancy by influencing the decidualization process mediated by Trem2 in mice.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11481393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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