Copy number variation of B1 controls awn length in wheat

Wheat awns contribute to photosynthesis and grain production.In this study,an F2population and F2:3families from a cross between the awned line 7D12 and the Chinese awnless variety Shiyou 20(SY20)were used to identify loci associated with awn length.Bulked-segregant RNA sequencing and linkage mapping identified a single dominant locus in a 0.3 cM interval on chromosome 5AL.Five genes were in the interval,including the recently cloned awn inhibitor B1.Although a single copy of the B1 gene was detected in 7D12,SY20 carried five copies of the gene.Increased copy number of B1 in SY20enhanced gene expression.Based on sequence variation among the promoter regions of five B1 gene copies in SY20,two dominant markers were developed and found to cosegregate with B1 in a population of 931 wheat accessions.All 77 awnless accessions harbored sequence variations in the B1 promoter regions similar to those of SY20 and thus carried multiple copies of the gene,whereas 15 randomly selected awned wheats carried only one copy.These results suggest that an increase in copy number of the B1 gene is associated with inhibition of awn length.

A proteomic approach to investigate the qualitative and quantitative polymorphism of <i>β</i>-lactoglobulin in ovine milk: Inference on gene copy-number variations

The rationale of this work is based on recent evidences suggesting that: 1) both qualitative and quantitative β-lactoglobulin (β-LG) polymorphism may be found in bovine milk;2) quantitative polymorphisms are often the result of expression gradients in multiple copies of a gene;3) the β-LG gene is duplicated in the dog and bovine genome;4) mammary genes are highly conserved across Mammalia. Thus, an investigation was conducted on ovine β-LG polymorphism checking phenotypic evidence for copy-number variants of β-LG in sheep. To the purpose, 206 milk samples were collected, during a small-scale survey within sheep farms breeding Southern Italian breeds. PAGIF screening of the samples revealed that approximately 50% individuals exhibited β-LG polymorphism and 4 different quantitative patterns, which were characterized in detail by a proteomic approach relying on combined chromatographic and mass spectrometric techniques. The expected figures based on the expression gradient models were compared with well-established α-globin gene arrangements in sheep. The different phenotypes suggest the presence of both duplicate and triplicate BLG haplotypes. The occurrence of a triplicate haplotype was supported by population data. The current study supports the helpfulness of up-to-date proteomics for inferring copy number polymorphisms through the characterization of the phenotypic expression.

Association between TLR7 copy number variations and hepatitis B virus infection outcome in Chinese

AIM To explore whether copy number variations (CNVs) of toll-like receptor 7 (TLR7) are associated with susceptibility to chronic hepatitis B virus (HBV) infection. METHODS This study included 623 patients (495 males and 128 females) with chronic hepatitis B virus infection (CHB) and 300 patients (135 females and 165 males) with acute hepatitis B virus infection (AHB) as controls. All CHB patients were further categorized according to disease progression after HBV infection (CHB, liver cirrhosis, or hepatocellular carcinoma). Copy numbers of the TLR7 gene were measured using the AccuCopy method chi(2) tests were used to evaluate the association between TLR7 CNVs and infection type. P values, odds ratios, and 95% confidence intervals (CIs) were used to estimate the effects of risk. RESULTS Among male patients, there were significant differences between the AHB group and CHB group in the distribution of TLR7 CNVs. Low copy numberof TLR7 was significantly associated with chronic HBV infection (OR = 0.329, 95% CI: 0.229-0.473, P > 0.001). Difference in TLR7 copy number was also found between AHB and CHB female patients, with low copy number again associated with an increased risk of chronic HBV infection (OR = 0.292, 95% CI: 0.173- 0.492, P < 0.001). However, there were no significant differences in TLR7 copy number among the three types of chronic HBV infection (CHB, liver cirrhosis, or hepatocellular carcinoma). In addition, there was no association between TLR7 copy number and titer of the HBV e antigen. CONCLUSION Low TLR7 copy number is a risk factor for chronic HBV infection but is not associated with later stages of disease progression.

Next‑Generation Sequencing‑Based Copy Number Variation Analysis in Chinese Patients with Primary Ciliary Dyskinesia Revealed Novel DNAH5 Copy Number Variations

Primary ciliary dyskinesia(PCD)is a rare disorder characterized by extensive genetic heterogeneity.However,in the genetic pathogenesis of PCD,copy number variation(CNV)has not received sufcient attention and has rarely been reported,especially in China.Next-generation sequencing(NGS)followed by targeted CNV analysis was used in patients highly suspected to have PCD with negative results in routine whole-exome sequencing(WES)analysis.Quantitative real-time polymerase chain reaction(qPCR)and Sanger sequencing were used to confrm these CNVs.To further characterize the ciliary phenotypes,high-speed video microscopy analysis(HSVA),transmission electron microscopy(TEM),and immunofuorescence(IF)analysis were used.Patient 1(F1:II-1),a 0.6-year-old girl,came from a nonconsanguineous family-I.She presented with situs inversus totalis,neonatal respiratory distress,and sinusitis.The nasal nitric oxide level was markedly reduced.The respiratory cilia beat with reduced amplitude.TEM revealed shortened outer dynein arms(ODA)of cilia.chr5:13717907-13722661del spanning exons 71–72 was identifed by NGS-based CNV analysis.Patient 2(F2:IV-4),a 37-year-old man,and his eldest brother Patient 3(F2:IV-2)came from a consanguineous family-II.Both had sinusitis,bronchiectasis and situs inversus totalis.The respiratory cilia of Patient 2 and Patient 3 were found to be uniformly immotile,with ODA defects.Two novel homozygous deletions chr5:13720087_13733030delinsGTTTTC and chr5:13649539_13707643del,spanning exons 69–71 and exons 77–79 were identifed by NGS-based CNV analysis.Abnormalities in DNA copy number were confrmed by qPCR amplifcation.IF showed that the respiratory cilia of Patient 1 and Patient 2 were defcient in dynein axonemal heavy chain 5(DNAH5)protein expression.This report identifed three novel DNAH5 disease-associated variants by WES-based CNV analysis.Our study expands the genetic spectrum of PCD with DNAH5 in the Chinese population.

Integrated Analysis of the Gene Expression Profiling and Copy Number Aberration of the Ovarian Cancer

Objective: DNA copy number alterations and difference expression are frequently observed in ovarian cancer. The purpose of this way was to pinpoint gene expression change that was associated with alterations in DNA copy number and could therefore enlighten some potential oncogenes and stability genes with functional roles in cancers, and investigated the bioinformatics significance for those correlated genes. Method: We obtained the DNA copy number and mRNA expression data from the Cancer Genomic Atlas and identified the most statistically significant copy number alteration regions using the GISTIC. Then identified the significance genes between the tumor samples within the copy number alteration regions and analyzed the correlation using a binary matrix. The selected genes were subjected to bioinformatics analysis using GSEA tool. Results: GISTIC analysis results showed there were 45 significance copy number amplification regions in the ovarian cancer, SAM and Fisher’s exact test found there have 40 genes can affect the expression level, which located in the amplification regions. That means we obtained 40 genes which have a correlation between copy number amplification and drastic up- and down-expression, which p-value < 0.05 (Fisher’s exact test) and an FDR < 0.05. GSEA enrichment analysis found these genes were overlapped with the several published studies which were focused on the gene study of tumorigenesis. Conclusion: The use of statistics and bioinformatics to analyze the microarray data can found an interaction network involved. The combination of the copy number data and expression has provided a short list of candidate genes that are consistent with tumor driving roles. These would offer new ideas for early diagnosis and treat target of ovarian cancer.

Deciphering the role of FSCN family genes in cancer:a pan-cancer bioinformatics study

Background:The Fascin(FSCN)family,comprising actin-bundling proteins,plays vital roles in cytoskeletal reorganization and cell migration.FSCN1,FSCN2,and FSCN3 are implicated in cancer progression through cell motility,invasion,and metastasis.However,their specific contributions across different cancer types remain unclear.Methods:We conducted a pan-cancer bioinformatics analysis of FSCN genes using data from The Cancer Genome Atlas.This included differential expression patterns,copy number variations(CNVs),mutations,methylation status,and correlations with tumor mutational burden,microsatellite instability,and immune checkpoint molecule expression.Differential expression was analyzed using DESeq2,while CNV and mutation analyses utilized GISTIC2.0 and MuTect2.Methylation data were assessed using the Illumina Human Methylation 450K BeadChip.Results:FSCN1 and FSCN2 showed significant differential expression in multiple cancers,often correlating with poor prognosis.FSCN3 exhibited less variability but a protective role in certain contexts.CNV analysis indicated frequent gene gains in FSCN genes,correlating with increased expression.FSCN3 had a higher mutation rate,suggesting genetic instability.Methylation analysis showed hypomethylation of FSCN1 and FSCN2 in tumors compared to normal tissues,whereas FSCN3 had minor changes.Significant associations were found between FSCN gene expression and tumor mutational burden,microsatellite instability,and immune checkpoint molecules,suggesting their involvement in tumor immunogenicity and the immune microenvironment.Conclusions:This pan-cancer analysis highlights the multifaceted roles of FSCN genes in cancer biology,emphasizing their potential as biomarkers and therapeutic targets.FSCN1 and FSCN2 are associated with poor prognosis and aggressive phenotypes,while FSCN3 shows protective roles in specific contexts.These findings offer new avenues for cancer diagnosis and treatment,particularly in personalized medicine.Future studies should validate these findings and explore the underlying mechanisms to fully harness the clinical potential of FSCN family proteins in oncology.

人恶性胸膜间皮瘤DNA从头测序及基因突变分析

通过DNA从头测序分析人胸膜间皮瘤发生的高关联度突变基因。提取恶性胸膜间皮瘤(MPM)组织和正常胸膜组织DNA,构建基因文库,用Illumina HiSeqX Ten PE 150平台测序,将测序结果与人类基因组数据库的参考序列进行比对、注释,并对测序结果进行过滤、错误率分布检查、GC含量分布检查分析。MPM组织DNA平均过滤37829946 bp,错误率小于0.12%,GC含量占41.17%,而正常胸膜组织DNA平均过滤39089681 bp,错误率小于0.1%,GC含量占41.7%,两者测序质量均在Q 30(≥80%)以上,MPM为87.43%,正常胸膜为88.36%。以上高质量测序数据通过BWA比对到参考基因组(GRCh 37/hg 19),得到最初比对序列,利用重复标记后的比对序列进行覆盖度、深度等统计,覆盖深度达到10 X以上该突变位点可信。结果显示,实验病例XL14覆盖深度达到10 X的占98.59%,覆盖率达到99.83%;对照病例Z5占98.50%,覆盖率达到99.79%。对该序列进行基因注释分析,发现一系列单核苷酸多态性、基因插入缺失、基因结构变异、基因拷贝数变异,筛选出总变异位点数29277个,可能致病的变异位点数22个,致病性的变异位点数5个,不确定变异有害性的位点数为3353个,其余变异位点均为良性。进一步对突变基因进行富集、关联性分析,预测出突变基因TXNDC2与人胸膜间皮瘤的发生高度相关,相关系数达到0.8以上;突变基因PIEN、ABCC1、UGT1A7、UGT1A3、UGT1A4、UGT1A9、ALDH3B1、UGT1A5等与人胸膜间皮瘤有一定关联性,关联度在0~0.2之间。基因TXNDC2、PIEN、ABCC1、UGT1A7、UGT1A3、UGT1A4、UGT1A9、ALDH3B1、UGT1A5的变异可能与人胸膜间皮瘤的发生发展有关。本实验为人胸膜间皮瘤分子诊断提供了参考。

LMNB1相关常染色体显性遗传成人型脑白质营养不良家系分析

目的总结一个LMNB1相关常染色体显性遗传成人型脑白质营养不良(adult-onset autosomal dominant leukodystrophy,ADLD)家系的临床、影像学特点,并进行致病性变异分析。方法选取2023年11月首都医科大学宣武医院确诊为ADLD患者1例,收集先证者及家系其他患者的临床和影像学资料,对先证者进行全外显子组测序分析及LMNB1基因的多重连接探针扩增(multiplex ligation-dependent probe amplification,MLPA)检测,并进行致病性分析和表型匹配分析。结果本例患者(先证者)男,44岁,因“大小便障碍3年,双下肢乏力2年余”就诊,基因检测示LMNB1基因1-11号外显子重复变异,评定为致病性变异,表型与ADLD匹配,先证者(Ⅲ:9)和Ⅲ:6以自主神经功能障碍起病,系ADLD典型表现,Ⅱ:11首发症状为头部震颤,与其他患者不同。结论ADLD患者的LMNB1基因1-11号外显子重复变异,符合常染色体显性遗传方式。成年患者以自主神经功能障碍起病,随后累及小脑、锥体束,MRI示广泛对称的脑白质病变、脊髓萎缩时应考虑ADLD,建议行LMNB1基因检测。

KIT杂合大片段缺失导致斑驳病一家系的临床表型

目的鉴定一个斑驳病家系的致病基因突变。方法收集斑驳病患者及其家系成员的临床资料,采集外周血,进行全外显子组测序。通过qPCR验证目的基因的缺失;采用gap-PCR结合Sanger测序法确定具体缺失的大小以及位点。结果在先证者4号染色体上存在约1.74 Mb的杂合大片段缺失突变,其中包括了全部KIT(斑驳病的致病基因)。该缺失在家系中呈基因型-表型共分离,在dbSNV数据库中未见该区域的缺失报道。该缺失是目前报道的最小的因KIT全长缺失而导致斑驳病表型的片段缺失。结论KIT缺失是导致该家系斑驳病表型的原因。

阿什旦牦牛MEF2A基因拷贝数变异与生长性状关联分析

为探究MEF2A基因拷贝数变异对阿什旦牦牛生长性状的影响,测定了92头阿什旦牦牛6月龄、12月龄、18月龄、30月龄的体重、体高、体长、胸围,采用qPCR检测了MEF2A基因的相对表达量,并利用SPSS软件进行了关联分析。结果表明,MEF2A基因拷贝数变异与阿什旦牦牛的18月龄胸围、6月龄体长呈极显著相关(P<0.01),与18月龄体高呈显著相关(P<0.05);6月龄体长正常型极显著高于其他两个类型(P<0.01),18月龄体高正常型显著低于增加型(P<0.05)、胸围缺失型和正常型极显著高于增加型(P<0.01);MEF2A基因在阿什旦牦牛肌肉组织中的表达量极显著高于其他组织(P<0.01)。综上,MEF2A基因拷贝数变异可影响阿什旦牦牛的生长发育。

拷贝数变异在卵巢癌中的研究进展

遗传变异是导致癌症发生和发展的重要因素之一。拷贝数变异是遗传多样性的重要来源,在结构上表现为基因的扩增或缺失,与肿瘤的发生和发展有关。采用高通量测序和基因芯片技术可以检测拷贝数的变异情况,提供相关的肿瘤分子特征、预后和治疗相关的信息,有利于临床上对患者进行更准确的诊断和治疗决策。卵巢癌在女性生殖系统疾病中的病死率极高,了解其发病机制对提高卵巢癌患者的生存率至关重要。目前拷贝数变异在卵巢癌中的具体作用和机制仍然不清楚,文章就现有的研究结果对与卵巢癌相关的拷贝数变异进行综述,以期为卵巢癌的预防、诊断及治疗等方面提供新的思路和方法。

Deletion and down-regulation of SMAD4 gene in colorectal cancers in a Chinese population

Objective： Colorectal cancer（CRC） is one of the most common types of human cancers. As a tumor suppressor, SMAD4 plays a key role in colorectal carcinogenesis and invasiveness. Copy number variations（CNVs） of the SMAD4 gene have been reported to be associated with cancer pathogenesis in array-based studies in different populations. Here we aimed to investigate the CNVs of the SMAD4 gene in a relatively large number of CRC patients from China. Methods： In the present study, we collected 147 Chinese CRC tumors as well as self-paired normal control tissues. Quantitative PCR was carried out to examine the copy number as well as the m RNA expression of the SMAD4 gene. Results： Our results showed that the copy number deletions of SMAD4 were frequent in a relatively high percentage of CRC samples（34.7%, 51 out of 147）. There was a positive correlation between the copy number decrease of SMAD4 and tumor progression in CRCs. Furthermore, copy number loss of SMAD4 was correlated with decreased m RNA expression.Conclusions： These findings suggested that the copy number deletions of SMAD4 were frequent in CRC patients from China and had the potential to serve as a diagnostic indicator, alone or in combination with other markers, for CRC.

SPTB基因CNV缺失导致的遗传性球形红细胞增多症家系遗传学分析

目的:对一个遗传性球形红细胞增多症家系进行临床表征及基因变异分析,并探讨其发病的分子机制。方法:先证者因黄疸、贫血于2021年5月就诊于潍坊市益都中心医院,采集其家系6人外周血,采用二代测序对先证者及其家系患病成员及3名健康成员进行致病基因变异筛查,选取有临床意义的变异位点,结合有关数据库对变异位点进行分析;对候选变异基因的m RNA表达水平进行RT-q PCR分析。利用Uni Prot与SMART数据库分析SPTB蛋白的结构与功能。结果:含近700个基因的二代测序结果筛查到SPTB基因CNV缺失与该家系患者表型共分离。通过UCSC数据库分析确定该缺失区域主要位于SPTB基因exon2-3。RT-q PCR分析表明患者SPTB m RNA水平明显低于健康对照。Uni Prot与SMART数据库分析表明缺失CH1、CH2结构域的SPTB蛋白不能与红细胞膜肌动蛋白结合。结论:SPTB基因CNV缺失可能是导致该家系遗传性球形红细胞增多症的原因。

不明原因发育迟缓/精神发育迟缓儿童基因检测结果研究

背景 发育迟缓(DD)/精神发育迟缓(MR)病因复杂,临床表现多样、异质性强,该类患儿的早期精准诊断十分困难,目前国内鲜有大样本分析该类患儿的临床资料及基因检测结果。目的 分析DD/MR患儿基因检测结果,为DD/MR患儿确定遗传学诊断、制订治疗方案和判断预后提供依据。方法 选取2017年9月至2021年9月于昆明市儿童医院康复科就诊的致病原因尚不明确的93例DD/MR患儿为研究对象,对患儿进行全外显子组测序(WES)和拷贝数变异(CNV)检测,分析与患儿临床表现相关的致病性基因突变位点和CNV特点,分析基因突变检出情况。结果 93例患儿临床表现包括运动发育落后、智力低下或全面性发育落后,发育水平落后于正常发育里程碑。共检出遗传变异74例,检出率为79.6%,其中40例(43.0%)为致病性基因突变,13例(14.0%)为基因CNV,21例(22.6%)为突变意义未明。基因检测结果共涉及50种基因,所致疾病中SMN1基因突变引起的脊髓性肌萎缩症所占比例最高(10.0%,4/40),其次为COL6A2基因突变引起的Bethlem综合征1型(7.5%,3/40)及CSPP1基因突变所致的Joubert综合征21型(5.0%,2/40)。结论 致病基因突变和基因CNV可能是导致DD/MR的主要病因,SMN1、COL6A2、CSPP1为DD/MR患者常见突变基因,WES结合CNV检测对明确DD/MR的病因,特别是对诊断表型和临床表现不典型的患儿有重要意义。

人肝癌细胞系HepG2和Huh7中的基因组拷贝数变异分析

目的利用人肝细胞癌拷贝数变异和转录组实验,结合临床公共数据,探索肝细胞癌的拷贝数变异对肝癌发生发展的影响。方法用光学基因组图谱技术识别肝癌细胞系HepG2和Huh7中的拷贝数变异,随后分析两种细胞系拷贝数变异基因的功能,并根据富集通路绘制蛋白质相互作用网络。选取两个细胞系核心网络中的关键基因,分析肝细胞癌拷贝数变异与基因表达之间的关系。GEPIA数据库分析基因表达与患者临床生存的关系。用RNA-seq实验和公共数据验证基因的表达水平。结果HepG2细胞主要存在拷贝数增加,相关基因富集在雌激素信号通路、金黄色葡萄球菌感染等通路;Huh7细胞系中既有拷贝数增加又有减少,相关基因主要富集嗅觉传导、细胞因子-细胞因子受体相互作用等通路。关键基因SRC、MAPK3和MAP3K7拷贝数与基因表达成正比,并且高表达这些基因的患者生存期显著降低(P<0.05)。相比于HEK293T细胞系,SRC、MAP3K7基因在两个肝癌细胞系的表达显著升高(P<0.001),提示了肝细胞癌的特异性变异,MAPK3无差异。结论肝细胞癌拷贝数变异基因SRC、MAP3K7的表达与患者的预后显著相关,可能影响肝细胞癌的发生发展和异质性。

基因芯片在胎儿超声软指标的异常中的应用研究

目的探讨基因芯片在胎儿超声软指标的异常中的应用研究。方法选择2020年8月至2022年8月于赣州市妇幼保健院收集且行产前超声发现胎儿异常的单胎孕妇76例作为研究对象,均抽取羊水进行染色体核型分析及基因芯片分析,根据基因芯片的检查方法、样本类型、超声类型、超声异常项数进行分组。比较各组孕妇的染色体异常检出率。采用Spearman分析超声类型、项数与染色体异常的相关性。结果不同检查方法的染色体异常检出率比较,差异无统计学意义(P>0.05)。不同超声类型的非整倍体异常检出率比较,差异有统计学意义(P<0.05),不同超声类型的致病性拷贝数变异(PCNVs)、杂合性缺失(LOH)及染色体异常总检出率比较,差异无统计学意义(P>0.05)。不同超声项数的PCNVs、染色体异常总检出率比较,差异有统计学意义(P<0.05)。不同超声项数的非整倍体异常、LOH异常检出率比较,差异无统计学意义(P>0.05);经Spearman分析,超声类型(r=0.288)、项数(r=0.334)与染色体异常均呈正相关(P<0.05)。结论引产胎儿多伴有染色体异常,基因芯片分析有助于提高超声异常胎儿染色体异常检出率,且非整倍体异常、PCNVs等染色体异常与超声类型、项数之间存在一定相关性。

高胰岛素血症/高氨血症综合征一家系的遗传学研究

目的分析高胰岛素血症/高氨血症(HI/HA)综合征一家系的临床和遗传学特征。方法采集先证者及其父母外周血行全外显子组及DNA拷贝数变异测序分析,初步确定候选致病基因,并通过Sanger测序在先证者及其父母、祖母中对突变位点进行验证。结果先证者因抽搐就诊,发现低血糖,其父亲和祖母同样有低血糖发作症状。先证者及其父亲、祖母在GLUD1基因11号外显子均存在c.1466C>T,p.P489L(p.Pro489Leu)杂合错义突变。结论GLUD1[c.1466C>T(p.P489L)]错义突变为该家系的致病原因,该突变在中国HI/HA综合征家系中首次发现。

数字PCR技术的发展和应用

数字PCR(digital PCR,dPCR)技术作为一种全新的核酸检测方法,通过把反应体系均分到大量反应单元中独立地进行PCR,并根据泊松分布和阳性比例来计算核酸数量。目前dPCR主要分为微滴式和芯片式两种。与传统PCR技术相比,dPCR具有高灵敏度、高精确度、高耐受性和绝对定量的优点。因此,dPCR技术在近年来得到了迅速的发展,广泛地应用于稀有突变检测、拷贝数变异分析和复杂样本基因表达检测等方面。

中国卵巢早衰妇女全基因组染色体拷贝数变异分析

目的：探讨卵巢早衰（premature ovarian failure， POF）患者染色体拷贝数的变异。方法：采用病例-对照研究方法对全基因组染色体拷贝数变异进行分析，用Affymetrix SNP6.0 芯片对30例POF患者和30例对照者进行对比研究。用定量PCR对芯片结果进行了验证，并在另外40例 POF 患者中进一步确证。结果：芯片共发现101个片段大小在0.1~5.6 MB的微缺失和扩增，包括8个新扩增和12个新的微缺失。实时定量PCR证实了位于染色体10q26.12，10q26.3，2p16.3和6p26的4个微缺失和位于染色体20p12.3和7p22.2的2个扩增。结论：本研究揭示了中国妇女POF 患者基因组拷贝数变异（copy number variants，CNV）的变化，在这些编码区发现有5个基因SYCE1,CYP2E1,NRXN1,PARK2和CARD11可能与POF有关。

基于33个遗传多样性水稻材料的泛基因组分析揭示“隐藏”的基因组变异

【目的】基因组结构变异(SV)和基因拷贝数变异(g CNV)是动植物中主要的遗传变异来源,全面准确地鉴定和分析SV和g CNV对挖掘优异等位基因、保障水稻粮食安全具有重要意义。【方法】利用长片段测序数据和基因组装方法(HERA),对31个具有遗传多样性的水稻栽培稻进行了高质量基因组组装,结合日本晴和蜀恢498高质量基因组,进行了系统的基因组比较分析。【结果】共鉴定到171072个非冗余SVs和25549个g CNVs,其中82.8%的PAV未在先前基于短序列测序数据获得的PAV中鉴定到。利用非洲栽培稻CG14作为外群,对发生在亚洲栽培稻群体的SV(d SV)进行了推断,发现大多数d SV位于基因非编码区,以及泛基因组中50%(32668)基因上下游2 kbp区域在32个亚洲栽培稻种至少有一个d SV。进一步结合转录组数据分析发现SVs和g CNVs对调控基因表达量对具有重要作用。对SV形成机制分析发现,SV主要由TEI(转座子插入)和NHEJ(非同源末端连接)两种机制形成,但不同类型SV的主要形成机制有所不同。该研究还构建了水稻中首个图形基因组,结合674份材料的二代测序和叶片早衰数据,发现17.5%的SV与其附近SNP的连锁度非常低,GWAS分析发现一个与叶片早衰显著相关的位点只能被SV检测到。相关研究成果以"Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations"为题于2021年5月发表在国际期刊Cell。【结论】提供了一个高质量泛基因组水平的基因组变异资源,将促进水稻的功能基因组和进化生物学研究、优异基因资源发掘和水稻育种。