REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

Background

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data.

Results

We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of recombination detection algorithms. A newly generated NGS dataset from a genetic cross of Toxoplasma gondii allowed us to demonstrate our pipeline. REDHORSE successfully extracted the relevant genetic markers and was able to transform the read alignments from NGS to the genome to generate multiple sequence alignments. Recombination detection algorithm in REDHORSE was able to detect conventional crossovers and double crossovers typically associated with gene conversions whilst filtering out artifacts that might have been introduced during sequencing or alignment. REDHORSE outperformed other commonly used recombination detection algorithms in finding conventional crossovers. In addition, REDHORSE was the only algorithm that was able to detect double crossovers.

Conclusion

REDHORSE is an efficient analytical pipeline that serves as a bridge between genomic alignments and existing recombination detection algorithms. Moreover, REDHORSE is equipped with a recombination detection algorithm specifically designed for Next-generation sequencing data. REDHORSE is portable, platform independent Java based utility that provides efficient analysis of genetic crosses based on Next-generation sequencing data. REDHORSE is available at http://redhorse.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1309-7) contains supplementary material, which is available to authorized users.     

近交系MIJ和HFJ大鼠部分生理数据测定和分析

目的测定近交系大鼠MIJ、HFJ和封闭群Wistar大鼠的脏器系数、体温、呼吸频率、肠管长度,观察两个近交系大鼠的生理表型。方法 采用常规方法对大鼠脏器系数、体温、呼吸频率及肠管长度进行测定,并对HFJ、MIJ、Wistar大鼠三者间进行比较。结果①体重:HFJ、MIJ、Wistar大鼠同性别间比较差异无显著性。②脏器系数:HFJ与Wistar大鼠雄性间心脏、肺,雌性间子宫、肝;MIJ与Wistar大鼠雄性间肺、脾,雌性间脑、脾,差异均有显著性。HFJ与MIJ大鼠雄性间脑,雌性间脑和脾差异有显著性。HFJ大鼠不同性别间肝、脑、眼球差异有显著性。MIJ大鼠不同性别间,脑、心脏、肾、肺、脾和眼球差异均有显著性。③体温:HFJ雌性大鼠明显高于Wistar雌性,雄性间差异无显著性。HFJ大鼠雌性高于雄性,差异有显著性。④呼吸频率:HFJ雌性大鼠低于同性Wistar大鼠,MIJ大鼠雌性和雄性均高于同性别Wistar大鼠,差异有显著性。⑤肠管长度:HFJ与Wistar同性别间比较,肠管总长和小肠差异有显著性。MIJ与Wistar大鼠雄性间肠管总长、大肠、小肠、盲肠差异均有显著性,雌性间肠管总长、小肠、盲肠差异有显著性。HFJ与MIJ大鼠同性别间差异均无显著性,不同性别的HFJ和MIJ的肠管总长、大肠和小肠差异有显著性。结论 MIJ和HFJ近交系大鼠的脏器系数、体温、呼吸频率、肠管长度都各有其独特的生理概貌。     

落葵薯粘液细胞分布及发育的解剖学研究

采用石蜡切片法对落葵薯(Anredera cordifolia(Tenore)Steenis)粘液细胞的分布及发育进行了研究。结果表明,粘液细胞普遍存在于落葵薯的茎、叶、叶柄中,粘液细胞单个散生分布于茎的髓及皮层组织中;叶的栅栏组织和海绵组织中都可见粘液细胞,且海绵组织中的数量明显多于栅栏组织中的;叶柄中的粘液细胞不多,主要分布在维管束四周的皮层组织中。粘液细胞的发育分为4个阶段:原始细胞阶段、液泡化阶段、成熟阶段和细胞质解体阶段。粘液细胞最早出现于第六叶原基,且其发育与茎、叶器官的组织分化不同步。     

Importancia de la determinación de variantes en el número de copias en neonatos con aneuploidías autosómicas

Introduction:

Aneuploidies are frequent genetic disorders in clinical practice. However, little is known about other genetic variants that may influence the final phenotype.

Objective:

To determine the variations in the number of copies and regions with homozygosity greater than 0.5% or larger than 10 Mb in newborns with autosomal aneuploidies.

Materials and methods:

We performed a chromosomal microarray analysis on newborns with autosomal aneuploidies (n=7), trisomy 21 (n=5), and trisomy 18 (n=2) evaluated at the Hospital Antonio Lorena and Hospital Regional of Cusco, Perú, during 2018.

Results:

We found pathogenic and probably pathogenic variants in the number of copies in other genomic regions different to chromosomes 21 or 18 in two neonates. Additionally, we found two variants bigger than 500 kpb of unknown pathogenicity.

Conclusions:

Although the number of analyzed individuals was small, it is important to highlight that we found other variants in the number of copies that have been described in association with neurodevelopmental disorders, congenital anomalies, deafness, and short/ tall stature, among others, in almost half of them, which will probably impact the phenotype negatively in patients with aneuploidies.     

贵州苏铁根的解剖学研究

对贵州苏铁（Cycas guizhouensis K.M.Lan et R.F.Zou）的根进行了解剖学研究,结果表明：（1）据外部形态和内部结构不同,贵州苏铁的根可分为正常根、珊瑚状根和肉质根三种类型。（2）正常根与肉质根的木栓形成层起源于表皮内方第1～2层皮层薄壁细胞,珊瑚状根的木栓形成层则起源于外方皮层的第2～3层细胞,而非中柱鞘。（3）首次发现肉质根一种新的增粗方式,是由周皮内方的皮层薄壁细胞恢复分裂能力,持续或周期性产生新的皮层薄壁细胞,引起根的增粗。     

Copy number variations (CNVs) in human pluripotent cell-derived neuroprogenitors

Results from the analysis of copy number variations (CNVs) in human pluripotent cell-derived neuroprogenitor cell lines (hiPSC and hESC-derived NPC) are presented. Two different types of CNVs were detected: a) CNVs inherited from the original source of pluripotent cells (hESC and hiPSC) and b) CNVs detected either in the original source of pluripotent cells or in the derived NPC cell lines but not in both at the same time. Our data suggest that submicroscopic chromosomal changes happened during culture and manipulation of cells and those differentiation procedures could result in gains and losses of genomic regions in pluripotent cell-derived neuroprogenitors. Overall, the results indicate that even chromosomally stable stem cell lines would need to be analyzed in detail by high resolution methodologies before their clinical use.     

长江刀鲚产卵洄游群体的年龄结构及其生物学特征变化

溯江产卵洄游中的刀鲚是目前长江最为名贵的水产品之一。本文分析了2009年4~5月采自长江九段沙、靖江和芜湖3个江段的299尾洄游型刀鲚样本。结果显示,3个群体的体长范围为15.8~32.8(平均23.32?3.49)cm,18~24cm体长组占总数的52.51%。体重范围为11.83~143.8 (平均48.19?24.89) g,10~50g体重组占总数的59.53%。芜湖群体的体长和体重均显著小于九段沙和靖江群体(ANOVA, p=0.000<0.001)。299尾个体包括1~4龄4个年龄组,其中51.28%的九段沙个体和53.97%的靖江个体均为3龄;而多达85.26%的芜湖个体则为2龄。不论体长、体重还是年龄结构,已较上世纪70年代同江段渔获物有明显下降。结果还显示,研究样本的雌雄性比为1:1.57,九段沙、靖江和芜湖群体的性比分别为1:1.28、1:1.46和1:1.97,显示出沿长江往上性比逐渐增加的现象。3个群体的平均丰满度为0.35?0.049,但即使是在同龄组间,靖江群体的丰满度也显著高于芜湖和九段沙群体,这可作为大个体刀鲚在这一江段最名贵高价的一种解释。     

Duplication of CXC chemokine genes on chromosome 4q13 in a melanoma-prone family

Copy number variations (CNVs) have been shown to contribute substantially to disease susceptibility in several inherited diseases including cancer. We conducted a genome-wide search for CNVs in blood-derived DNA from 79 individuals (62 melanoma patients and 17 spouse controls) of 30 high-risk melanoma-prone families without known segregating mutations using genome-wide comparative genomic hybridization (CGH) tiling arrays. We identified a duplicated region on chromosome 4q13 in germline DNA of all melanoma patients in a melanoma-prone family with three affected siblings. We confirmed the duplication using quantitative PCR and a custom-made CGH array design spanning the 4q13 region. The duplicated region contains 10 genes, most of which encode CXC chemokines. Among them, CXCL1 (melanoma growth-stimulating activity α) and IL8 (interleukin 8) have been shown to stimulate melanoma growth in vitro and in vivo. Our data suggest that the alteration of CXC chemokine genes may confer susceptibility to melanoma.     

Single Cell Genomics of the Brain: Focus on Neuronal Diversity and Neuropsychiatric Diseases

Single cell genomics has made increasingly significant contributions to our understanding of the role that somatic genome variations play in human neuronal diversity and brain diseases. Studying intercellular genome and epigenome variations has provided new clues to the delineation of molecular mechanisms that regulate development, function and plasticity of the human central nervous system (CNS). It has been shown that changes of genomic content and epigenetic profiling at single cell level are involved in the pathogenesis of neuropsychiatric diseases (schizophrenia, mental retardation (intellectual/leaning disability), autism, Alzheimer’s disease etc.). Additionally, several brain diseases were found to be associated with genome and chromosome instability (copy number variations, aneuploidy) variably affecting cell populations of the human CNS. The present review focuses on the latest advances of single cell genomics, which have led to a better understanding of molecular mechanisms of neuronal diversity and neuropsychiatric diseases, in the light of dynamically developing fields of systems biology and “omics”.     

热带喀斯特森林常绿和落叶榕树的水力特征和水分关系与抗旱策略

以热带喀斯特地区的直脉榕(Ficus orthoneura)和豆果榕(F.pisocarpa)为实验材料,研究了常绿和落叶树木枝条和叶片的解剖结构特征、光合水分特征和耐旱性的差异,目的在于探讨不同生活型榕树适应干旱生境的策略.直脉榕和豆果榕的叶片都有两层栅栏组织、游离状的海绵组织和钟乳体等旱生结构,同时叶片角质层蒸腾速率(gmin)和气孔导度(gs)相对较低.但与落叶的豆果榕相比,常绿的直脉榕的枝条木质部失去50％传导率的水势(P50)和gmin更低,表现出更保守的水分利用策略.总体上,两种榕树都表现出了对喀斯特干旱生境的良好适应,但是它们的适应策略表现出一定的差别.豆果榕通过落叶度过旱期,而直脉榕在结构和功能上比豆果榕更耐旱.抗旱策略和水分利用策略的不同导致两种榕树的生态位分异,减少了彼此间的水分竞争,有利于它们在喀斯特生境中共存.