Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.

/pdf/efficient-de-novo-assembly-of-highly-heterozygous-genomes-4vmguhvfxx.pdf

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus

/pdf/the-brassica-oleracea-genome-reveals-the-asymmetrical-2y7hgd5bni.pdf

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

Because lignin limits the use of wood for fiber, chemical, and energy production, strategies for its downregulation are of considerable interest. We have produced transgenic aspen (Populus tremuloides Michx.) trees in which expression of a lignin biosynthetic pathway gene Pt4CL1 encoding 4-coumarate:coenzyme A ligase (4CL) has been downregulated by antisense inhibition. Trees with suppressed Pt4CL1 expression exhibited up to a 45% reduction of lignin, but this was compensated for by a 15% increase in cellulose. As a result, the total lignin–cellulose mass remained essentially unchanged. Leaf, root, and stem growth were substantially enhanced, and structural integrity was maintained both at the cellular and whole-plant levels in the transgenic lines. Our results indicate that lignin and cellulose deposition could be regulated in a compensatory fashion, which may contribute to metabolic flexibility and a growth advantage to sustain the long-term structural integrity of woody perennials.

Biotechnology on genetic control of lignin biosynthesis in trees -Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees-

The invention provides an SNP (single nucleotide polymorphism) marker for identifying pear early blossoming on basis of a high-resolution melting curve and an application of the SNP marker and discloses SNP molecular marker primers closely related to the pear early blossoming and the application of the SNP molecular marker primers. The SNP marker Pef072-01 closely related to the pear early blossoming contains the primers represented as SEQ ID NO.1 and SEQ ID NO.2. The pear early blossoming time can be subjected to good typing by the specific primers on the basis of the high-resolution meltingcurve. The molecular marker primers for the pear early blossoming can be used for marker-assisted selection breeding for the pear early blossoming and have great theoretical and practical guiding significance for accelerating genetic improvement progress of the pear variety and improving breeding selection efficiency.

SNP (single nucleotide polymorphism) marker for identifying pear early blossoming on basis of high-resolution melting curve and application of SNP marker

Protein disulfide isomerase (PDI) is an important enzyme for protein folding in endoplasmic reticulum. The PDI gene family has been systematically studied in Arabidopsis, barley, rice, and bread wh...

https://bioone.org/journals/Canadian-Journal-of-Plant-Science/volume-98/issue-5/cjps-2017-0302/Phylogenetic-and-expression-analysis-of-protein-disulfide-isomerase-unravels-good/10.1139/cjps-2017-0302.pdf

Phylogenetic and expression analysis of protein disulfide isomerase unravels good reference genes for gene expression studies in pear and peach fruits

The invention discloses a SNP molecular marker primer closely related to the pear pulp low stone cell content. The SNP markers closely related to the pear pulp low stone cell content are Psc397-7, Psc397-12, and the primers are SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4. Based on a high resolution dissolution curve, the specific primers can well type the pulp low stone cell content. The pear pulp stone cell content molecular marker primer can be used in molecular marker assisted selection breeding of the pear pulp low stone cell content, and has great theoretical and practical guiding significance to speed up the genetic improvement process of pear varieties and improve the selection efficiency of breeding.

SNP marker based on high resolution dissolution curve for identifying pear pulp low stone cell content and application thereof

The invention discloses SNP (single-nucleotide polymorphism) molecular marker primers for pear fruit sepal state major QTL (quantitative trait locus) site and application thereof. According to the SNP marker Pybd06_026, the forward primer CALYX-F is disclosed as SEQ ID NO.1, and the reverse primer CALYX-R is disclosed as SEQ ID NO.2. The specific primers can be used for performing favorable typing on the sepal state on the basis of a high-resolution dissolution curve, i.e. detecting the difference between the polymorphism expression sepal states on the QTL site qCalyx. The molecular marker primers for pear fruit sepal state major QTL can be used for molecular marker assisted selective breeding of pear fruit sepal state, and have important theoretical and practical instruction meanings for accelerating the pear variety genetic improvement progress and enhancing the breeding selection efficiency.

SNP (single-nucleotide polymorphism) molecular marker primers for pear fruit sepal state major QTL (quantitative trait locus) site and application thereof

The invention discloses a pear transcription factor PbrMYB169 and an application thereof. The pear transcription factor PbrMYB169 is separated from Dangshan crisp pears, and has MYB family member PbrMYB169 genes capable of adjusting and controlling development of sclereid of pear fruits, the nucleotide sequence of the pear transcription factor PbrMYB169 is as shown in SEQID No.1, and the coding amino acid sequence of the pear transcription factor PbrMYB169 is as shown in a sequence table SEQID No.2. Through an agrobacterium tumefaciens mediated heredity conversion method, PbrMYB169 transcription factors are converted into arabidopsis thaliana, and transgenic plants are obtained; biological function verification indicates that the PbrMYB169 gene cloned through the pear transcription factorPbrMYB169 has the function of promoting synthesis of arabidopsis thaliana inflorescence stem lignin, besides, the PbrMYB169 transcription factor has the advantage of being capable of adjusting and controlling a plurality of genes, and an efficient way is provided for molecular breeding. New genetic resources are provided for reduction of molecular breeding of synthesis of organism lignin, new heredity resources are provided for implementing green agriculture, and reduction of the agriculture cost and realization of an environmental-friendly purpose can be facilitated through development and utilization of the heredity resources.

Mingyue Zhang

Papers

SNP (single nucleotide polymorphism) marker for identifying pear early blossoming on basis of high-resolution melting curve and application of SNP marker

Phylogenetic and expression analysis of protein disulfide isomerase unravels good reference genes for gene expression studies in pear and peach fruits

SNP marker based on high resolution dissolution curve for identifying pear pulp low stone cell content and application thereof

SNP (single-nucleotide polymorphism) molecular marker primers for pear fruit sepal state major QTL (quantitative trait locus) site and application thereof

Pear transcription factor PbrMYB169 and application thereof