scholarly journals Genome sequence and analysis of the eggplant (Solanum melongena L.)

2019 ◽  
Author(s):  
Dandan Li ◽  
Jun Qian ◽  
Wenjia Li ◽  
Yaqin Jiang ◽  
Guiyun Gan ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Economic Value ◽  
Solanum Melongena ◽  
Acid Synthesis ◽  
Total Production ◽  
Sequencing Data ◽  
Chromosomal Distribution ◽  
Reference Genome Sequence

SummaryThe eggplant (Solanum melongena L.) is one of the most important Solanaceae crops, ranking third in the total production and economic value in the genus Solanum. Here, we report a high-quality, chromosome-scale eggplant reference genome sequence of 1,155.8 Mb, with N50 of 93.9 Mb, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences occupied 70.1% of the assembly length, and 35,018 high-confidence protein-coding genes were annotated based on multiple evidence. Comparative analysis revealed 646 species-specific families and 364 positive selection genes, conferring distinguishing traits to the eggplant. We performed genome-wide identification of disease resistance genes and discovered an expanded gene family of bacterial spot resistance in the eggplant and pepper but not in tomato and potato. The genes involved in chlorogenic acid synthesis were comprehensively characterized. Highly similar chromosomal distribution patterns of polyphenol oxidase genes were observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only facilitate evolutionary studies in the Solanaceae but also facilitate their breeding and improvement.

scholarly journals Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring

2019 ◽  
Vol 20 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Susan B. Altenbach ◽  
Han-Chang Chang ◽  
Annamaria Simon-Buss ◽  
Toni Mohr ◽  
Naxin Huo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Hexaploid Wheat ◽  
Chinese Spring ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Proteomic Study

scholarly journals A novel genome-wide microsatellite resource for species ofEucalyptuswith linkage-to-physical correspondence on the reference genome sequence

2014 ◽  
Vol 15 (2) ◽  
pp. 437-448 ◽  
Author(s):  
Dario Grattapaglia ◽  
Eva M. C. Mamani ◽  
Orzenil B. Silva-Junior ◽  
Danielle A. Faria
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Genome Wide

scholarly journals Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers

2020 ◽  
Vol 7 (3) ◽  
pp. 88
Author(s):  
Rachael Thomas ◽  
Joan U Pontius ◽  
Luke B Borst ◽  
Matthew Breen
Keyword(s):  
Genome Sequence ◽  
Copy Number ◽  
Reference Genome ◽  
Microarray Platform ◽  
Domestic Cat ◽  
Dna Copy Number ◽  
Reference Genome Sequence ◽  
Copy Number Aberrations ◽  
Genome Sequence Assembly ◽  
Dna Copy Number Aberrations

The utility of the domestic cat as a model system for biomedical studies was constrained for many years by the absence of a comprehensive feline reference genome sequence assembly. While such a resource now exists, the cat continues to lag behind the domestic dog in terms of integration into the ‘One Health’ era of molecular medicine. Stimulated by the advances being made within the evolving field of comparative cancer genomics, we developed a microarray platform that allows rapid and sensitive detection of DNA copy number aberrations in feline tumors using comparative genomic hybridization analysis. The microarray comprises 110,456 unique oligonucleotide probes anchored at mean intervals of 22.6 kb throughout the feline reference genome sequence assembly, providing ~350-fold higher resolution than was previously possible using this technique. We demonstrate the utility of this resource through genomic profiling of a feline injection-site sarcoma case, revealing a highly disrupted profile of DNA copy number imbalance involving several key cancer-associated genes including KIT, TP53, PTEN, FAS and RB1. These findings were supported by targeted fluorescence in-situ hybridization analysis, which identified major alterations in chromosome structure, including complex intrachromosomal reorganization events typical of those seen in aggressive soft-tissue sarcomas of other species. We then characterized a second mass that was identified at a nearby site in the same patient almost 12 months later. This mass demonstrated a remarkably conserved genomic profile consistent with a recurrence of the original tumor; however the detection of subtle differences reflected evolution of the tumor over time. These findings exemplify the diverse potential of this microarray platform to incorporate domestic cat cancers into comparative and translational research efforts in molecular oncology.

scholarly journals Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.)

2019 ◽  
Vol 10 ◽  
Author(s):  
Denisa Šimoníková ◽  
Alžbeěta Němečková ◽  
Miroslava Karafiátová ◽  
Brigitte Uwimana ◽  
Rony Swennen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Chromosome Painting ◽  
Reference Genome ◽  
Reference Genome Sequence ◽  
Musa Spp

scholarly journals Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads

2018 ◽  
Author(s):  
Huilong Du ◽  
Chengzhi Liang
Keyword(s):  
Single Molecule ◽  
High Efficiency ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Sequencing Data ◽  
High Quality ◽  
Single Molecule Sequencing ◽  
Genome Maps ◽  
Long Reads ◽  
Novel Method

AbstractDue to the large number of repetitive sequences in complex eukaryotic genomes, fragmented and incompletely assembled genomes lose value as reference sequences, often due to short contigs that cannot be anchored or mispositioned onto chromosomes. Here we report a novel method Highly Efficient Repeat Assembly (HERA), which includes a new concept called a connection graph as well as algorithms for constructing the graph. HERA resolves repeats at high efficiency with single-molecule sequencing data, and enables the assembly of chromosome-scale contigs by further integrating genome maps and Hi-C data. We tested HERA with the genomes of rice R498, maize B73, human HX1 and Tartary buckwheat Pinku1. HERA can correctly assemble most of the tandemly repetitive sequences in rice using single-molecule sequencing data only. Using the same maize and human sequencing data published by Jiao et al. (2017) and Shi et al. (2016), respectively, we dramatically improved on the sequence contiguity compared with the published assemblies, increasing the contig N50 from 1.3 Mb to 61.2 Mb in maize B73 assembly and from 8.3 Mb to 54.4 Mb in human HX1 assembly with HERA. We provided a high-quality maize reference genome with 96.9% of the gaps filled (only 76 gaps left) and several incorrectly positioned sequences fixed compared with the B73 RefGen_v4 assembly. Comparisons between the HERA assembly of HX1 and the human GRCh38 reference genome showed that many gaps in GRCh38 could be filled, and that GRCh38 contained some potential errors that could be fixed. We assembled the Pinku1 genome into 12 scaffolds with a contig N50 size of 27.85 Mb. HERA serves as a new genome assembly/phasing method to generate high quality sequences for complex genomes and as a curation tool to improve the contiguity and completeness of existing reference genomes, including the correction of assembly errors in repetitive regions.

scholarly journals An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion

2017 ◽  
Vol 2 ◽  
pp. 42 ◽  
Author(s):  
Erica M Pasini ◽  
Ulrike Böhme ◽  
Gavin G. Rutledge ◽  
Annemarie Voorberg-Van der Wel ◽  
Mandy Sanders ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Malaria Parasite ◽  
Reference Genome ◽  
Sequence Data ◽  
Single Copy ◽  
Chromosome 9 ◽  
Reference Genome Sequence ◽  
Plasmodium Cynomolgi ◽  
Average Gene

Background: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres.  Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated a new reference genome sequence, PcyM, sourced from an Indian rhesus monkey. We compare the newly assembled genome sequence with those of several other Plasmodium species, including a re-annotated P. coatneyi assembly. Results: The new PcyM genome assembly is of significantly higher quality than the existing reference, comprising only 56 pieces, no gaps and an improved average gene length. Detailed manual curation has ensured a comprehensive annotation of the genome with 6,632 genes, nearly 1,000 more than previously attributed to P. cynomolgi. The new assembly also has an improved representation of the subtelomeric regions, which account for nearly 40% of the sequence. Within the subtelomeres, we identified more than 1300 Plasmodium interspersed repeat (pir) genes, as well as a striking expansion of 36 methyltransferase pseudogenes that originated from a single copy on chromosome 9. Conclusions: The manually curated PcyM reference genome sequence is an important new resource for the malaria research community. The high quality and contiguity of the data have enabled the discovery of a novel expansion of methyltransferase in the subtelomeres, and illustrates the new comparative genomics capabilities that are being unlocked by complete reference genomes.

scholarly journals A Reference Genome Sequence for Giant Sequoia

2020 ◽  
Vol 10 (11) ◽  
pp. 3907-3919
Author(s):  
Alison D. Scott ◽  
Aleksey V. Zimin ◽  
Daniela Puiu ◽  
Rachael Workman ◽  
Monica Britton ◽  
...  
Keyword(s):  
Sierra Nevada ◽  
Genome Sequence ◽  
Reference Genome ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Reference Genome Sequence ◽  
Oxford Nanopore ◽  
Sierra Nevada Mountains ◽  
Genomic Tools ◽  
Giant Sequoia

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, were used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.

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