Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Qifan Zeng; Qiang Fu; Yun Li; Geoff Waldbieser; Brian Bosworth; Shikai Liu; Yujia Yang; Lisui Bao; Zihao Yuan; Ning Li; Zhanjiang Liu

doi:10.1038/srep40347

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

Functional & Integrative Genomics ◽

10.1007/s10142-019-00694-z ◽

2019 ◽

Vol 20 (1) ◽

pp. 1-16 ◽

Cited By ~ 7

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

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

Molecular Ecology Resources ◽

10.1111/1755-0998.12317 ◽

2014 ◽

Vol 15 (2) ◽

pp. 437-448 ◽

Cited By ~ 18

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

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

Veterinary Sciences ◽

10.3390/vetsci7030088 ◽

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.

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

Frontiers in Plant Science ◽

10.3389/fpls.2019.01503 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 14

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

DASE: Condition-specific differential alternative splicing variants estimation method without reference genome sequence, and its application to non-model organisms

2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) ◽

10.1109/bibm.2016.7822540 ◽

2016 ◽

Author(s):

Kouki Yonezawa ◽

Tsukasa Mori ◽

Shuichi Shigeno ◽

Atsushi Ogura

Keyword(s):

Alternative Splicing ◽

Genome Sequence ◽

Reference Genome ◽

Estimation Method ◽

Model Organisms ◽

Reference Genome Sequence ◽

Splicing Variants

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

BMC Genomics ◽

10.1186/1471-2164-12-59 ◽

2011 ◽

Vol 12 (1) ◽

Cited By ~ 113

Author(s):

Frank M You ◽

Naxin Huo ◽

Karin R Deal ◽

Yong Q Gu ◽

Ming-Cheng Luo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genome Sequence ◽

Reference Genome ◽

Aegilops Tauschii ◽

Next Generation ◽

Snp Discovery ◽

Reference Genome Sequence ◽

Genome Wide ◽

Generation Sequencing

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

Wellcome Open Research ◽

10.12688/wellcomeopenres.11864.1 ◽

2017 ◽

Vol 2 ◽

pp. 42 ◽

Cited By ~ 22

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.

A Reference Genome Sequence for Giant Sequoia

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401612 ◽

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.

P1009 Sheep reference genome sequence updates: Texel improvements and Rambouillet progress

Journal of Animal Science ◽

10.2527/jas2016.94supplement418b ◽

2016 ◽

Vol 94 (suppl_4) ◽

pp. 18-19 ◽

Cited By ~ 1

Author(s):

Y. Liu ◽

S. C. Murali ◽

R. A. Harris ◽

A. C. English ◽

X. Qin ◽

...

Keyword(s):

Genome Sequence ◽

Reference Genome ◽

Reference Genome Sequence

Chromosome Level Genome Assembly Reveals Cassia Tora May Be an Ancient Species in Leguminosae

10.21203/rs.3.rs-134025/v1 ◽

2020 ◽

Author(s):

Caicai Lin ◽

Piyi Xing ◽

Changhao Zhou ◽

Xingfeng Li ◽

Zhenqiao Song

Keyword(s):

Genome Evolution ◽

Genome Sequence ◽

Reference Genome ◽

Chromatin Interaction ◽

Leguminous Plant ◽

Future Research ◽

Comparative Genomic ◽

Cassia Tora ◽

Reference Genome Sequence ◽

Legume Crops

Abstract Background: Cassia tora L. is an annual leguminous plant. Its seeds had wide utility in herbal medicine in Asian, but is usually regard as a potent, invasive weed which even helps farmers eliminate other parasitic weed species. However, compared with other important legume crops, C. tora is far from fully developed and the genetic basis is greatly lacking. A reference genome sequence will be great valuable resource for its genome evolution, genetic breeding and development.Results: Here, we de novo assembled a chromosome-scale genome for C. tora by combining PacBio sequencing technology with chromatin interaction mapping, resulting in 621-Mb genome with a contig N50 of 2.5 Mb, of which 77.44% was ordered and oriented on 13 pseudochromosomes. The genome contained 32,361 protein-coding genes with a repetitive DNA content of approximately 58.15%. Gypsy-type LTRs constituted the largest subfamily. LTR insertion events seldom occurred in this genome over the past 10 million years. Comparative genomic analyses showed that C. tora diverged ~95 million years ago (MYA), which revealed it has the most distant genetic relationship with 11 other legumes. Compared with other legume crops, Cassia tora is maybe an ancient species in Leguminosae.Conclusions: The high-quality reference genome sequence reported here furnishes unprecedented insights into genome dynamics and provides an important basis for future research on legume genome evolution.