scholarly journals An improved pig reference genome sequence to enable pig genetics and genomics research

2019 ◽  
Author(s):  
Amanda Warr ◽  
Nabeel Affara ◽  
Bronwen Aken ◽  
H. Beiki ◽  
Derek M. Bickhart ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genomic Research ◽  
Biomedical Model ◽  
Model Species ◽  
Domestic Pig ◽  
Genomics Research ◽  
Long Read ◽  
Genetics And Genomics ◽  
Genome Assemblies ◽  
Chromosome Level

AbstractThe domestic pig (Sus scrofa) is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

scholarly journals An improved pig reference genome sequence to enable pig genetics and genomics research

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Amanda Warr ◽  
Nabeel Affara ◽  
Bronwen Aken ◽  
Hamid Beiki ◽  
Derek M Bickhart ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genomic Research ◽  
Biomedical Model ◽  
Model Species ◽  
Domestic Pig ◽  
Genomics Research ◽  
Long Read ◽  
Genetics And Genomics ◽  
Genome Assemblies ◽  
Chromosome Level

Abstract Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

scholarly journals Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Alan Smith
Keyword(s):  
Evolutionary History ◽  
Lentinula Edodes ◽  
Reference Genome ◽  
Genomic Change ◽  
Diverse Species ◽  
The World ◽  
Cultivated Mushroom ◽  
Genome Assemblies ◽  
High Degree ◽  
Chromosome Level

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

scholarly journals Human genetics and genomics research in Ecuador: historical survey, current state, and future directions

2019 ◽  
Vol 13 (1) ◽  
Author(s):  
Marlon S. Zambrano-Mila ◽  
Spiros N. Agathos ◽  
Juergen K. V. Reichardt
Keyword(s):  
Human Genetics ◽  
Genetic Diseases ◽  
Historical Record ◽  
Genomic Research ◽  
Current Status ◽  
Forensic Sciences ◽  
Resource Limited ◽  
Genomics Research ◽  
Comprehensive Picture ◽  
Genetics And Genomics

Abstract Background In South America, the history of human genetics is extensive and its beginnings go back to the onset of the twentieth century. In Ecuador, the historical record of human genetics and genomics research is limited. In this context, our work analyzes the current status and historical panorama of these fields, based on bibliographic searches in Scopus, Google Scholar, PubMed, and Web of Science. Results Our results determined that the oldest paper in human genetics coauthored by an Ecuadorian institution originates from the Central University of Ecuador in 1978. From a historical standpoint, the number of articles has increased since the 1990s. This growth has intensified and it is reflected in 137 manuscripts recorded from 2010 to 2019. Areas such as human population genetics, phylogeography, and forensic sciences are the core of genetics and genomics-associated research in Ecuador. Important advances have been made in the understanding of the bases of cancer, some genetic diseases, and congenital disorders. Fields such as pharmacogenetics and pharmacogenomics have begun to be explored during the last years. Conclusions This work paints a comprehensive picture and provides additional insights into the future panorama of human genetic and genomic research in Ecuador as an example of an emerging, resource-limited country with interesting phylogeographic characteristics and public health implications.

scholarly journals RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

2020 ◽  
Author(s):  
Yuxuan Yuan ◽  
Philipp E. Bayer ◽  
Robyn Anderson ◽  
HueyTyng Lee ◽  
Chon-Kit Kenneth Chan ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Chinese Spring ◽  
Complete Genome ◽  
Reference Genome ◽  
Computing Time ◽  
Link Type ◽  
Recent Advances ◽  
Long Read ◽  
Genome Assemblies

AbstractRecent advances in long-read sequencing have the potential to produce more complete genome assemblies using sequence reads which can span repetitive regions. However, overlap based assembly methods routinely used for this data require significant computing time and resources. Here, we have developed RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step. During benchmarking, we assembled the wheat Chinese Spring (CS) genome using publicly available PacBio reads in parallel in 168 wall hours on a 250 CPU system. The maximum RAM used was 300 Gb and the computing time was 42,000 CPU hours. The approach opens applications for the assembly of other large and complex genomes with much-reduced computing requirements. The RefKA pipeline is available at https://github.com/AppliedBioinformatics/RefKA

scholarly journals A new and improved genome sequence of Cannabis sativa

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Shivraj Braich ◽  
Rebecca C. Baillie ◽  
German C. Spangenberg ◽  
Noel O. I. Cogan
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Cannabis Sativa ◽  
Draft Genome ◽  
Diploid Species ◽  
Sequence Assembly ◽  
Draft Genome Sequence ◽  
Genome Sequence Assembly ◽  
Long Read ◽  
Genome Assemblies

Cannabis is a diploid species (2n = 20), the estimated haploid genome sizes of the female and male plants using flow cytometry are 818 and 843 Mb respectively. Although the genome of Cannabis has been sequenced (from hemp, wild and high-THC strains), all assemblies have significant gaps. In addition, there are inconsistencies in the chromosome numbering which limits their use. A new comprehensive draft genome sequence assembly (∼900 Mb) has been generated from the medicinal cannabis strain Cannbio-2, that produces a balanced ratio of cannabidiol and delta-9-tetrahydrocannabinol using long-read sequencing. The assembly was subsequently analysed for completeness by ordering the contigs into chromosome-scale pseudomolecules using a reference genome assembly approach, annotated and compared to other existing reference genome assemblies. The Cannbio-2 genome sequence assembly was found to be the most complete genome sequence available based on nucleotides assembled and BUSCO evaluation in Cannabis sativa with a comprehensive genome annotation. The new draft genome sequence is an advancement in Cannabis genomics permitting pan-genome analysis, genomic selection as well as genome editing.

scholarly journals Improved Apis mellifera reference genome based on the alternative long-read-based assemblies

2021 ◽  
Author(s):  
Milyausha Kaskinova ◽  
Bayazit Yunusbayev ◽  
Radick Altinbaev ◽  
Rika Raffiudin ◽  
Madeline H. Carpenter ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Reference Genome ◽  
De Novo ◽  
Gene Annotation ◽  
Model Organism ◽  
Functional Genomic ◽  
Long Read ◽  
Chromosome Level

ABSTRACTApis mellifera L., the western honey bee is a major crop pollinator that plays a key role in beekeeping and serves as an important model organism in social behavior studies. Recent efforts have improved on the quality of the honey bee reference genome and developed a chromosome-level assembly of sixteen chromosomes, two of which are gapless. However, the rest suffer from 51 gaps, 160 unplaced/unlocalized scaffolds, and the lack of 2 distal telomeres. The gaps are located at the hard-to-assemble extended highly repetitive chromosomal regions that may contain functional genomic elements. Here, we use de-novo re-assemblies from the most recent reference genome Amel_HAv_3.1 raw reads and other long-read-based assemblies (INRA_AMelMel_1.0, ASM1384120v1, and ASM1384124v1) of the honey bee genome to resolve 13 gaps, five unplaced/unlocalized scaffolds and, the lacking telomeres of the Amel_HAv_3.1. The total length of the resolved gaps is 848,747 bp. The accuracy of the corrected assembly was validated by mapping PacBio reads and performing gene annotation assessment. Comparative analysis suggests that the PacBio-reads-based assemblies of the honey bee genomes failed in the same highly repetitive extended regions of the chromosomes, especially on chromosome 10. To fully resolve these extended repetitive regions, further work using ultra-long Nanopore sequencing would be needed. Our updated assembly facilitates more accurate reference-guided scaffolding and marker/sequence mapping in honey bee genomics studies.

scholarly journals EquCab3, an Updated Reference Genome for the Domestic Horse

2018 ◽  
Author(s):  
Theodore S. Kalbfleisch ◽  
Edward S. Rice ◽  
Michael S. DePriest ◽  
Brian P. Walenz ◽  
Matthew S. Hestand ◽  
...  
Keyword(s):  
Reference Genome ◽  
Reference Sequence ◽  
Large Animal ◽  
Domestic Horse ◽  
Sequencing Technology ◽  
Proximity Ligation ◽  
Genomics Research ◽  
Long Read ◽  
Solid Foundation ◽  
Work Done

AbstractEquCab2, a high-quality reference genome for the domestic horse, was released in 2007. Since then, it has served as the foundation for nearly all genomic work done in equids. Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference assemblies of large animal and plant genomes in terms of contiguity and composition. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. The result, EquCab3, is presented here. The count of non-N bases in the incorporated chromosomes is improved from 2.33Gb in EquCab2 to 2.41Gb from EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

scholarly journals Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

2021 ◽  
Author(s):  
Hollis A Dahn ◽  
Jacquelyn Mountcastle ◽  
Jennifer Balacco ◽  
Sylke Winkler ◽  
Iliana Bista ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Long Range ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Preservation Methods ◽  
Long Read ◽  
Genome Assemblies ◽  
Ultra High Molecular Weight ◽  
Chromosome Level

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.

Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae

2021 ◽  
Author(s):  
Yun‐Tao Ji ◽  
Zhihui Xiu ◽  
Chun‐Hai Chen ◽  
Youru Wang ◽  
Jing‐Xia Yang ◽  
...  
Keyword(s):  
Reference Genome ◽  
Toona Sinensis ◽  
The Family ◽  
Long Read ◽  
Chromosome Level
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