Conference Announcement | January 12-17, GrandOmics sincerely invites you to participate in the 2024 PAG event!

International Plant & Animal Genome (PAG Conference) is an internationally renowned top academic conference on animal and plant genomics research, held from January 12th to 17th, 2024 in San Diego, CA, USA. The PAG consists of scientific workshops, plenary speakers, industry workshops, digital tools and resources sessions, posters sessions, and exhibits with vendors presenting industry related productions and services. It is designed to provide a forum on recent developments and future plans for plant and animal genome projects. Conference is an excellent opportunity to exchange ideas and applications on this internationally important project. This conference covers the latest research progress in genomics of major crops, cutting-edge developments in bioinformatics and high-throughput sequencing technology, and provides a high-level communication platform for genetic researchers in multiple disciplines and fields.

Meeting Information
Location: San Diego, CA, USA
Time: January 12-17, 2024
Website: https://intlpag.org/31/

Program Overview
Day One / Friday, January 12, 2024

8:00 AM – 9:00 PMMeeting Management Office Open
8:00 AM – 9:00 PMSpeaker Ready Room Open
9:00 AM – 9:00 PMRegistration Open
9:30 AM – 10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
1:30 PM – 3:40 PMWorkshop Session*
2:00 PM – 9:00 PMPoster Hanging Access
3:00 PM – 4:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
Day Two / Saturday, January 13, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:30 AM – 7:00 PMRegistration Open
7:30 AM – 9:00 PMPoster Hanging Access
8:00 AM – 10:10 AMWorkshop Session*
8:00 AM – 12:40 PMWorkshop Session*
8:00 AM – 6:10 PMWorkshop Session*
9:30 AM – 10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
12:00 PM – 9:00 PMPoster Viewing Access
12:00 PM – 1:30 PMLunch
1:30 PM – 3:40 PMWorkshop Session*
1:30 PM – 3:40 PMDigital Tools and Resources Workshop #1
3:00 PM – 4:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:00 PM – 6:30 PMCoffee Break
6:20 PM – 8:30 PMWorkshop Session*
Day Three / Sunday, January 14, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:30 AM – 12:00 PMPoster Hanging Access
7:30 AM – 5:00 PMRegistration Open
8:00 AM – 10:10 AMWorkshop Session*
8:00 AM – 12:40 PMWorkshop Session*
9:30 AM – 10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
12:00 PM – 1:30 PMLunch
12:00 PM – 8:45 PMExhibits Open
1:30 PM – 3:40 PMWorkshop Session*
1:30 PM – 6:20 PMWorkshop Session*
3:00 PM – 4:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:30 PM – 7:15 PMPlenary Lecture – Appolinaire DjikengDirector General, International Livestock Research Institute (ILRI), Kenya
Talk Title: “Livestock and the Food Systems: A Focus on Smallholder Systems in the Global South”
7:15 PM – 8:45 PMOpening Reception
Day Four / Monday, January 15, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:00 AM – 9:30 PMPoster Viewing Access
7:30 AM – 5:00 PMRegistration Open
8:00 AM – 8:45 AMPlenary Lecture – Scott EdwardsProfessor and Chair, Department of Organismic and Evolutionary Biology, Harvard University; Curator of Ornithology, Museum of Comparative Zoology, USATalk Title: “Comparative Population Pangenomes: A New Frontier for the Evolutionary Analysis of Birds”
8:45 AM – 9:30 AMPlenary Lecture – Lucy Van DorpUCL Excellence Fellow, University College London, UKTalk Title: “Tracking Pathogens in Space and Time”
9:30 AM – 11:30 AMCoffee Break
9:30 AM – 5:00 PMExhibits Open
10:00 AM – 11:30 AMPoster Session – Even Numbers
11:30 PM – 1:00 PMLunch
12:50 PM – 3:00 PMWorkshop Session*
12:50 PM – 3:00 PMDigital Tools and Resources Workshop #2
3:00 PM – 4:30 PMPoster Session – Odd Numbers
3:00 PM – 4:30 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:00 PM – 6:30 PMCoffee Break
6:20 PM – 8:30 PMWorkshop Session*
Day Five / Tuesday, January 16, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 7:00 PMMeeting Management Office Open
7:00 AM – 7:00 PMSpeaker Ready Room Open
7:00 AM – 3:00 PMPoster Viewing Access
7:30 AM – 3:00 PMRegistration Open
8:00 AM – 8:45 AMPlenary Lecture – Katrien DevosDistinguished Research Professor, University of Georgia, USATalk Title: “Ensuring Food Security in a Changing Climate: Adopt an Orphan” (Preliminary Title)
8:45 AM – 9:30 AMPlenary Lecture – Amy Marshall ColonAssociate Professor, Department of Plant Biology, University of Illinois Urbana-Champaign, USATalk Title: “Integrative Modeling for the Development of in Silico Crops”
9:30 AM – 10:30 AMCoffee Break
9:30 AM – 3:00 PMExhibits Open
10:30 AM – 12:40 PMWorkshop Session*
10:30 AM – 6:10 PMWorkshop Session*
10:30 AM – 12:40 PMDigital Tools and Resources Workshop #3
12:00 PM – 1:30 PMLunch
1:30 PM – 3:40 PMWorkshop Session*
2:00 PM – 3:00 PMCoffee Break
4:00 PM – 6:10 PMWorkshop Session*
6:00 PM – 6:30 PMCoffee Break
6:20 PM – 8:30 PMWorkshop Session*
6:20 PM – 9:30 PMWorkshop Session*
Day Six / Wednesday, January 17, 2024
7:00 AM – 8:00 AMContinental Breakfast
7:00 AM – 2:00 PMSpeaker Ready Room Open
7:00 AM – 5:00 PMMeeting Management Office Open
7:00 AM – 12:00 PMPoster Viewing Access
7:30 AM – 12:00 PMRegistration Open
8:00 AM – 8:45 AMPlenary Lecture – Dirk InzeDirector, VIB-UGent Center for Plant Systems Biology, BelgiumTalk Title: “Multiplex Engineering of Yield Traits in Maize”
8:45 AM-9:30 AMPlenary Lecture – Virginia WalbotProfessor Emerita, Stanford University, USATalk Title: “Building a Maize Anther”
9:30 AM-10:30 AMCoffee Break
10:30 AM – 12:40 PMWorkshop Session*
10:30 AM – 12:40 PMDigital Tools and Resources Workshop #4
12:00 PM – 1:30 PMLunch
7:15 PM – 11:55 PMBanquet Dinner

Join us in #PAG31
Our booth No. 504
Excited to see you here!

We will participate with you to explore the application of multi-omics technologies in animal and plant research, and work together to promote the development and innovation of genomics, with our extensive reading of omics products and experience in animal and plant genome projects!

GrandOmics X PacBio Revio – Higher throughput, more HiFi reads, but cost effeciently

GrandOmics is happy to share that two latest PacBio sequencers -Revio have arrived on 4 Arpil. The new platforms provide 15-fold increase in productivity compared to Sequel II/IIe, shortening turnaround time and reducing cost by almost 3-fold.

The Revio system uses a high-density, 25 million SMRT Cell, up to 4 SMRT Cells in parallel sequencing to provide 360 Gb of HiFi reads per day. In addition, With the Revio system, you can achieve higher throughput to support large studies and develop novel applications.

GrandOmics is releasing sequencing services using this latest sequencing platforms by Revio:

  • Genome Sequencing
  • Single Cell Full-length Transcriptome Sequencing
  • T2T assembly
  • Pangenomic Sequencing
  • Metagenomics Research

… More to explore.

Contact us: inquiry@grandomics.com

GrandOmics collaborates with Oxford Nanopore to deliver dbSV-100k, a project to deliver 100,000 affordable nanopore long-read human genomes

Strategic collaboration between two organisations represents largest nanopore sequencing project to date, capitalising on recent developments bringing ultra-high yields with PromethION

GrandOmics, a leading sequencing company in China, has announced a populational-scale project, dbSV100k, to understand the impact of structural variation on human disease. The project aims to sequence 20,000 human genomes in 2019, with a goal of 50,000 by the end of 2020 and total of 100,000 by the end of 2021. This uses high-throughput nanopore sequencing on the PromethION device and the project will explore viable opportunities for the development of clinical applications, with a view to ultimately providing clinical genetic diagnosis services in the future.

This research project aims to gain a complete understanding of genetic variations associated with human health and disease. Oxford Nanopore has entered into a Memorandum of Understanding with GrandOmics in support of their plan to build genome medicine services at an affordable price with high-quality that is accessible for anyone, anywhere.

The highest yields, with long reads

The performance of PromethION, the newest nanopore sequencing device, has now accelerated sufficiently to allow >7Tb on human samples using a complete set of 48 flow cells – the equivalent of 86Gb of real time sequencing data per hour, or ~1 human genome at 30X coverage.

PromethION, as with other nanopore sequencers, sequences the complete nucleic acid fragment and therefore provides very long reads – the current record is 2.3Mb in a single read and this represents the full fragment rather than multiple repeat passes of a smaller fragment.  With real time data and modular flow cells, the performance of the technology has developed while flow cell costs have remained the same. Flow cells now deliver ultra-high yields, and the latest R10 nanopore has delivered Q50 (99.999% consensus accuracy) in a small genome in internal company experiments. R10 is now being trialled by GrandOmics.

GrandOmics: delivering high throughput nanopore genomics

To date, GrandOmics has sequenced more than a thousand human genome samples (G1k) and several hundreds of plants, animals, and microbial genomes using nanopore technology, servicing a network of over a thousand customers throughout the world. This has resulted in new discoveries in genome science and genomic medicine, in more than 50 publications for the last two years. This includes publications using nanopore technology, with more prospect papers in the near future.

This high-throughput infrastructure will be expanded to deliver dbSV-100K.

“GrandOmics’s mission is to provide innovative and precise genomics solutions for disease research and diagnosis. We have been running our PromethION devices to full capacity, and have developed our own bioinformatics pipelines to drive breakthrough projects to achieve new standards.” Said Mr. Depeng Wang, CEO of GrandOmics.

Dr. Gordon Sanghera, CEO of Oxford Nanopore said: “We are glad to form a strategic and ongoing collaboration with GrandOmics to support genomic medicine and personalized medicine for China. At Oxford Nanopore last week, the PromethION 48 has achieved 7.3Tb of data using a single set of 48 flow cells, and our development pathway offers higher future capacity. We are excited to see GrandOmics drive innovative solutions for offering accessible ‘de novo personal genomes’ to customers using high-throughput PromethION sequencing.”

“This is so far the largest high-throughput nanopore sequencing project in the world, and is the outcome of extensive effort between two parties in developing a strategic alliance for the last several months. This is achieved by a shared vision to create an opportunity to revolutionize genome medicine in the UK, China and the rest of the world.” Min S. Park, Director of GrandOmics Institute.

About GrandOmics

GrandOmics is a world-leading sequencing company in Beijing, China. It was one of the earliest to apply nanopore technology for commercial DNA sequencing in the world, and also the first in China and the second in the world to be certified to provide PromethION sequencing services using Nanopore technology.

GrandOmics provides comprehensive solutions for genome science and genomic medicine. The company aims to utilise advanced sequencing-based solutions for rare genetic diseases, complex diseases, microbial diseases, and cancer, by integrating nanopore long reads and optical mapping to detect and characterize complex mutations in clinical samples of patient genomes. GrandOmics has been establishing one of the world’s largest nanopore long-reads based structural variation databases (www.dbsv.com).

NextOmics, a subsidiary company of GrandOmics, has one of the most complete third-generation sequencing, optical and 3D mapping platforms. NextOmics delivers genome assemblies and analysis pipelines for animal, plant, microbial and human genomes, in research areas such as transcriptomics, metagenomics and epigenetics.

About Oxford Nanopore 

Oxford Nanopore Technologies aims to disrupt the paradigm of biological analysis by making high performance, novel DNA/RNA sequencing technology that is accessible and easy to use. Our goal is to enable the genetic analysis of any living thing, by any person, in any environment.

Our novel, electronics-based DNA/RNA sequencing technology is being used in more than 80 countries, for a range of biological research applications and is also being explored beyond research.

Oxford Nanopore’s proprietary technology is fully scalable for any requirement. Small formats such as Flongle address the need for on-demand, rapid, smaller tests or experiments, and can be used in labs or in the field. The pocket-sized MinION is a powerful and portable sequencing device that can deliver high volumes of long read sequence data. The benchtop GridION X5 can run up to five MinION Flow Cells at a time, on-demand, for larger genomics projects. The recently launched PromethION is the largest format for nanopore sequencing, designed to offer on-demand use of up to 24 or 48 flow cells – each of which can offer more than 100Gb of sequencing data in field.

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Nature Genetics        Published:30 July 2018

Abstract:Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73,was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might ca considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

Read the original articlehttps://www.nature.com/articles/s41588-018-0182-0

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Nature Plants                             Published:02 July 2018

Abstract: Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns—one at the base of ‘core leptosporangiates’ and one specific to Azolla. One fernspecific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla–cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

Read the original articlehttps://www.nature.com/articles/s41477-018-0188-8

Adaptation and conservation insights from the koala genome

Nature Genetics    Published: 02 July 2018

Abstract:The koala, the only extant species of the marsupial family Phascolarctidae, is classified as ‘vulnerable’ due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala’s ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala’s survival in the wild.

Read the original article: https://www.nature.com/articles/s41588-018-0153-5

Oak genome reveals facets of long lifespan

Nature Plant       Published: 18 June 2018

Abstract:Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times. With 450 species spread throughout Asia, Europe and America, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical and modelling approaches have shown that intra-organismal genetic heterogeneity can be selected for and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Read the original article: https://www.nature.com/articles/s41477-018-0172-3

High-resolution comparative analysis of great ape genomes

Science           08 June 2018

Abstract:Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single– to mega–base pair–sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

Read the original article: http://science.sciencemag.org/content/360/6393/eaar6343

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Nature          Published: 25 April 2018

AbstractHere we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

Read the original article: https://www.nature.com/articles/s41586-018-0063-9