$40m plant genome sequencing effort targets the best science

Advances in genome sequencing technologies have created a new genomic era of life sciences research worldwide in which a number of modern and sophisticated techniques and tools have been developed and employed. Many countries have invested in plant genome sequencing as part of a sustainable development strategy. Each year, the number of plant genomes and transcriptomes sequenced has increased. The results obtained offer opportunities for fundamental and applied research, provide valuable data for identification of genes or molecular markers linked to traits that are important for selection, cultivation, and/or production. In Vietnam, partial or complete genome sequencing of crops has been recently conducted, primarily as part of international collaborative projects. The genus Panax L. (Araliaceae family) is comprised of several species of commercial value with narrow distributions such as P. bipinnatifidus Seem., P. stipuleanatus H.T.Tsai & K.M.Feng, and Panax vietnamensis Ha et Grushv. Despite their very important roles in traditional medicine, understanding of their genetic characteristics is still limited. Molecular studies on the genus have, so far, only evaluated limited markers for phylogenetic analysis. Therefore, genome sequencing of these important herbal plants is needed to understand their genetic characteristics, their evolutionary history and the genes and biochemical pathways contributing to medicinally important metabolites. This review summarizes all related genome sequencing technologies including the most recent advances in the last decade and their applications in genome and transcriptome sequencing of plants in general and in the genus Panax L. in particular.

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Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽

10.3390/plants8080270 ◽

2019 ◽

Vol 8 (8) ◽

pp. 270 ◽

Cited By ~ 4

Author(s):

Yun Gyeong Lee ◽

Sang Chul Choi ◽

Yuna Kang ◽

Kyeong Min Kim ◽

Chon-Sik Kang ◽

...

Keyword(s):

Plant Species ◽

Genome Sequencing ◽

Reference Genome ◽

Genome Structure ◽

Plant Genome ◽

Sequence Information ◽

Sequencing Analysis ◽

Oxford Nanopore ◽

A Genome ◽

Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

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Genome sequences of horticultural plants: past, present, and future

Horticulture Research ◽

10.1038/s41438-019-0195-6 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 14

Author(s):

Fei Chen ◽

Yunfeng Song ◽

Xiaojiang Li ◽

Junhao Chen ◽

Lan Mo ◽

...

Keyword(s):

Data Storage ◽

Genome Sequencing ◽

Herbal Medicines ◽

Genome Project ◽

Plant Genome ◽

Quality Data ◽

Sequencing Data ◽

Sequencing Technologies ◽

Horticultural Plant ◽

Horticultural Plants

Abstract Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials for beverages, and herbal medicines and by acting as ornamentals. They have also shaped human art, culture, and environments and thereby have influenced the lifestyles of humans. With the advent of sequencing technologies, there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication. Here we summarize the advances in the genome sequencing of horticultural plants, the reconstruction of pan-genomes, and the development of horticultural genome databases. We also discuss past, present, and future studies related to genome sequencing, data storage, data quality, data sharing, and data visualization to provide practical guidance for genomic studies of horticultural plants. Finally, we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.

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Plant genome sequencing — applications for crop improvement

Current Opinion in Biotechnology ◽

10.1016/j.copbio.2013.08.019 ◽

2014 ◽

Vol 26 ◽

pp. 31-37 ◽

Cited By ~ 105

Author(s):

Marie E Bolger ◽

Bernd Weisshaar ◽

Uwe Scholz ◽

Nils Stein ◽

Björn Usadel ◽

...

Keyword(s):

Genome Sequencing ◽

Crop Improvement ◽

Plant Genome

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Progress in plant genome sequencing: research directions

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj19.459 ◽

2019 ◽

Vol 23 (1) ◽

pp. 38-48 ◽

Cited By ~ 1

Author(s):

M. K. Bragina ◽

D. A. Afonnikov ◽

E. A. Salina

Keyword(s):

Genome Sequencing ◽

Plant Traits ◽

Plant Genome ◽

Targeted Sequencing ◽

Genome Sequences ◽

Crop Species ◽

High Coverage ◽

Protein Coding ◽

Sequencing Technologies ◽

A Genome

Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.

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Twenty years of plant genome sequencing: achievements and challenges

Trends in Plant Science ◽

10.1016/j.tplants.2021.10.006 ◽

2021 ◽

Author(s):

Yanqing Sun ◽

Lianguang Shang ◽

Qian-Hao Zhu ◽

Longjiang Fan ◽

Longbiao Guo

Keyword(s):

Genome Sequencing ◽

Plant Genome

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Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

Rice ◽

10.1186/s12284-020-00432-1 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Veronica Roman-Reyna ◽

Dale Pinili ◽

Frances N. Borja ◽

Ian L. Quibod ◽

Simon C. Groen ◽

...

Keyword(s):

Genome Sequencing ◽

Crop Improvement ◽

Rice Genome ◽

Plant Genome ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Rice Leaf ◽

Relative Contribution ◽

Bacterial Microbiome ◽

Host Microbe Interactions

Abstract Background The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3024 rice accessions. Findings By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

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