scholarly journals Progress in plant genome sequencing: research directions

2019 ◽  
Vol 23 (1) ◽  
pp. 38-48 ◽  
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.

scholarly journals Genome sequencing in plants and the genus Panax L.

2016 ◽  
Vol 14 (1) ◽  
pp. 1-13
Author(s):  
Lê Thị Thu Hiền ◽  
Hugo De Boer ◽  
Vincent Manzanilla ◽  
Hà Văn Huân ◽  
Nông Văn Hải
Keyword(s):  
Development Strategy ◽  
Genome Sequencing ◽  
Evolutionary History ◽  
Applied Research ◽  
Plant Genome ◽  
Related Genome ◽  
Genetic Characteristics ◽  
Biochemical Pathways ◽  
Sequencing Technologies ◽  
Herbal Plants

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.

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

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
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.

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

2019 ◽  
Vol 6 (1) ◽  
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.

scholarly journals Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions

2015 ◽  
Vol 36 (8) ◽  
pp. 815-822 ◽  
Author(s):  
Stefan H. Lelieveld ◽  
Malte Spielmann ◽  
Stefan Mundlos ◽  
Joris A. Veltman ◽  
Christian Gilissen
Keyword(s):  
Genome Sequencing ◽  
Protein Coding ◽  
Coding Regions ◽  
Sequencing Technologies

scholarly journals Impact of short-read sequencing on the misassembly of a plant genome

2021 ◽  
Author(s):  
Peipei Wang ◽  
Fanrui Meng ◽  
Bethany M. Moore ◽  
Shin-Han Shiu
Keyword(s):  
Great Majority ◽  
Plant Genome ◽  
High Coverage ◽  
Short Read ◽  
Short Read Sequencing ◽  
Sequencing Technologies ◽  
Long Read ◽  
Downstream Analysis ◽  
Genomic Regions ◽  
Simple Sequence

Abstract Background: Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively.Results: To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions: Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads.

scholarly journals Impact of short-read sequencing on the misassembly of a plant genome

2020 ◽  
Author(s):  
Peipei Wang ◽  
Fanrui Meng ◽  
Bethany M. Moore ◽  
Shin-Han Shiu
Keyword(s):  
Great Majority ◽  
Plant Genome ◽  
High Coverage ◽  
Short Read ◽  
Short Read Sequencing ◽  
Sequencing Technologies ◽  
Long Read ◽  
Downstream Analysis ◽  
Genomic Regions ◽  
Simple Sequence

Abstract Background Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively. Results To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads.

scholarly journals Oxford Nanopore sequencing: new opportunities for plant genomics?

2020 ◽  
Vol 71 (18) ◽  
pp. 5313-5322 ◽  
Author(s):  
Kathryn Dumschott ◽  
Maximilian H-W Schmidt ◽  
Harmeet Singh Chawla ◽  
Rod Snowdon ◽  
Björn Usadel
Keyword(s):  
Plant Genome ◽  
Third Generation ◽  
Plant Genomics ◽  
High Coverage ◽  
Plant Genomes ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Oxford Nanopore ◽  
Long Read ◽  
Generation Sequencing

Abstract DNA sequencing was dominated by Sanger’s chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.

Deciphering the Parts List for the Mechanical Plant

Daedalus ◽  
2012 ◽  
Vol 141 (3) ◽  
pp. 89-97
Author(s):  
Chris Somerville
Keyword(s):  
Climate Change ◽  
Ecosystem Services ◽  
Genetic Manipulation ◽  
Plant Genome ◽  
Biological Research ◽  
Rapid Progress ◽  
Genome Sequences ◽  
Sequencing Technologies ◽  
Mechanistic Basis ◽  
Mechanical Plant

The development of inexpensive DNA sequencing technologies has revolutionized all aspects of biological research. The proliferation of plant genome sequences, in conjunction with the parallel development of robust tools for directed genetic manipulation, has given momentum and credibility to the goal of understanding several model plants as the sum of their parts. A broad inventory of the functions and interrelationships of the parts is currently under way, and the first steps toward computer models of processes have emerged. These approaches also provide a framework for the mechanistic basis of plant diversity. It is hoped that rapid progress in this endeavor will facilitate timely responses to expanding demand for food, feed, fiber, fuel, and ecosystem services in a period of climate change.

scholarly journals Impact of short-read sequencing on the misassembly of a plant genome

2021 ◽  
Author(s):  
Peipei Wang ◽  
Fanrui Meng ◽  
Bethany M. Moore ◽  
Shin-Han Shiu
Keyword(s):  
Great Majority ◽  
Plant Genome ◽  
High Coverage ◽  
Short Read ◽  
Short Read Sequencing ◽  
Sequencing Technologies ◽  
Long Read ◽  
Downstream Analysis ◽  
Genomic Regions ◽  
Simple Sequence

Abstract Background: Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively.Results: To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions: Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads and the generality of these causes and factors should be tested further in other species.

scholarly journals Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri

2020 ◽  
Author(s):  
Kazuaki Yamaguchi ◽  
Yuichiro Hara ◽  
Kaori Tatsumi ◽  
Osamu Nishimura ◽  
Jeramiah J. Smith ◽  
...  
Keyword(s):  
Single Copy ◽  
Sequence Information ◽  
High Coverage ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Genome Wide ◽  
Mate Pair ◽  
A Genome ◽  
Gene Models ◽  
High Utility

AbstractThe group of hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and is one of the only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming at reconstructing a high-coverage coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of resulting gene models promises a high utility in various comparative analyses including phylogenomics and phylome exploration.

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