Genome sequence assembly: algorithms and issues

Computer ◽  
2002 ◽  
Vol 35 (7) ◽  
pp. 47-54 ◽  
Author(s):  
M. Pop ◽  
S.L. Salzberg ◽  
M. Shumway
Keyword(s):  
Genome Sequence ◽  
Sequence Assembly ◽  
Genome Sequence Assembly ◽  
Assembly Algorithms

scholarly journals Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 518
Author(s):  
Zequn Chen ◽  
Xiwu Qi ◽  
Xu Yu ◽  
Ying Zheng ◽  
Zhiqi Liu ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Essential Oils ◽  
Gene Family ◽  
Genome Sequence ◽  
Sequence Assembly ◽  
Terpene Synthase ◽  
Genome Sequence Assembly ◽  
Mentha Longifolia ◽  
Specific Expansion ◽  
Species Specific

Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha.

scholarly journals Limitations of next-generation genome sequence assembly

2010 ◽  
Vol 8 (1) ◽  
pp. 61-65 ◽  
Author(s):  
Can Alkan ◽  
Saba Sajjadian ◽  
Evan E Eichler
Keyword(s):  
Genome Sequence ◽  
Sequence Assembly ◽  
Next Generation ◽  
Genome Sequence Assembly

scholarly journals Draft Genome Sequence and Annotation of the Apicomplexan Parasite Besnoitia besnoiti

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Gereon Schares ◽  
Pratap Venepally ◽  
Hernán A. Lorenzi
Keyword(s):  
Genome Sequence ◽  
Causative Agent ◽  
Definitive Host ◽  
Draft Genome ◽  
Sequence Assembly ◽  
Apicomplexan Parasite ◽  
Draft Genome Sequence ◽  
Besnoitia Besnoiti ◽  
Genome Sequence Assembly ◽  
Bovine Besnoitiosis

ABSTRACT The apicomplexan parasite Besnoitia besnoiti is the causative agent of bovine besnoitiosis that affects livestock, particularly cattle. The definitive host of B. besnoiti is unknown and its transmission only partially understood. Here, we report the first draft genome sequence, assembly, and annotation of this parasite.

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 A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly

2015 ◽  
Vol 14 (4) ◽  
pp. 13096-13104 ◽  
Author(s):  
N.B. Stafuzza ◽  
B.C.M. Naressi ◽  
E. Yang ◽  
J.J. Cai ◽  
M.E.J. Amaral-Trusty
Keyword(s):  
Genome Sequence ◽  
Radiation Hybrid ◽  
Sequence Assembly ◽  
Chromosome 1 ◽  
Genome Sequence Assembly ◽  
Radiation Hybrid Map

scholarly journals High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 585 ◽  
Author(s):  
Bertrand Servin ◽  
Thomas Faraut ◽  
Nathalie Iannuccelli ◽  
Diana Zelenika ◽  
Denis Milan
Keyword(s):  
High Resolution ◽  
Genome Sequence ◽  
Radiation Hybrid ◽  
Sequence Assembly ◽  
Genome Sequence Assembly ◽  
Pig Genome

scholarly journals PSVII-39 Late-Breaking Abstract: Enhancing production and Aleutian disease resilience in mink through advanced genomics

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 342-342
Author(s):  
Younes Miar ◽  
Graham Plastow ◽  
Zhiquan Wang ◽  
Mehdi Sargolzaei
Keyword(s):  
Genome Sequence ◽  
Genetic Relationships ◽  
American Mink ◽  
Sequence Assembly ◽  
Whole Genome Sequence ◽  
High Price ◽  
Whole Genome ◽  
Next Generation ◽  
Genome Sequence Assembly ◽  
Wide Range

Abstract The fur industry is one of the oldest and the most historically significant industries in Canada. The industry has used American mink (Neovison vison) as the major source of fur for decades because of their high-quality fur and wide range of colours. This project will seek to (1) create the first accurate whole-genome sequence assembly of mink using next-generation sequencing technology to help understanding the biology and evolution of the order Carnivora, (2) design a robust and informative SNP assay for genomics discovery in mink, (3) discover genome structure and signature of selection as well as identify new genetic variants explaining variation in economically important traits, and (4) identify the genetic relationships among these traits including feed efficiency, Aleutian disease resilience, fur quality, reproductive performance, growth rate and pelt size. One hundred mink DNA samples from the Canadian Centre for Fur Animal Research at Dalhousie Agriculture Campus (Truro, Nova Scotia), and one breeding population (Millbank Fur Farm Limited, Rockwood, Ontario) were sequenced using next-generation whole-genome sequencing with more than 30x coverage to create the first SNP assay for American mink. A DNA panel composed of these sequenced mink from five color-types were assembled to identify the most homozygous individual as the reference animal for whole-genome sequence assembly development. The phenotypic data and DNA samples from 3,323 animals were collected and will be genotyped using the customized assay. The ultimate objective is to develop new tools for implementation of marker assisted selection or genomic selection in mink breeding programs for development of superior, highly efficient, and healthy animals. This approach will help improve the overall performance of the North American mink industry, which is now in difficulty due to several economic factors such as the high price of feed, declining price of fur and prevalence of diseases.

scholarly journals A New and Improved Genome Sequence of Cannabis sativa

2020 ◽  
Author(s):  
Shivraj Braich ◽  
Rebecca C. Baillie ◽  
German 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.

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