scholarly journals A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia x Vitis cinerea) and its Exploitation for Marker Development and Targeted Mapping

2019 ◽  
Author(s):  
Daniela Holtgräwe ◽  
Thomas Rosleff Sörensen ◽  
Ludger Hausmann ◽  
Boas Pucker ◽  
Prisca Viehöver ◽  
...  
Keyword(s):  
Genetic Marker ◽  
Genome Sequence ◽  
Plant Protection ◽  
Draft Genome ◽  
Plasmopara Viticola ◽  
Sequence Assembly ◽  
Resistance Locus ◽  
Sources Of Resistance ◽  
Vitis Riparia ◽  
Genome Sequence Assembly

AbstractGrapevine breeding becomes highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. Therefore, in modern breeding programs genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x V. cinerea Arnold, available as the rootstock cultivar ‘Börner’, carries several relevant resistance loci. We applied next generation sequencing to enable the reliable identification of simple sequence repeats (SSR) and also generated a draft genome sequence assembly of ‘Börner’ to access genome wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the ‘Börner’ genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

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 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.

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 of Plasmopara viticola , the Grapevine Downy Mildew Pathogen

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yann Dussert ◽  
Jérôme Gouzy ◽  
Sylvie Richart-Cervera ◽  
Isabelle D. Mazet ◽  
Laurent Delière ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Genome Sequence ◽  
Genome Analysis ◽  
Plant Pathogen ◽  
Host Resistance ◽  
Draft Genome ◽  
Plasmopara Viticola ◽  
Host Specialization ◽  
Grapevine Downy Mildew ◽  
Plant Pathogen Interactions

Plasmopara viticola is a biotrophic pathogenic oomycete responsible for grapevine downy mildew. We present here the first draft of the P. viticola genome. Analysis of this sequence will help in understanding plant-pathogen interactions in oomycetes, especially pathogen host specialization and adaptation to host resistance.

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
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