scholarly journals Whole Genome Sequence Comparisons and "Full-Length" cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation

2004 ◽  
Vol 14 (3) ◽  
pp. 406-413 ◽  
Author(s):  
V. Castelli
Keyword(s):  
Genome Sequence ◽  
Genome Annotation ◽  
Full Length ◽  
Arabidopsis Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Combined Approach ◽  
Sequence Comparisons ◽  
Full Length Cdna ◽  
Cdna Sequences

scholarly journals Whole genome sequence and genome annotation of Colletotrichum acutatum , causal agent of anthracnose in pepper plants in South Korea

Genomics Data ◽  
2016 ◽  
Vol 8 ◽  
pp. 45-46 ◽  
Author(s):  
Joon-Hee Han ◽  
Jae-Kyung Chon ◽  
Jong-Hwa Ahn ◽  
Ik-Young Choi ◽  
Yong-Hwan Lee ◽  
...  
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Genome Annotation ◽  
Causal Agent ◽  
Whole Genome Sequence ◽  
Colletotrichum Acutatum ◽  
Whole Genome ◽  
Pepper Plants

scholarly journals Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Ainong Shi ◽  
Devi R. Kandel ◽  
Nora Solís-Gracia ◽  
Jorge Alberto da Silva ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genome Sequence ◽  
Reference Genome ◽  
Whole Genome Sequence ◽  
Large Set ◽  
Whole Genome ◽  
Genome Sequences ◽  
Sequence Comparisons ◽  
Ssr Loci ◽  
Simple Sequence

AbstractThe availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.

scholarly journals De Novo Whole-Genome Sequence and Genome Annotation of Lichtheimia ramosa

2014 ◽  
Vol 2 (5) ◽  
Author(s):  
J. Linde ◽  
V. Schwartze ◽  
U. Binder ◽  
C. Lass-Florl ◽  
K. Voigt ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Annotation ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lichtheimia Ramosa

Whole-genome sequence comparisons reveal the evolution of Vibrio cholerae O1

2015 ◽  
Vol 23 (8) ◽  
pp. 479-489 ◽  
Author(s):  
Eun Jin Kim ◽  
Chan Hee Lee ◽  
G. Balakrish Nair ◽  
Dong Wook Kim
Keyword(s):  
Vibrio Cholerae ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Comparisons ◽  
Vibrio Cholerae O1

scholarly journals Whole-Genome Sequence and Fosfomycin Resistance of Bacillus sp. Strain G3(2015) Isolated from Seawater off the Coast of Malaysia

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Xin-Yue Chan ◽  
Jian-Woon Chen ◽  
Tan-Guan-Sheng Adrian ◽  
Kar-Wai Hong ◽  
Chien-Yi Chang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Annotation ◽  
Bacterial Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Bacillus Sp ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Resistant Gene ◽  
Fosfomycin Resistance

ABSTRACT Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In this study, the genome of marine Bacillus sp. strain G3(2015) was sequenced using MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome annotation.

Whole Genome Sequence Comparisons in Taxonomy

2011 ◽  
pp. 409-436 ◽  
Author(s):  
Rainer Borriss ◽  
Christian Rueckert ◽  
Jochen Blom ◽  
Oliver Bezuidt ◽  
Oleg Reva ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Comparisons
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