Journal: International Journal of Molecular Sciences

Article Title: Plasticity in Gene Expression Patterns and CYPSF Gene Possibly Involved in the Etofenprox-Resistant Population of White-Backed Planthopper, Sogatella furcifera

doi: 10.3390/ijms252413605

Figure Lengend Snippet: Statistics of initial assembled, and unigene contig.

Article Snippet: The statistics for the initial assembled contig, longest contig, and unigene contig are detailed in , which highlights key metrics such as the number of genes, number of transcripts, GC content (%), N 50 values, average contig length (bp), and total assembled bases.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Plasticity in Gene Expression Patterns and CYPSF Gene Possibly Involved in the Etofenprox-Resistant Population of White-Backed Planthopper, Sogatella furcifera

doi: 10.3390/ijms252413605

Figure Lengend Snippet: Statistics of initial assembled, and unigene contig.

Article Snippet: The unigene contig assembly, which aimed to consolidate unique gene sequences, included 194,501 genes and transcripts.

Techniques:

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Diploid (AA) M. acuminata accessions contrasting in resistance to Mycosphaerella leaf spot diseases selected for use in SSR marker validation .

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques: Marker

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques: Sequencing

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Species distribution of M. acuminata unigenes shown as the percentage of the total homologous monocotyledon plant sequences. The best BLAST hits of each sequence were analysed.

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques: Sequencing

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Representation of M. acuminata unigenes classified in functional groups. The GO hits were assigned to categories (A) molecular function, (B) biological process and (C) cellular component.

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques: Functional Assay

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Northern blot analysis of expression of selected defence-related M. acuminata unigenes during the time course interaction with Mf . Arrows show differential gene expression between the tested cultivars for each gene probe.

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques: Northern Blot, Expressing

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Summary of M. acuminata unigenes mapped in KEGG pathways .

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques:

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Abundance and diversity of expressed TEs in M. acuminata EST datasets .

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques:

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Overview of SSR repeat abundance in M. acuminata ESTs and primer design statistics .

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques:

Journal: AoB Plants

Article Title: Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

doi: 10.1093/aobpla/pls030

Figure Lengend Snippet: Characteristics of polymorphic microsatellite loci isolated from M. acuminata Calcutta 4 and Cavendish Grande Naine EST data .

Article Snippet: Fig. 2 Summary of EST quality and sequence assembly from combined MAC4 and MACV datasets. (A) Length distribution of the M. acuminata ESTs; (B) length distribution of the assembled M. acuminata unigene contigs; (C) length distribution of the M. acuminata unigene singletons; (D) frequency and distribution of ESTs in assembled M. acuminata unigene contigs.

Techniques: Isolation

Journal: BMC Plant Biology

Article Title: Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [ Cajanus cajan (L.) Millspaugh]

doi: 10.1186/1471-2229-11-17

Figure Lengend Snippet: Size distribution of the TSA contigs from two pigeonpea varieties generated using Newbler assembler and then aligned together using Lasergene SeqMan Pro™ software

Article Snippet: A total of 3,771 SSR loci were identified in 3,327 TSA contigs, representing 7.6% of the total 43,324 unigene TSA contigs (Figure ).

Techniques: Generated

Journal: BMC Plant Biology

Article Title: Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [ Cajanus cajan (L.) Millspaugh]

doi: 10.1186/1471-2229-11-17

Figure Lengend Snippet: Wet laboratory validation of in silico identified genic-SSR length polymorphism between pigeonpea parental lines . Pigeonpea genic-SSR locus ASSR-8 showing: a. in silco polymorphism between the aligned TSA contigs of parental lines Asha (A) and UPAS 120 (U), b. agarose gel analysis of segregation of the ASSR-8 alleles in F 2 population. Positions of flanking primers and the polymorphic SSR sequence are highlighted.

Article Snippet: A total of 3,771 SSR loci were identified in 3,327 TSA contigs, representing 7.6% of the total 43,324 unigene TSA contigs (Figure ).

Techniques: In Silico, Agarose Gel Electrophoresis, Sequencing

Journal: BMC Plant Biology

Article Title: Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [ Cajanus cajan (L.) Millspaugh]

doi: 10.1186/1471-2229-11-17

Figure Lengend Snippet: Details of pigeonpea transcriptome shotgun sequence reads and their assembly into TSA contigs using 454-Newbler assembler

Article Snippet: A total of 3,771 SSR loci were identified in 3,327 TSA contigs, representing 7.6% of the total 43,324 unigene TSA contigs (Figure ).

Techniques: Sequencing

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: Comparison of the results of two physical map assembly algorithms used to assemble chromosome 1AS fingerprints, FPC and LTC.

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques: Clone Assay

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: Repetitive BAC clones within the BAC fingerprints were problematic for the FPC assembly, leading to non-linear contig patterns. The reassembly of fingerprints using the LTC assembly program resolved non-linear contigs. The dashed line indicates where the non-linear contig was cut into two contig segments, because the two segments are only connected by a single BAC clone (indicated by all connections converging in one point.

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques: Clone Assay

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: Final composition of the BAC clone backbone of the wheat 1AS physical map.

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques:

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: a. The BAC clones constituting the contig ltc5279 are depicted at the top. Underneath, FPC contigs which cover corresponding regions are displayed. Gray lines connect the start points of corresponding BACs. Contig ltc5279 (approximately 2,161 kb in size) which is the fusion product of eight smaller FPC contigs. Overall, the relative positions of BAC clones within LTC and FPC contigs are very similar. b. Example of three small FPC contigs which are merged into one LTC contig (ltc132). This LTC contig also includes BACs which were singletons in the FPC assembly (blue). Note that in a and b the scales are different. c. Size distribution of overlaps of FPC contigs which were merged in the LTC assembly. The x-axis indicates the size range of overlaps of two FPC clones that were merged by LTC. The y-axis shows how many cases were identified in each size range. The gray series shows the size distribution of all overlaps. The blue series shows only those cases where additional singletons were included to merge FPC contigs while the red series shows the cases where no additional clones were used for the merging.

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques: Clone Assay

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: The figure integrates multiple sequence resources. a. Chromosome 1AS deletion bin map with the three bins shown in (yellow, green and gray). ESTs from the three deletion bins which were mapped to Brachypodium reference zipper genes are indicated with boxes with colour of the corresponding bin. If more than one EST mapped to the same Brachypodium gene, the boxes were stacked on top of each other. This information was used to estimate the boundaries of each deletion bin in the Brachypodium reference zipper (dashed lines). b. Brachypodium reference zipper. c. Physical map of the 1AS chromosme arm. BAC contigs are symbolised with blue lines (see enlarged legend at the right). The length of the line reflects the number of putative syntenic genes found on the contig, not its physical size. Syntenic genes are also symbolised by black boxes. The number of non-syntenic genes for each contig is indicated with a stack of red boxes. Grey boxes indicate place holders for contigs that contained no syntenic genes but were anchored by means other than synteny (e.g. genetic markers of centromere-specific repeats. d. Published genetic markers from chromosome 1AS that were used to deduce an estimated genetic map (marker and map names and genetic distances are detailed in ).

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques: Sequencing, Marker

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: On level 1, genes were anchored to physical BAC contigs using positive hybridisation probe matches, BAC-end sequences and Illumina contigs. Individual anchoring procedures are indicated by capital letters in circles and described in the text. For level 2 anchoring, all BAC contigs which contain genes which have their homologs in the 1AS syntenic region of Brachypodium , rice or sorghum were anchored to the reference zipper. This means that the order of genes in wheat was assumed to be the same as in Brachypodium , rice or sorghum. In the final step (level 3), data from genetic markers were used to anchor BAC contigs to previously published genetic maps.

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques: Hybridization

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: Numbers of genes which were assigned to 1AS BAC contigs during level 1 anchoring.

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques:

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: Statistics on level 2 anchoring of BAC contigs in the 1AS physical map.

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques:

Journal: PLoS ONE

Article Title: A Physical Map of the Short Arm of Wheat Chromosome 1A

doi: 10.1371/journal.pone.0080272

Figure Lengend Snippet: Two assembled physical contigs (ltc132 and ltc5245) were linked together using a previously published 178 kb sequence from chromosome 1AS (cv. Chinese Spring) covering the the Pm3 locus (Wicker et al. 2007). Approximate locations of NimbleGen transcriptome hybridisation probes are shown in blue. The Pm3 and the low molecular weight (LMW) glutenin loci are known to be closely linked (Wicker et al. 2003; Wang et al. 2010). The inset shows a phylogenetic analysis that compares glutenin UniGene sequences with previously published glutenin genes from 1AS (TmGluA3, green), 1BS (TaGluB) and 1DS (TaGluD).

Article Snippet: These allow the characterisation of expressed genes as well as the assembly of so-called UniGene EST contigs.

Techniques: Sequencing, Hybridization, Molecular Weight