Using Whole-Genome Sequence Information to Foster Conservation Efforts for the European Dark Honey Bee, Apis mellifera mellifera

AbstractIn this paper we extend multi-locus iterative peeling to be a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, called hybrid peeling, uses multi-locus iterative peeling to estimate shared chromosome segments between parents and their offspring, and then uses single-locus iterative peeling to aggregate genomic information across multiple generations. Using a synthetic dataset, we first analysed the performance of hybrid peeling for calling and phasing alleles in disconnected families, families which contained only a focal individual and its parents and grandparents. Second, we analysed the performance of hybrid peeling for calling and phasing alleles in the context of the full pedigree. Third, we analysed the performance of hybrid peeling for imputing whole genome sequence data to the remaining individuals in the population. We found that hybrid peeling substantially increase the number of genotypes that were called and phased by leveraging sequence information on related individuals. The calling rate and accuracy increased when the full pedigree was used compared to a reduced pedigree of just parents and grandparents. Finally, hybrid peeling accurately imputed whole genome sequence information to non-sequenced individuals. We believe that this algorithm will enable the generation of low cost and high accuracy whole genome sequence data in many pedigreed populations. We are making this algorithm available as a standalone program called AlphaPeel.

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A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79.2.15 ◽

2019 ◽

Vol 79 (02) ◽

Author(s):

Humira Sonah ◽

Hasthi Ram ◽

Bikram Pratap Singh ◽

Jawaharlal Katara ◽

Radha Chopra ◽

...

Keyword(s):

Quantitative Pcr ◽

Genome Sequence ◽

Sequence Variation ◽

Whole Genome Sequence ◽

Pcr Analysis ◽

Sequence Information ◽

Whole Genome ◽

Intron Length Polymorphism ◽

Genome Wide ◽

A Genome

Whole genome sequence availability in rice has provided several advantages for genomics as well as other omics assisted applications. Genome-wide molecular markers are one of such availability that has exceptional importance in modern plant breeding. In the present study, a resource of intron-spanning primers (ISPs) was developed using whole genome sequence information of two rice subspecies, japonica (cv. Nipponbare) and indica (cv. 93-11). The ISPs were designed in a way that the PCR using a cDNA template will yield 60 to 100 base pair size amplicon ideal for the quantitative PCR analysis. Whereas, PCR using genomic DNA will amplify the introns, which are more prone to sequence variation. The sequence variation in the intron serves as an excellent marker resource. The application of ISPs was demonstrated by characterizing 12 diverse rice cultivars. A total of eight out of ten ISPs were found to be polymorphic. The resource will be helpful for the rice molecular biologist and breeder community.

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Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense

10.1101/2021.06.17.448907 ◽

2021 ◽

Author(s):

Kenta Shirasawa ◽

Nobuo Kobayashi ◽

Akira Nakatsuka ◽

Hideya Ohta ◽

Sachiko Isobe

Keyword(s):

Genome Sequence ◽

Single Molecule ◽

Sequence Information ◽

Whole Genome ◽

Closely Related Species ◽

Chiba Prefecture ◽

Genome Sequence Assembly ◽

Genome Sequence Information ◽

Relationship Of ◽

Long Fragment Read

To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analyzed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars, respectively; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time (SMRT) sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read (stLFR) sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely-related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.

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Enhancing PCR Capacity To Detect ‘Candidatus Liberibacter asiaticus’ Utilizing Whole Genome Sequence Information

Plant Disease ◽

10.1094/pdis-05-19-0931-re ◽

2020 ◽

Vol 104 (2) ◽

pp. 527-532 ◽

Cited By ~ 4

Author(s):

Minli Bao ◽

Zheng Zheng ◽

Xiaoan Sun ◽

Jianchi Chen ◽

Xiaoling Deng

Keyword(s):

Genome Sequence ◽

Biological Information ◽

Whole Genome Sequence ◽

Rrna Gene ◽

Sequence Information ◽

Whole Genome ◽

Candidatus Liberibacter Asiaticus ◽

Genomic Locus ◽

Candidatus Liberibacter ◽

Liberibacter Asiaticus

‘Candidatus Liberibacter asiaticus’ (CLas) is an unculturable α-proteobacterium associated with citrus Huanglongbing (HLB; yellow shoot disease). PCR procedures that accurately confirm or exclude CLas infection in citrus tissue/Asian citrus psyllid (ACP) samples are critical for HLB management. When CLas was described in 1994, a 23-bp signature oligonucleotide sequence (OI1) in the 16S rRNA gene (rrs, three genomic copies) was identified based on Sanger sequencing. OI1 contains single nucleotide polymorphisms (SNPs) distinguishing CLas from non-CLas species. The SNPs were used to design the primer HLBas, a key primer for a commonly used TaqMan PCR system (HLBas-PCR) for CLas detection. Recent developments in next-generation sequencing technology have led to the identification of 15 CLas whole genome sequence strains (WGSs). Analyses of CLas WGSs have generated a significant amount of biological information that could help to improve CLas detection. Utilizing the WGS information, this study re-evaluated the sequence integrity of OI1/HLBas and identified and/or confirmed a missing nucleotide G in the two primers. Replacement primers for OI1 and HLBas are proposed. At low cycle threshold (Ct) values (e.g., <30), HLBas-PCR remained reliable in CLas determination. At high Ct values (e.g., >30), HLBas-PCR alone was unreliable in differentiating whether samples contain low CLas titers or whether CLas is not present. The availability of ribonucleotide reductase (RNR)-PCR derived from the five-copy nrdB gene helped to resolve this problem. To further enhance low CLas titer detection, a 4CP-PCR system, based on a four-copy genomic locus, was developed. Evaluation of 107 HLB samples (94 citrus and 13 ACP) showed that 4CP-PCR was more sensitive than HLBas-PCR and shared similar sensitivity with RNR-PCR.

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