Transcriptome based genetic resources from Rabbiteye and Southern Highbush blueberries

2021 ◽  
pp. 1-13
Author(s):  
Chuyan Wang ◽  
Jie Yu ◽  
Jun Wang ◽  
Jigang Zhang ◽  
Liuqing Yang ◽  
...  
Keyword(s):  
Genetic Resources ◽  
De Novo ◽  
Present Report ◽  
Rapid Development ◽  
Homology Search ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Wide Range ◽  
Highbush Blueberries ◽  
Southern Highbush

BACKGROUND: Blueberry is among the fastest growing fruit crops in the world, which is beneficial to human health and attracts extensive interests. In contrast to its rapid development and utilization, availability of molecular and genetic resources for blueberries are still scarce. OBJECTIVE: In present report, transcriptomic profiling of four widely cultivated varieties of Rabbiteye and Southern Highbush blueberries were characterized to assist the breeding programs. METHODS: Both de novo and reference-based assembly were conducted to generate the genetic resources that can be used in the further functional and breeding studies. RESULTS: De novo and reference-based assembly found average 136,350 and 158,123 non-redundant transcripts, respectively. Average 57,668 de novo assembled transcripts can be functionally annotated by homology search with different databases. We further detected 6,268 polymorphic simple sequence repeats, 566,913 high-quality single nucleotide polymorphisms and 88,662 insertion and deletions among the four varieties with comparison to a recently released reference genome of blueberry. Differentially expressed genes analysis showed that varieties of same species show less differences within species but larger differences between species. CONCLUSIONS: These comprehensive and high-quality genetic resources will contribute to a wide range of genetics and molecular breeding studies in blueberries.

scholarly journals De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1342
Author(s):  
Shaghayegh Mehravi ◽  
Gholam Ali Ranjbar ◽  
Ghader Mirzaghaderi ◽  
Anita Alice Severn-Ellis ◽  
Armin Scheben ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Snps ◽  
The Family ◽  
Double Digestion ◽  
Flanking Sequences ◽  
Downstream Analysis

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

scholarly journals LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology

2021 ◽  
Author(s):  
Patrick Driguez ◽  
Salim Bougouffa ◽  
Karen Carty ◽  
Alexander Putra ◽  
Kamel Jabbari ◽  
...  
Keyword(s):  
De Novo ◽  
Rapid Development ◽  
Plant Genome ◽  
Plant Genomics ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Tissue Samples ◽  
Sequencing Technologies ◽  
The Cost ◽  
New Generation

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.

scholarly journals Exploring the Phylogeography of Ancient Platycladus orientalis in China by Specific-Locus Amplified Fragment Sequencing

2019 ◽  
Vol 20 (16) ◽  
pp. 3871
Author(s):  
Ermei Chang ◽  
Yuxin Tian ◽  
Caiyun Wang ◽  
Nan Deng ◽  
Zeping Jiang ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Phylogenetic Trees ◽  
De Novo ◽  
Climatic Factors ◽  
Geographical Location ◽  
Nucleotide Polymorphisms ◽  
Platycladus Orientalis ◽  
Sequencing Method ◽  
History Of ◽  
Specific Locus

Platycladus orientalis (i.e., Chinese thuja) is famous for its lifespan spanning hundreds, and even thousands, of years. Most ancient P. orientalis populations are widely distributed in China, with accessible historical records, making them valuable genetic resources. In this study, the distribution pattern of ancient P. orientalis in China was analyzed based on 13 bioclimatic factors. Additionally, a specific-locus amplified fragment (SLAF) sequencing method was applied to detect single nucleotide polymorphisms (SNPs) in the genomes of 100 accessions from 13 populations. The resulting data revealed that the suitable areas for the distribution of ancient P. orientalis populations were accurately predicted with four main climatic factors. A total of 81,722 SNPs were identified from 461,867 SLAFs for 100 individuals, with an average sequencing depth of 10.11-fold and a Q30 value of 82.75%. The pair-wise genetic distance and genetic differentiation of 13 populations indicated that the BT-T population exhibited the largest divergence from the other populations. A neighbor-joining phylogenetic tree suggested the relationship between many individuals was inconsistent with the geographical location, possibly indicative of a history of transplantation and cultivation. All individuals were clustered into nine genotypes according to a structural analysis and the relationships between individuals were clarified in phylogenetic trees. This study highlights the importance of the de novo genome sequencing of ancient P. orientalis and may provide the basis for the conservation of P. orientalis genetic resources, the identification of supergene families, and the evaluation of related genetic resources.

scholarly journals A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia

2020 ◽  
Vol 10 (4) ◽  
pp. 1159-1166 ◽  
Author(s):  
Swarnali Louha ◽  
David A. Ray ◽  
Kevin Winker ◽  
Travis C. Glenn
Keyword(s):  
Biomedical Research ◽  
Genome Assembly ◽  
De Novo ◽  
Genome Structure ◽  
Melospiza Melodia ◽  
Song Sparrow ◽  
Comparative Genomic ◽  
High Quality ◽  
Wide Range

The song sparrow, Melospiza melodia, is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species’ pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We have generated a high-quality de novo genome assembly of M. melodia using Illumina short read sequences from genomic and in vitro proximity-ligation libraries. The assembled genome is 978.3 Mb, with a physical coverage of 24.9×, N50 scaffold size of 5.6 Mb and N50 contig size of 31.7 Kb. Our genome assembly is highly complete, with 87.5% full-length genes present out of a set of 4,915 universal single-copy orthologs present in most avian genomes. We annotated our genome assembly and constructed 15,086 gene models, a majority of which have high homology to related birds, Taeniopygia guttata and Junco hyemalis. In total, 83% of the annotated genes are assigned with putative functions. Furthermore, only ∼7% of the genome is found to be repetitive; these regions and other non-coding functional regions are also identified. The high-quality M. melodia genome assembly and annotations we report will serve as a valuable resource for facilitating studies on genome structure and evolution that can contribute to biomedical research and serve as a reference in population genomic and comparative genomic studies of closely related species.

scholarly journals Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]

2020 ◽  
Vol 10 (8) ◽  
pp. 2565-2572 ◽  
Author(s):  
Xiaozhu Wang ◽  
Yogeshwar D. Kelkar ◽  
Xiao Xiong ◽  
Ellen O. Martinson ◽  
Jeremy Lynch ◽  
...  
Keyword(s):  
De Novo ◽  
Rapid Development ◽  
Laboratory Strain ◽  
Whole Genome Sequence ◽  
High Quality ◽  
Important Species ◽  
A Genome ◽  
Behavioral Expression ◽  
Genomic Studies ◽  
Low Coverage

Jewel wasps in the genus of Nasonia are parasitoids with haplodiploidy sex determination, rapid development and are easy to culture in the laboratory. They are excellent models for insect genetics, genomics, epigenetics, development, and evolution. Nasonia vitripennis (Nv) and N. giraulti (Ng) are closely-related species that can be intercrossed, particularly after removal of the intracellular bacterium Wolbachia, which serve as a powerful tool to map and positionally clone morphological, behavioral, expression and methylation phenotypes. The Nv reference genome was assembled using Sanger, PacBio and Nanopore approaches and annotated with extensive RNA-seq data. In contrast, Ng genome is only available through low coverage resequencing. Therefore, de novo Ng assembly is in urgent need to advance this system. In this study, we report a high-quality Ng assembly using 10X Genomics linked-reads with 670X sequencing depth. The current assembly has a genome size of 259,040,977 bp in 3,160 scaffolds with 38.05% G-C and a 98.6% BUSCO completeness score. 97% of the RNA reads are perfectly aligned to the genome, indicating high quality in contiguity and completeness. A total of 14,777 genes are annotated in the Ng genome, and 72% of the annotated genes have a one-to-one ortholog in the Nv genome. We reported 5 million Ng-Nv SNPs which will facility mapping and population genomic studies in Nasonia. In addition, 42 Ng-specific genes were identified by comparing with Nv genome and annotation. This is the first de novo assembly for this important species in the Nasonia model system, providing a useful new genomic toolkit.

scholarly journals High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jiali Yu ◽  
Amanda M. Hulse-Kemp ◽  
Ebrahiem Babiker ◽  
Margaret Staton
Keyword(s):  
Small Rna ◽  
Reference Genome ◽  
Anthocyanin Biosynthesis ◽  
Vaccinium Corymbosum ◽  
Small Rna Sequencing ◽  
High Quality ◽  
Protein Coding ◽  
Haplotype Assembly ◽  
Highbush Blueberries ◽  
Southern Highbush

AbstractVaccinium darrowii Camp (2n = 2x = 24) is a native North American blueberry species and an important source of traits such as low chill requirement in commercial southern highbush blueberry breeding (Vaccinium corymbosum, 2n = 4x = 48). We present a chromosomal-scale genome of V. darrowii generated by the combination of PacBio sequencing and high throughput chromatin conformation capture (Hi–C) scaffolding technologies, yielding a total length of 1.06 Gigabases (Gb). Over 97.8% of the genome sequences are scaffolded into 24 chromosomes representing the two haplotypes. The primary haplotype assembly of V. darrowii contains 34,809 protein-coding genes. Comparison to a V. corymbosum haplotype assembly reveals high collinearity between the two genomes with small intrachromosomal rearrangements in eight chromosome pairs. With small RNA sequencing, the annotation was further expanded to include more than 200,000 small RNA loci and 638 microRNAs expressed in berry tissues. Transcriptome analysis across fruit development stages indicates that genes involved in photosynthesis are downregulated, while genes involved in flavonoid and anthocyanin biosynthesis are significantly increased at the late stage of berry ripening. A high-quality reference genome and accompanying annotation of V. darrowii is a significant new resource for assessing the evergreen blueberry contribution to the breeding of southern highbush blueberries.

scholarly journals A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs

2014 ◽  
Vol 2014 ◽  
pp. 1-4 ◽  
Author(s):  
Mingming Liu ◽  
Zach N. Adelman ◽  
Kevin M. Myles ◽  
Liqing Zhang
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Rapid Development ◽  
High Quality ◽  
High Coverage ◽  
Sequencing Technologies ◽  
Sequence Variations ◽  
Downstream Analysis ◽  
Genome Assemblies ◽  
Redundant Contigs

With the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. Sequence assembly approaches have been modified to meet the requirements for de novo transcriptomes, which have complications not found in traditional genome assemblies such as variation in coverage for each candidate mRNA and alternative splicing. As a consequence, de novo assembly strategies tend to generate a large number of redundant contigs due to sequence variations, which adversely affects downstream analysis and experiments. In this work we proposed TransPS, a transcriptome post-scaffolding method, to generate high quality, nonredundant de novo transcriptomes. TransPS shows promising results on the test transcriptome datasets, where redundancy is greatly reduced by more than 50% and, at the same time, coverage is improved considerably. The web server and source code are available.

scholarly journals Anthracnose on Southern Highbush Blueberry

EDIS ◽  
2018 ◽  
Vol 2018 (3) ◽  
Author(s):  
Douglas A Phillips ◽  
Maria C. Velez-Climent ◽  
Philip F. Harmon ◽  
Patricio R. Munoz
Keyword(s):  
Plant Pathology ◽  
Fungal Pathogens ◽  
Highbush Blueberry ◽  
Pathology Department ◽  
Wide Range ◽  
Highbush Blueberries ◽  
Southern Highbush

Information contained in this 4-page publication is intended for Florida blueberry growers to use as a guide in the identification of anthracnose, a group of fungal pathogens that affects a wide range of plants, including southern highbush blueberries (SHB). Written by Douglas A. Phillips, Maria C. Velez-Climent, Philip F. Harmon, and Patricio R. Munoz and published by the UF/IFAS Plant Pathology Department, May 2018.https://edis.ifas.ufl.edu/pp337

scholarly journals A high-quality genome assembly of the North American Song Sparrow, Melospiza melodia

2019 ◽  
Author(s):  
Swarnali Louha ◽  
David A. Ray ◽  
Kevin Winker ◽  
Travis Glenn
Keyword(s):  
Biomedical Research ◽  
Genome Assembly ◽  
De Novo ◽  
Genome Structure ◽  
Melospiza Melodia ◽  
Song Sparrow ◽  
Comparative Genomic ◽  
High Quality ◽  
Wide Range

AbstractThe song sparrow, Melospiza melodia, is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species’ pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We have generated a high-quality de novo genome assembly of M. melodia using Illumina short read sequences from genomic and in vitro proximity-ligation libraries. The assembled genome is 978.3 Mb, with a coverage of 24.9×, N50 scaffold size of 5.6 Mb and N50 contig size of 31.7 Kb. Genes within our genome assembly are largely complete, with 87.5% full-length genes present out of a set of 4,915 universal single-copy orthologs present in most avian genomes. We annotated our genome assembly and constructed 15,086 gene models, a majority of which have high homology to related birds, Taeniopygia guttata and Junco hyemalis. In total, 83% of the annotated genes are assigned with putative functions. Furthermore, only ~7% of the genome is found to be repetitive; these regions and other non-coding functional regions are also identified. The high-quality M. melodia genome assembly and annotations we report will serve as a valuable resource for facilitating studies on genome structure and evolution that can contribute to biomedical research and serve as a reference in population genomic and comparative genomic studies of closely related species.

scholarly journals Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits

2020 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Agronomic Traits ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Wide Range ◽  
Breeding Research ◽  
High Quality Genome

Abstract BackgroundCultivated soybean (Glycine max) is an important source for protein and oil. Each soybean strain has its own genetic diversity, and the availability of more soybean genomes may enhance comparative genomic analysis of soybean.ResultsIn this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with high contiguity, completeness, and accuracy. We annotated 59,629 gene models and reconstructed 235,109 high-quality full-length transcripts. We have molecularly characterized the genotypes of some important agronomic traits of JD17 by taking advantage of these newly established genomic resources.ConclusionsWe reported a high-quality genome and annotations of a wide range of cultivars, and used them to analyze the genotypes of genes related to important agronomic traits of soybean in JD17. We have demonstrated that high-quality genome assembly can serve as a valuable reference for soybean genomics and breeding research community.

Sign in / Sign up

Export Citation Format

Share Document