scholarly journals Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

2021 ◽  
Author(s):  
Nikolay Alabi ◽  
Yihan Wu ◽  
Oliver Bossdorf ◽  
Loren H Rieseberg ◽  
Robert I Colautti
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Genome Mapping ◽  
Draft Genome ◽  
Alliaria Petiolata ◽  
Conservation Strategies ◽  
Ecological Knowledge ◽  
Garlic Mustard ◽  
A Genome ◽  
Invasion Genetics

Abstract The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

scholarly journals A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

2021 ◽  
Author(s):  
Nikolay Alabi ◽  
Yihan Wu ◽  
Oliver Bossdorf ◽  
Loren H. Rieseberg ◽  
Robert I. Colautti
Keyword(s):  
Western Europe ◽  
De Novo ◽  
Genome Mapping ◽  
Draft Genome ◽  
Alliaria Petiolata ◽  
Ecological Knowledge ◽  
Garlic Mustard ◽  
Draft Genome Assembly ◽  
A Genome ◽  
Invasion Genetics

AbstractThe emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ~70× coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121Mb; L50 = 2) with 99.7% of the 1.1Gb genome mapping to contigs of at least 50Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe Almost, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite a genome-wide average of < 2% heterozygosity. The continuity and gene space quality of our draft genome assembly will enable genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation efforts.

scholarly journals Employing whole genome mapping for optimal de novo assembly of bacterial genomes

2014 ◽  
Vol 7 (1) ◽  
pp. 484 ◽  
Author(s):  
Basil Xavier ◽  
Julia Sabirova ◽  
Moons Pieter ◽  
Jean-Pierre Hernalsteens ◽  
Henri de Greve ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Genome Mapping ◽  
Whole Genome ◽  
Bacterial Genomes ◽  
Whole Genome Mapping

scholarly journals The Draft Genome Assembly of the Critically Endangered Nyssa yunnanensis, a Plant Species with Extremely Small Populations Endemic to Yunnan Province, China

2020 ◽  
Author(s):  
Weixue Mu ◽  
Jinpu Wei ◽  
Ting Yang ◽  
Yannan Fan ◽  
Le Cheng ◽  
...  
Keyword(s):  
Plant Species ◽  
Tree Species ◽  
Yunnan Province ◽  
De Novo ◽  
Higher Plants ◽  
Draft Genome ◽  
Critically Endangered ◽  
Deciduous Tree ◽  
Conservation Strategies ◽  
Small Populations

Nyssa yunnanensis is a deciduous tree in family Nayssaceae within the order Cornales. As only 8 individuals in 2 sites recorded in Yunnan province of China, the species was listed as the China&rsquo;s national grade-I protection species in 1999, and also as one of 120 PSESP(Plant Species with Extremely Small Populations) in Implementation Plan of Rescuing and Conserving China&rsquo;s Plant Species with extremely Small Populations(PSESP) (2011-2-15). N. yunnanensis was also been evaluated as Critically Endangered in IUCN red list and Threatened Species List of China's Higher Plants. Hence understanding the genomic characteristics of this highly endangered Tertiary relict tree species is essential, especially for developing conservation strategies. Here we sequenced and annotated the genome of N. yunnanensis using 10X genomics linked-reads sequencing data. The de novo assembled genome is 1474Mb in length with a scaffold N50 length of 985.59kb. We identified 823.51Mb of non-redundant sequence as repetitive elements and annotated 39,803 protein-coding genes in the assembly. Our result provided the genomic characteristics of N. yunnanensis, which will provide valuable resources for future genomic and evolutionary studies, especially for conservation biology studies of this extremely threatened tree species.

scholarly journals Enhanced De Novo Assembly of High Throughput Pyrosequencing Data Using Whole Genome Mapping

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e61762 ◽  
Author(s):  
Fatma Onmus-Leone ◽  
Jun Hang ◽  
Robert J. Clifford ◽  
Yu Yang ◽  
Matthew C. Riley ◽  
...  
Keyword(s):  
High Throughput ◽  
De Novo Assembly ◽  
De Novo ◽  
Genome Mapping ◽  
Whole Genome ◽  
Whole Genome Mapping

scholarly journals De Novo Genome Sequence of “ Candidatus Liberibacter solanacearum” from a Single Potato Psyllid in California

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
F. Wu ◽  
X. Deng ◽  
G. Liang ◽  
C. Wallis ◽  
J. T. Trumble ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Open Reading Frames ◽  
Potato Psyllid ◽  
Bactericera Cockerelli ◽  
Solanacearum Strain ◽  
A Genome ◽  
Candidatus Liberibacter ◽  
Rna Genes

The draft genome sequence of “ Candidatus Liberibacter solanacearum” strain RSTM from a potato psyllid ( Bactericera cockerelli ) in California is reported here. The RSTM strain has a genome size of 1,286,787 bp, a G+C content of 35.1%, 1,211 predicted open reading frames (ORFs), and 43 RNA genes.

scholarly journals The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

2022 ◽  
Author(s):  
Shinichi Morita ◽  
Tomoko F. Shibata ◽  
Tomoaki Nishiyama ◽  
Yuuki Kobayashi ◽  
Katsushi Yamaguchi ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Genetic Regulation ◽  
Draft Genome ◽  
Evolutionary Developmental Biology ◽  
Rhinoceros Beetle ◽  
Insect Order ◽  
Trypoxylus Dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

scholarly journals Draft Genome Assembly and Annotation of Red Raspberry Rubus Idaeus

2019 ◽  
Author(s):  
Haley Wight ◽  
Junhui Zhou ◽  
Muzi Li ◽  
Sridhar Hannenhalli ◽  
Stephen M. Mount ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Rubus Idaeus ◽  
Slow Process ◽  
Red Raspberry ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Protein Coding Genes ◽  
A Genome ◽  
Exceptional Value

AbstractThe red raspberry, Rubus idaeus, is widely distributed in all temperate regions of Europe, Asia, and North America and is a major commercial fruit valued for its taste, high antioxidant and vitamin content. However, Rubus breeding is a long and slow process hampered by limited genomic and molecular resources. Genomic resources such as a complete genome sequencing and transcriptome will be of exceptional value to improve research and breeding of this high value crop. Using a hybrid sequence assembly approach including data from both long and short sequence reads, we present the first assembly of the Rubus idaeus genome (Joan J. variety). The de novo assembled genome consists of 2,145 scaffolds with a genome completeness of 95.3% and an N50 score of 638 KB. Leveraging a linkage map, we anchored 80.1% of the genome onto seven chromosomes. Using over 1 billion paired-end RNAseq reads, we annotated 35,566 protein coding genes with a transcriptome completeness score of 97.2%. The Rubus idaeus genome provides an important new resource for researchers and breeders.

scholarly journals IterCluster: a barcode clustering algorithm for long fragment read analysis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8431
Author(s):  
Jiancong Weng ◽  
Tian Chen ◽  
Yinlong Xie ◽  
Xun Xu ◽  
Gengyun Zhang ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Clustering Algorithm ◽  
De Novo ◽  
Recall Rate ◽  
Divide And Conquer ◽  
Data Set ◽  
Target Region ◽  
Additional Information ◽  
A Genome ◽  
Long Fragment Read

Recent advances in long fragment read (LFR, also known as linked-read technologies or read-cloud) technologies, such as single tube long fragment reads (stLFR), 10X Genomics Chromium reads, and TruSeq synthetic long-reads, have enabled efficient haplotyping and genome assembly. However, in the case of stLFR and 10X Genomics Chromium reads, the long fragments of a genome are covered sparsely by reads in each barcode and most barcodes are contained in multiple long fragments from different regions, which results in inefficient assembly when using long-range information. Thus, methods to address these shortcomings are vital for capitalizing on the additional information obtained using these technologies. We therefore designed IterCluster, a novel, alignment-free clustering algorithm that can cluster barcodes from the same target region of a genome, using -mer frequency-based features and a Markov Cluster (MCL) approach to identify enough reads in a target region of a genome to ensure sufficient target genome sequence depth. The IterCluster method was validated using BGI stLFR and 10X Genomics chromium reads datasets. IterCluster had a higher precision and recall rate on BGI stLFR data compared to 10X Genomics Chromium read data. In addition, we demonstrated how IterCluster improves the de novo assembly results when using a divide-and-conquer strategy on a human genome data set (scaffold/contig N50 = 13.2 kbp/7.1 kbp vs. 17.1 kbp/11.9 kbp before and after IterCluster, respectively). IterCluster provides a new way for determining LFR barcode enrichment and a novel approach for de novo assembly using LFR data. IterCluster is OpenSource and available on https://github.com/JianCong-WENG/IterCluster.

scholarly journals De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aysenur Soyturk ◽  
Fatima Sen ◽  
Ali Tevfik Uncu ◽  
Ibrahim Celik ◽  
Ayse Ozgur Uncu
Keyword(s):  
Ab Initio ◽  
De Novo ◽  
Draft Genome ◽  
Mirna Precursor ◽  
Machine Learning Algorithms ◽  
Genomic Research ◽  
Support Vector ◽  
Cydonia Oblonga ◽  
Protein Coding ◽  
A Genome

AbstractQuince (Cydonia oblonga Mill.) is the sole member of the genus Cydonia in the Rosacea family and closely related to the major pome fruits, apple (Malus domestica Borkh.) and pear (Pyrus communis L.). In the present work, whole genome shotgun paired-end sequencing was employed in order to assemble the first draft genome of quince. A genome assembly that spans 488.4 Mb of sequence corresponding to 71.2% of the estimated genome size (686 Mb) was produced in the study. Gene predictions via ab initio and homology-based sequence annotation strategies resulted in the identification of 25,428 and 30,684 unique putative protein coding genes, respectively. 97.4 and 95.6% of putative homologs of Arabidopsis and rice transcription factors were identified in the ab initio predicted genic sequences. Different machine learning algorithms were tested for classifying pre-miRNA (precursor microRNA) coding sequences, identifying Support Vector Machine (SVM) as the best performing classifier. SVM classification predicted 600 putative pre-miRNA coding loci. Repetitive DNA content of the assembly was also characterized. The first draft assembly of the quince genome produced in this work would constitute a foundation for functional genomic research in quince toward dissecting the genetic basis of important traits and performing genomics-assisted breeding.

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