Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1

Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).

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Whole-genome sequencing of 182 Bursaphelenchus xylophilus strains generates first long read based de novo genome assembly and reveals temperature associated population structure

10.22541/au.159352211.19983305 ◽

2020 ◽

Author(s):

Xiaolei Ding ◽

Yunfei Guo ◽

Jianren Ye ◽

Xiaoqin Wu ◽

Sixi Lin ◽

...

Keyword(s):

Population Structure ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Bursaphelenchus Xylophilus ◽

Whole Genome ◽

De Novo Genome Assembly ◽

Long Read

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In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Genome Research ◽

10.1101/gr.178319.114 ◽

2014 ◽

Vol 24 (12) ◽

pp. 2041-2049 ◽

Cited By ~ 87

Author(s):

Andrew Adey ◽

Jacob O. Kitzman ◽

Joshua N. Burton ◽

Riza Daza ◽

Akash Kumar ◽

...

Keyword(s):

Long Range ◽

Genome Assembly ◽

De Novo ◽

Sequence Information ◽

De Novo Genome Assembly

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Chromosome‐level de novo genome assembly and whole‐genome resequencing of threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

Molecular Ecology Resources ◽

10.1111/1755-0998.13562 ◽

2021 ◽

Author(s):

Bo Xu ◽

Min Liao ◽

Heng‐ning Deng ◽

Chao‐chao Yan ◽

Lv Yun‐yun ◽

...

Keyword(s):

Threatened Species ◽

Genome Assembly ◽

De Novo ◽

Biodiversity Hotspot ◽

Whole Genome ◽

Alpine Plant ◽

Genome Resequencing ◽

De Novo Genome Assembly ◽

Whole Genome Resequencing ◽

Chromosome Level

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The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus

10.1101/2021.04.25.441282 ◽

2021 ◽

Author(s):

Mike Ruigrok ◽

Andrew Catanach ◽

Deepa Bowatte ◽

Marcus Davey ◽

Roy Storey ◽

...

Keyword(s):

New Zealand ◽

Sex Determination ◽

Genome Assembly ◽

De Novo ◽

Read Depth ◽

Chromosome 21 ◽

Whole Genome ◽

De Novo Genome Assembly ◽

Teleost Species ◽

Sex Marker

Background: The genetic control of sex determinism in teleost species is poorly understood. This is partly because of the diversity of sex determining mechanisms in this large group, including constitutive genes linked to sex chromosomes, polygenic constitutive mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly of New Zealand silver trevally (Pseudocaranx georgianus) together with whole genome sequencing to detect sexually divergent regions, identify candidate genes and develop molecular makers. Results: The de novo assembly of an unsexed trevally (Trevally_v1) resulted in an assembly of 579.4 Mb in length, with a N50 of 25.2 Mb. Of the assembled scaffolds, 24 were of chromosome scale, ranging from 11 to 31 Mb. A total of 28416 genes were annotated after 12.8% of the assembly was masked with repetitive elements. Whole genome re-sequencing of 13 sexed trevally (7 males, 6 females) identified sexually divergent regions located on two scaffolds, including a 6 kb region at the proximal end of chromosome 21. Blast analyses revealed similarity between one region and the aromatase genes cyp19 (a1a/b). Males contained higher numbers of heterozygous variants in both regions, while females showed regions of very low read-depth, indicative of deletions. Molecular markers tested on 96 histologically-sexed fish (42 males, 54 females). Three markers amplified in absolute correspondence with sex. Conclusions: The higher number of heterozygous variants in males combined with deletions in females support a XY sex-determination model, indicating the trevally_v1 genome assembly was based on a male. This sex system contrasts with the ZW-type sex system documented in closely related species. Our results indicate a likely sex-determining function of the cyp19b-like gene, suggesting the molecular pathway of sex determination is somewhat conserved in this family. Our genomic resources will facilitate future comparative genomics works in teleost species, and enable improved insights into the varied sex determination pathways in this group of vertebrates. The sex marker will be a valuable resource for aquaculture breeding programmes, and for determining sex ratios and sex-specific impacts in wild fisheries stocks of this species.

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Whole-Genome Sequencing for Comparative Genomics and De Novo Genome Assembly

Methods in Molecular Biology - Mycobacteria Protocols ◽

10.1007/978-1-4939-2450-9_1 ◽

2015 ◽

pp. 1-16 ◽

Cited By ~ 5

Author(s):

Andrej Benjak ◽

Claudia Sala ◽

Ruben C. Hartkoorn

Keyword(s):

Comparative Genomics ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Whole Genome ◽

De Novo Genome Assembly

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A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00586-y ◽

2021 ◽

Author(s):

Seyoung Mun ◽

Songmi Kim ◽

Wooseok Lee ◽

Keunsoo Kang ◽

Thomas J. Meyer ◽

...

Keyword(s):

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Personal Genome ◽

Human Populations ◽

Whole Genome ◽

Structural Variations ◽

Insert Size ◽

Human Genomes ◽

Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

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