Genome Improvement and Genetic Map Construction for , the First Divergent Branch in the Brassicaceae Family

Overview

Journal G3 (Bethesda)

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2019 Sep 27

PMID 31554715

Citations 7

Authors

Thu-Phuong Nguyen

Cornelia Muhlich

Setareh Mohammadin

Erik van den Bergh

Adrian E Platts

Fabian B Haas

Stefan A Rensing

M Eric Schranz

Affiliations

Soon will be listed here.

Abstract

The genus is a sister-group to the core-group of the Brassicaceae family that includes and the Brassica crops. Thus, is phylogenetically well-placed for the investigation and understanding of genome and trait evolution across the family. We aimed to improve the quality of the reference genome draft version of the annual species Second, we constructed the first genetic map. The improved reference genome and genetic map enabled the development of each other. We started with the initially published genome (version 2.5). PacBio and MinION sequencing together with genetic map v2.5 were incorporated to produce the new reference genome v3.0. The improved genome contains 203 MB of sequence, with approximately 94% of the assembly made up of called (non-gap) bases, assembled into 2,883 scaffolds (with only 6% of the genome made up of non-called bases (Ns)). The N (10.3 MB) represents an 80-fold increase over the initial genome release. We generated a Recombinant Inbred Line (RIL) population that was derived from two ecotypes: Cyprus and Turkey (the reference genotype. Using a Genotyping by Sequencing (GBS) approach, we generated a high-density genetic map with 749 (v2.5) and then 632 SNPs (v3.0) was generated. The genetic map and reference genome were integrated, thus greatly improving the scaffolding of the reference genome into 11 linkage groups. We show that long-read sequencing data and genetics are complementary, resulting in an improved genome assembly in They will facilitate comparative genetic mapping work for the Brassicaceae family and are also valuable resources to investigate wide range of life history traits in .

Citing Articles

The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures.

Chandler J, Wilhelmsson P, Fernandez-Pozo N, Graeber K, Arshad W, Perez M Plant Cell. 2024; 36(7):2465-2490.

PMID: 38513609 PMC: 11218780. DOI: 10.1093/plcell/koae085.

Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae.

Liu J, Zhou S, Liu Y, Zhao B, Yu D, Zhong M Plant Commun. 2024; 5(7):100878.

PMID: 38475995 PMC: 11287156. DOI: 10.1016/j.xplc.2024.100878.

Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae.

Palos K, Nelson Dittrich A, Yu L, Brock J, Railey C, Wu H Plant Cell. 2022; 34(9):3233-3260.

PMID: 35666179 PMC: 9421480. DOI: 10.1093/plcell/koac166.

Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research.

Fernandez-Pozo N, Metz T, Chandler J, Gramzow L, Merai Z, Maumus F Plant J. 2021; 106(1):275-293.

PMID: 33453123 PMC: 8641386. DOI: 10.1111/tpj.15161.

Single Nucleotide Polymorphism Charting of Reveals Accumulation of Somatic Mutations During Culture on the Scale of Natural Variation by Selfing.

Haas F, Fernandez-Pozo N, Meyberg R, Perroud P, Gottig M, Stingl N Front Plant Sci. 2020; 11:813.

PMID: 32733496 PMC: 7358436. DOI: 10.3389/fpls.2020.00813.

References

Merai Z, Graeber K, Wilhelmsson P, Ullrich K, Arshad W, Grosche C . Aethionema arabicum: a novel model plant to study the light control of seed germination. J Exp Bot. 2019; 70(12):3313-3328. PMC: 6598081. DOI: 10.1093/jxb/erz146. View

Beilstein M, Al-Shehbaz I, Mathews S, Kellogg E . Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited. Am J Bot. 2011; 95(10):1307-27. DOI: 10.3732/ajb.0800065. View

Lenser T, Graeber K, Cevik O, Adiguzel N, Donmez A, Grosche C . Developmental Control and Plasticity of Fruit and Seed Dimorphism in Aethionema arabicum. Plant Physiol. 2016; 172(3):1691-1707. PMC: 5100781. DOI: 10.1104/pp.16.00838. View

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

Hiss M, Meyberg R, Westermann J, Haas F, Schneider L, Schallenberg-Rudinger M . Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute. Plant J. 2017; 90(3):606-620. DOI: 10.1111/tpj.13501. View

Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J . SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2013; 1(1):18. PMC: 3626529. DOI: 10.1186/2047-217X-1-18. View

Huson D, Beier S, Flade I, Gorska A, El-Hadidi M, Mitra S . MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol. 2016; 12(6):e1004957. PMC: 4915700. DOI: 10.1371/journal.pcbi.1004957. View

Keilwagen J, Wenk M, Erickson J, Schattat M, Grau J, Hartung F . Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 2016; 44(9):e89. PMC: 4872089. DOI: 10.1093/nar/gkw092. View

Li H, Durbin R . Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26(5):589-95. PMC: 2828108. DOI: 10.1093/bioinformatics/btp698. View

10.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

11.

Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E . A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011; 6(5):e19379. PMC: 3087801. DOI: 10.1371/journal.pone.0019379. View

12.

. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2015; 44(D1):D7-19. PMC: 4702911. DOI: 10.1093/nar/gkv1290. View

13.

Franzke A, Lysak M, Al-Shehbaz I, Koch M, Mummenhoff K . Cabbage family affairs: the evolutionary history of Brassicaceae. Trends Plant Sci. 2010; 16(2):108-16. DOI: 10.1016/j.tplants.2010.11.005. View

14.

Lang D, Ullrich K, Murat F, Fuchs J, Jenkins J, Haas F . The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant J. 2017; 93(3):515-533. DOI: 10.1111/tpj.13801. View

15.

Guo X, Liu J, Hao G, Zhang L, Mao K, Wang X . Plastome phylogeny and early diversification of Brassicaceae. BMC Genomics. 2017; 18(1):176. PMC: 5312533. DOI: 10.1186/s12864-017-3555-3. View

16.

Glaubitz J, Casstevens T, Lu F, Harriman J, Elshire R, Sun Q . TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One. 2014; 9(2):e90346. PMC: 3938676. DOI: 10.1371/journal.pone.0090346. View

17.

Watson M, Thomson M, Risse J, Talbot R, Santoyo-Lopez J, Gharbi K . poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics. 2014; 31(1):114-5. PMC: 4271141. DOI: 10.1093/bioinformatics/btu590. View

18.

Huang C, Sun R, Hu Y, Zeng L, Zhang N, Cai L . Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution. Mol Biol Evol. 2015; 33(2):394-412. PMC: 4866547. DOI: 10.1093/molbev/msv226. View

19.

Wu T, Nacu S . Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010; 26(7):873-81. PMC: 2844994. DOI: 10.1093/bioinformatics/btq057. View

20.

Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View