Dataset Information

Whole genome sequencing and assembly data of Moricandia moricandioides and M. arvensis.

ABSTRACT: Moricandia is a genus belonging to the family Brassicaceae. C₃ and C_3-C₄ photosynthesis Moricandia species exist in a close phylogenetic proximity, as well as to Brassica crops. Here, we performed PacBio genome sequencing on M. moricandioides and M. arvensis. The genomes were assembled using Flye assembler, then polished with Illumina reads and reduced duplication with Purge Haplotigs. The total length of genome assemblies of M. moricandioides and M. arvensis was 498 Mbp and 759 Mbp, respectively. These data will be useful for studies of the genetic control of C_3-C₄ characteristics, therefore gaining new insights into the early evolutionary steps of C₄ photosynthesis. Further, it can be integrated into Brassica crop breeding. The data can be accessed at ENA under the project number PRJEB39764.

SUBMITTER: Lin MY

PROVIDER: S-EPMC7966999 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Whole genome sequencing and assembly data of Moricandia moricandioides and M. arvensis.

Lin Meng-Ying MY Koppers Nils N Denton Alisandra A Schlüter Urte U Weber Andreas P M APM

Data in brief 20210301

Moricandia is a genus belonging to the family Brassicaceae. C3 and C3-C4 photosynthesis Moricandia species exist in a close phylogenetic proximity, as well as to Brassica crops. Here, we performed PacBio genome sequencing on M. moricandioides and M. arvensis. The genomes were assembled using Flye assembler, then polished with Illumina reads and reduced duplication with Purge Haplotigs. The total length of genome assemblies of M. mor ...[more]

PMID: 33748364

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Project description:Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with "subunits of ATP synthase" (atpB), "subunits of NADH-dehydrogenase" (ndhG and ndhE), and "self-replication" (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species.

Project description:Background In large-scale high-throughput sequencing projects and biobank construction, sample tagging is essential to prevent sample mix-ups. Despite the availability of fingerprint panels for DNA data, little research has been conducted on sample tagging of whole genome bisulfite sequencing (WGBS) data. This study aims to construct a pipeline and identify applicable fingerprint panels to address this problem. Results Using autosome-wide A/T polymorphic single nucleotide variants (SNVs) obtained from whole genome sequencing (WGS) and WGBS of individuals from the Third China National Stroke Registry, we designed a fingerprint panel and constructed an optimized pipeline for tagging WGBS data. This pipeline used Bis-SNP to call genotypes from the WGBS data, and optimized genotype comparison by eliminating wildtype homozygous and missing genotypes, and retaining variants with identical genomic coordinates and reference/alternative alleles. WGS-based and WGBS-based genotypes called from identical or different samples were extensively compared using hap.py. In the first batch of 94 samples, the genotype consistency rates were between 71.01%-84.23% and 51.43%-60.50% for the matched and mismatched WGS and WGBS data using the autosome-wide A/T polymorphic SNV panel. This capability to tag WGBS data was validated among the second batch of 240 samples, with genotype consistency rates ranging from 70.61%-84.65% to 49.58%-61.42% for the matched and mismatched data, respectively. We also determined that the number of genetic variants required to correctly tag WGBS data was on the order of thousands through testing six fingerprint panels with different orders for the number of variants. Additionally, we affirmed this result with two self-designed panels of 1351 and 1278 SNVs, respectively. Furthermore, this study confirmed that using the number of genetic variants with identical coordinates and ref/alt alleles, or identical genotypes could not correctly tag WGBS data. Conclusion This study proposed an optimized pipeline, applicable fingerprint panels, and a lower boundary for the number of fingerprint genetic variants needed for correct sample tagging of WGBS data, which are valuable for tagging WGBS data and integrating multi-omics data for biobanks. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-023-09413-2.

Dataset Information

Whole genome sequencing and assembly data of Moricandia moricandioides and M. arvensis.

Publications

Whole genome sequencing and assembly data of <i>Moricandia moricandioides</i> and <i>M. arvensis</i>.

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