The complete chloroplast genome of common walnut (<i>Juglans regia</i>)

Hu, Yiheng; Woeste, Keith; Dang, Meng; Zhou, Tao; Feng, Xiaojia; Zhao, Guifang; Liu, Zhan‐Lin; Li, Zhong-Hu; Zhao, Peng

doi:10.1080/23802359.2015.1137804

Cited by 13 publications

(17 citation statements)

References 8 publications

(8 reference statements)

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“…We sequenced the complete chloroplast genome of J. regia with the Illumina MiSeq sequencing platform (Sangon Biotech, Shanghai, China). We assembled the chloroplast genomes using SPAdes v3.6.2 (Bankevich et al, 2012) (http://bioinf.spbau.ru/spades) and annotated them with CpGAVAS (http://www.biomedcentral.com/1471-2164/13/715) (Liu et al, 2012a; Hu et al, 2016). We sequenced the complete Cpg of four Juglans species using Illumina HiSeq 2500 sequencing technology via a combination of de novo and reference-guided assembly based on the Cpg of J. regia (Hu et al, 2016, NCBI Accession number: KT963008).…”

Section: Methodsmentioning

confidence: 99%

“…We assembled the chloroplast genomes using SPAdes v3.6.2 (Bankevich et al, 2012) (http://bioinf.spbau.ru/spades) and annotated them with CpGAVAS (http://www.biomedcentral.com/1471-2164/13/715) (Liu et al, 2012a; Hu et al, 2016). We sequenced the complete Cpg of four Juglans species using Illumina HiSeq 2500 sequencing technology via a combination of de novo and reference-guided assembly based on the Cpg of J. regia (Hu et al, 2016, NCBI Accession number: KT963008). A paired-end (PE) library with 350-bp insert size was constructed using the Illumina PE DNA library kit according to the manufacturer's instructions and sequenced using an Illumina Hiseq2500 by Novogene (http://www.novogene.com, China).…”

Section: Methodsmentioning

confidence: 99%

“…Small gaps in the assemblies were bridged by designing custom primers for PCR (Table S1) based on their flanking sequences, followed by conventional Sanger sequencing. The PCR primers were designed using J. regia sequences when they appeared identical to our original de novo assembly (Hu et al, 2016). Eleven primer pairs were used to validate junctions using PCR based sequencing in each of five Juglans Cpgs.…”

Section: Methodsmentioning

confidence: 99%

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Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

2017

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Juglans L. (walnuts and butternuts) is an economically and ecologically important genus in the family Juglandaceae. All Juglans are important nut and timber trees. Juglans regia (Common walnut), J. sigillata (Iron walnut), J. cathayensis (Chinese walnut), J. hopeiensis (Ma walnut), and J. mandshurica (Manchurian walnut) are native to or naturalized in China. A strongly supported phylogeny of these five species is not available due to a lack of informative molecular markers. We compared complete chloroplast genomes and determined the phylogenetic relationships among the five Chinese Juglans using IIumina sequencing. The plastid genomes ranged from 159,714 to 160,367 bp encoding 128 functional genes, including 88 protein-coding genes and 40 tRNA genes each. A complete map of the variability across the genomes of the five Juglans species was produced that included single nucleotide variants, indels (insertions and deletions), and large structural variants, as well as differences in simple sequence repeats (SSR) and repeat sequences. Molecular phylogeny strongly supported division of the five walnut species into two previously recognized sections (Juglans/Dioscaryon and Cardiocaryon) with a 100% bootstrap (BS) value using the complete cp genomes, protein coding sequences (CDS), and the introns and spacers (IGS) data. The availability of these genomes will provide genetic information for identifying species and hybrids, taxonomy, phylogeny, and evolution in Juglans, and also provide insight into utilization of Juglans plants.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

2017

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“…The PCR products were constructed as short-insert (300 bp) libraries using Illumina Nextera XT and then sequenced using the HiSeq ×10 platform (Illumina). Raw reads were filtered using NGSQC Tool kit v2.3.3 to obtain high-quality reads, and then, the chloroplast genomes were assembled by NOVOPlasty using clean data and annotated with CpGAVAS (Hu et al, 2016). The chloroplast genome of P. persica (NCBI Accession number NC_014697.1) was used as the reference genome in this study.…”

Section: Chloroplast Genome Resequencingmentioning

confidence: 99%

Association between blooming time and climatic adaptation in Prunus mume

Shi

Luo

et al. 2019

Ecology and Evolution

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Prunus mume Sieb. et Zucc. is an important fruit crop of the subtropical region, originating in China. It blooms earlier than other deciduous fruit trees, but different regions have different blooming periods. The time of anthesis is related to the dormancy period, and a certain amount of chilling promotes bud break and blooming. To identify the relationship between blooming time and the climatic adaptation of P. mume cultivars in China, the nuclear and chloroplast genomes of 19 cultivars from the main cultivation areas of P. mume in China were resequenced. The average depth of coverage was 34X–76X, and a total of 388,134 single nucleotide polymorphisms were located within the coding regions of the gene (CDs). Additionally, the 19 cultivar accessions were divided into three groups based on their blooming time: early, mid, and late. Associated with the blooming time groups, 21 selective sweep regions were identified, which could provide evidence supporting the possible model of P. mume domestication originating due to natural selection. Furthermore, we identified a flowering gene, FRIGIDA‐LIKE 3 (FRL3), seems to affect the blooming time and the climatic adaptation of P. mume cultivars. This study is a major step toward understanding the climatic adaptation of P. mume cultivars in China.

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“…The walnut genome sequence was recently obtained from the cultivar Chandler [2]. Also, the complete chloroplast sequence (GenBank: KT963008) was annotated with CpGAVAS [3], revealing 86 protein-coding genes [4].…”

Section: Introductionmentioning

confidence: 99%

YeATSAM analysis of the chloroplast genome of walnut reveals several putative un-annotated genes and mis-annotation of the trans-spliced rps12 gene in other organisms

Chakraborty¹

2016

Preprint

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An open reading frame (ORF) is genomic sequence that can be translated into amino acids, and does not contain any stop codon. Previously, YeATSAM analyzed ORFs from the RNA-seq derived transcriptome of walnut, and revealed several genes that were not annotated by widely-used methods.Here, a similar ORF-based method is applied to the chloroplast genome from walnut (Accid:KT963008). This revealed, in addition to the ∼84 protein coding genes, ∼100 additional putative protein coding genes with homology to RefSeq proteins. Some of these genes have corresponding transcripts in the previously derived transcriptome from twenty different tissues, establishing these as bona fide genes. Other genes have introns, and need to be manually annotated. Importantly, this analysis revealed the mis-annotation of the rps12 gene in several organisms which have used an automated annotation flow. This gene has three exons -exon1 is ∼28kbp away from exon2 and exon3 -and is assembled by transsplicing. Automated annotation tools are more likely to select an ORF closer to exon2 to complete a possible protein, and are unlikely to properly annotate trans-spliced genes. A database of trans-spliced genes would greatly benefit annotations. Thus, the current work continues previous work establishing the proper identification of ORFs as a simple and important step in many applications, and the requirement of validation of annotations.

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The complete chloroplast genome of common walnut (Juglans regia)

Cited by 13 publications

References 8 publications

Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

Association between blooming time and climatic adaptation in Prunus mume

YeATSAM analysis of the chloroplast genome of walnut reveals several putative un-annotated genes and mis-annotation of the trans-spliced rps12 gene in other organisms

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