Corrigendum to “Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton<i> Gossypium raimondii</i> by Comparative Genomics Approaches”

Bi, Changwei; Paterson, Andrew H.; Wang, Xuelin; Xu, Yiqing; Wu, Dongyang; Qu, Yi; Jiang, Anna; Ye, Qiaolin; Ye, Ning

doi:10.1155/2019/9691253

Cited by 21 publications

(31 citation statements)

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“…), and it is not as large as that described in Bi et al . (). However, the mitochondrial sequence of G. raimondii (D 5 ) submitted to GenBank by Bi was only 494,101 bp (accession no: NC 029998.1).…”

Section: Discussionmentioning

confidence: 97%

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Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

et al. 2017

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Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D ) and G. arboreum (A ) are the putative contributors to the progenitor of G. hirsutum (AD ), the economically important fibre-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analysed in orderly. Gossypium raimondii (D ) and G. arboreum (A ) mitochondrial genomes were provided in this study. The mitochondrial genomes of two diploid species harboured circular genome of 643,914 bp (D ) and 687,482 bp (A ), respectively. They differ in size and number of repeat sequences, both contain illuminating triplicate sequences with 7317 and 10,246 bp, respectively, demonstrating dynamic difference and rearranged genome organisations. Comparing the D and A mitogenomes with mitogenomes of tetraploid Gossypium species (AD , G. hirsutum; AD , G. barbadense), a shared 11 kbp fragment loss was detected in allotetraploid species, three regions shared by G. arboreum (A ), G. hirsutum (AD ) and G. barbadense (AD ), while eight regions were specific to G. raimondii (D ). The presence/absence variations and gene-based phylogeny supported that A-genome is a cytoplasmic donor to the progenitor of allotetraploid species G. hirsutum and G. barbadense. The results present structure variations and phylogeny of Gossypium mitochondrial genome evolution.

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Section: Discussionmentioning

confidence: 97%

“…Here we assembled the G. raimondii (D 5 ) mitochondrial genome of 643,914 bp with six large repeats (>1 kb; Table 1, Fig. 1), and it is not as large as that described in Bi et al (2016). However, the mitochondrial sequence of G. raimondii (D 5 ) submitted to GenBank by Bi was only 494,101 bp (accession no: NC 029998.1).…”

Section: Discussionmentioning

confidence: 99%

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

et al. 2017

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“…Among these, the gene petL had both start and stop codons undetermined, as well as it was 73 nucleotides long. Similarly, gene mttB was expected to have non ATG start codon based on previous studies [48][49][50][51]. Protein-coding genes varied largely in size and intervals, ranging from a few hundreds of nucleotides and a single interval (one exon), to thousands of nucleotides and up to 5 intervals (i.e.…”

Section: Genome Architecture and Gene Contentmentioning

confidence: 99%

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

Diaz‐Garcia¹,

Rodríguez-Bonilla²,

Smith

et al. 2019

Preprint

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Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry and could be useful to improve fruit quality such as phytochemical content, and given their northern distribution, could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V.microcarpum. Finally, we provided important data regarding the polyploid origin of V.oxycoccos.

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“…Mitochondrial genome sizes in Papilionoideae range from 217 kb in Medicago truncatula Gaertn. (Bi et al 2016) to 588 kb in Vicia faba L. (Negruk 2013). These mitochondrial genomes share 30 protein-coding genes and three rRNA genes (Shi et al 2018), as well as the loss of three ribosomal protein genes (rps2, rps11 and rps13).…”

Section: Introductionmentioning

confidence: 99%

Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae)

et al. 2019

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Plant mitochondrial genomes are often difficult to assemble because of frequent recombination mediated by repeats. Only a few mitochondrial genomes have been characterised in subfamily Papilionoideae of Leguminosae. Here, we report the complete mitochondrial genome of Castanospermum australe A.Cunn. & C.Fraser, an important medicinal and ornamental species in the Aldinoid clade of Papilionoideae. By mapping paired-end reads, seven hypothetical subgenomic conformations were rejected and two hypothetical complete isometric mitochondrial genome conformations that differed by a 64-kb inversion were strongly supported. Quantitative assessment of repeat-spanning read pairs showed a major conformation (MC1) and a minor conformation (MC2). The complete mitochondrial genome of C. australe was, thus, generated as 542079bp in length, with a high depth of coverage (~389.7×). Annotation of this mitochondrial genome yielded 58 genes encoding 37 proteins, 18 tRNAs and three rRNAs, as well as 17 introns and three medium-sized repeats (133, 119 and 114bp). Comparison of 10 mitochondrial genomes from Papilionoideae demonstrated significant variation in genome size, structure, gene content and RNA editing sites. In addition, mitochondrial genes were shown to be potentially useful in resolving the deep relationships of Papilionoideae.

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Corrigendum to “Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches”

Cited by 21 publications

References 1 publication

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A‐genome species as cytoplasmic donor of the allotetraploid species

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

Assembly and comparative analyses of the mitochondrial genome of Castanospermum australe (Papilionoideae, Leguminosae)

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