Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions

Jia, Chang; Bei, Jinlong; Shao, Qi; Wang, Hemu; Fan, Hong-Tao; Yau, Tung On; Bu, Wenjun; Ruan, Jishou; Wei, Dongsheng; Gao, Shan

doi:10.3389/fmicb.2022.855666

Cited by 8 publications

(8 citation statements)

References 15 publications

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“…With the wide application of PacBio and Nanopore DNA-seq ( Xu et al, 2019 ), a great number of complete or even full-length genomes have been increasingly submitted to the public databases ( Chang et al, 2022 ). These genomes are facilitating the discovery or identification of transposons in various species.…”

Section: Introductionmentioning

confidence: 99%

The first discovery of Tc1 transposons in yeast

Jia

Duan²,

Li³

et al. 2023

Front. Microbiol.

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BackgroundIdentification of transposons without close homologs is still a difficult task. IS630/Tc1/mariner transposons, classified into a superfamily, are probably the most widespread DNA transposons in nature. Tc1/mariner transposons have been discovered in animals, plants, and filamentous fungi, however, not in yeast.ResultsIn the present study, we report the discovery of two intact Tc1 transposons in yeast and filamentous fungi, respectively. The first one, named Tc1-OP1 (DD40E), represents Tc1 transposons in Ogataea parapolymorpha. The second one, named Tc1-MP1 (DD34E), represents Tc1 transposons in the Rhizopodaceae and Mucoraceae families. As a homolog of Tc1-OP1 and Tc1-MP1, IS630-AB1 (DD34E) was discovered as an IS630 transposon in Acinetobacter spp.ConclusionTc1-OP1 is not only the first reported Tc1 transposon in yeast, but also the first reported nonclassical Tc1 transposon. Tc1-OP1 is the largest of IS630/Tc1/mariner transposons reported to date and significantly different from others. Notably, Tc1-OP1 encodes a serine-rich domain and a transposase, extending the current knowledge of Tc1 transposons. The phylogenetic relationships of Tc1-OP1, Tc1-MP1 and IS630-AB1 indicated that these transposons had evolved from a common ancestor. Tc1-OP1, Tc1-MP1 and IS630-AB1 can be used as reference sequences to facilitate the identification of IS630/Tc1/mariner transposons. More Tc1/mariner transposons will be identified in yeast, following our discovery.

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Section: Introductionmentioning

confidence: 99%

The first discovery of Tc1 transposons in yeast

Jia

Duan²,

Li³

et al. 2023

Front. Microbiol.

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“…Long (> 20 Kb) PacBio subreads were used to validate the structure of DXWR159 cpDNA and all detected SVs. As the draft genome using high-depth PacBio data may still contain two types of errors in the low complexity and STR regions, respectively ( Chang et al., 2022 ), 1,223,905 pairs of Illumina DNA-seq reads were properly aligned to the DXWR159 cpDNA and only one error in a STR region was corrected. The DXWR159 cpDNA is a full-length genome ( Supplementary File 1 ), as defined to has no gaps and ambiguous nucleotides ( Chang et al., 2022 ).…”

Section: Resultsmentioning

confidence: 99%

Full-length chloroplast genome of Dongxiang wild rice reveals small single-copy region switching

et al. 2022

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BackgroundPlant chloroplast DNA (cpDNA) typically has a circular structure, including a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (IR1 and IR2). The organization of these four elementary regions LSC-IR1-SSC-IR2 is highly conserved across all plant cpDNAs. Very few structural variations (SVs) occurring at the elementary-region level have been reported.ResultsIn the present study, we assembled the full-length cpDNA of Dongxiang wild rice line 159 (DXWR159). Using the long PacBio subreads, we discovered a large inversion of SSC and a large duplication of IR in DXWR159 cpDNAs. Significantly, we reported for the first time forward and reverse SSCs of cpDNAs in similar proportions and named the frequent inversion of a whole SSC as SSC switching.ConclusionsOur study helps researchers to correctly assemble the chloroplast genomes. Our recombination model explained the formation of large SVs in cpDNAs and provided insights into a novel scientific question that if there are common mechanisms in the formation or translocation of all kinds of transposon-like elements (TLEs). We propose that: (1) large inversion is the most accepted mutation type of SVs in cpDNAs; (2) SSC switching ubiquitous occurs in plant cpDNAs; and (3) further investigation of molecular mechanism underlying SSC switching may reveal new driving forces for large SVs.

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“…Finally, 6,480,424 bp cleaned Illumina DNA-seq data were aligned to the DXWR159 cpDNA and only one error in a STR region was corrected. The DXWR159 cpDNA is a full-length genome (Figure 1), which is defined to has no gaps and ambiguous nucleotides [10].…”

Section: Genome Sequencing Assembly and Annotationmentioning

confidence: 99%

Full-length chloroplast genome of Dongxiang wild rice reveals single-copy region switching in cpDNAs

Jian-guang

Chen

Zhang

et al. 2022

Preprint

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Background: Plant chloroplast DNA (cpDNA) typically has a circular structure, including a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (IR1 and IR2). The organization of these four elementary regions LSC-IR1-SSC-IR2 is highly conserved across all plant cpDNAs. Only very a few structural variations (SVs) occurring at the elementary-region level have been reported. Results: In the present study, we assembled the full-length cpDNA of Dongxiang wild rice line 159 (DXWR159). Using the long PacBio subreads, we discovered a large inversion of SSC and a large duplication of IR in DXWR159 cpDNAs. The large inversion of SSC results in a reverse orientation of SSC. According to the orientation of SSC, the structures of rice cpDNAs can be classified into the forward SSC (SSC-F) and reverse SSC (SSC-R) types. As the most significant finding, both SSC-F and SSC-R type cpDNAs were detected in several seedlings of DXWR159. The inversion of SSC was named as SSC switching. Conclusions: The frequencies of short tandem repeats (STRs) and large SVs were under-estimated in plant cpDNAs. STRs may not be useful as molecular markers in phylogenetic studies, particularly at low taxonomic levels. SSC switching is not a rarely occurring event and is active in cell growth. We propose that SSC switching ubiquitous occurs in plant cpDNAs and further investigation may reveal novel and important functions associated with SSC switching.

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Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions

Cited by 8 publications

References 15 publications

The first discovery of Tc1 transposons in yeast

The first discovery of Tc1 transposons in yeast

Full-length chloroplast genome of Dongxiang wild rice reveals small single-copy region switching

Full-length chloroplast genome of Dongxiang wild rice reveals single-copy region switching in cpDNAs

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