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Research article
Ying Yang
Institute of Botany Jiangsu Province and Chinese Academy of Sciences
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: Chloroplast(cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.
Results: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the three cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat(TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Ycf1 was the only one gene that has an indel in CDS, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes.
Conclusions: This study would advance our understanding of the complexity, dynamics, and evolution of cp genome in Cupressophytes.
Keywords
Taxodium, chloroplast genome, repeat, indel, single nucleotide polymorphisms, arrangement
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CURRENT STATUS: Published
Version 1
Posted 15 Dec, 2019
Published
On 31 Jan, 2020
No community comments so far
Review #1 received
Received 08 Jan, 2020
Review #2 received
Received 06 Jan, 2020
Reviewer #2 agreed
On 19 Dec, 2019
Reviewers invited
Invitations sent on 16 Dec, 2019
Reviewer #1 agreed
On 16 Dec, 2019
First submitted
On 27 Nov, 2019
Editor assigned
On 27 Nov, 2019
Submission checks complete
On 26 Nov, 2019
Editor invited
On 26 Nov, 2019
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Ying Yang
Institute of Botany Jiangsu Province and Chinese Academy of Sciences
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 1
Posted 15 Dec, 2019
Published
On 31 Jan, 2020
No community comments so far
Review #1 received
Received 08 Jan, 2020
Review #2 received
Received 06 Jan, 2020
Reviewer #2 agreed
On 19 Dec, 2019
Reviewers invited
Invitations sent on 16 Dec, 2019
Reviewer #1 agreed
On 16 Dec, 2019
First submitted
On 27 Nov, 2019
Editor assigned
On 27 Nov, 2019
Submission checks complete
On 26 Nov, 2019
Editor invited
On 26 Nov, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: Chloroplast(cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.
Results: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the three cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat(TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Ycf1 was the only one gene that has an indel in CDS, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes.
Conclusions: This study would advance our understanding of the complexity, dynamics, and evolution of cp genome in Cupressophytes.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
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