Comprehensive analysis of complete mitochondrial genome of Sapindus mukorossi Gaertn.: an important industrial oil tree species in China

Wang, Xin; Zhang, Rengang; Yun, Quanzheng; Xu, Yuanyuan; Zhao, Guochun; Liu, Jiming; Shi, Shuanglong; Chen, Zhong; Jia, Liming

doi:10.1016/j.indcrop.2021.114210

Cited by 21 publications

(17 citation statements)

References 79 publications

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“…We followed previous approaches ( Wang et al., 2021 ) and took advantage of the GetOrganelle pipeline and second- and third- generation sequencing data to achieve high-quality assembly of the complex chloroplast genomes of Carex . First, we used GetOrganelle ( Jin et al., 2020 ) ( ) to extract the Illumina sequencing data belonging to the chloroplast and assembled it into a unitig graph that was manually optimized using Bandage software ( Wick et al., 2015 ) to eliminate mitochondria- and nucleus-derived unitig nodes.…”

Section: Methodsmentioning

confidence: 99%

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

Teng

Zhang

et al. 2023

Front. Plant Sci.

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The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa.

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Section: Methodsmentioning

confidence: 99%

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

Teng

Zhang

et al. 2023

Front. Plant Sci.

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“…In contrast to other plant mitogenomes in Populus , the rps14 and trnK-CUU were lost from P. simonii , where trnK-CUU was transferred into its nuclear genome, and rps14 was complete lost from P. simonii mitogenome during evolution. These lost genes can experience different fates; they may be completely lost from the cell ( Adams, 2003 ), or functionally substituted by the same functional genes from plastids, nuclei, or the cytosol ( Lei et al, 2013 ; Wang et al, 2021 ). Previous studies have reported that most mitochondrial lost tRNA genes were generally compensated by the corresponding cp-derived tRNA genes, such as trnH-GUG , trnN-GUU , trnS-GGA , and trnW-CCA ( Bi et al, 2016 ; Wang et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…These lost genes can experience different fates; they may be completely lost from the cell ( Adams, 2003 ), or functionally substituted by the same functional genes from plastids, nuclei, or the cytosol ( Lei et al, 2013 ; Wang et al, 2021 ). Previous studies have reported that most mitochondrial lost tRNA genes were generally compensated by the corresponding cp-derived tRNA genes, such as trnH-GUG , trnN-GUU , trnS-GGA , and trnW-CCA ( Bi et al, 2016 ; Wang et al, 2021 ). Additionally, some lost genes ( rps2 , rps11 , and rps19 ) were transferred to the nucleus during evolution, which was the main pathway for PCGs loss in plant mitogenomes ( Adams et al, 2002 ; Park et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

Bi¹,

Qu²,

Hou³

et al. 2022

Front. Plant Sci.

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Mitochondria, inherited maternally, are energy metabolism organelles that generate most of the chemical energy needed to power cellular various biochemical reactions. Deciphering mitochondrial genome (mitogenome) is important for elucidating vital activities of species. The complete chloroplast (cp) and nuclear genome sequences of Populus simonii (P. simonii) have been reported, but there has been little progress in its mitogenome. Here, we assemble the complete P. simonii mitogenome into three circular-mapping molecules (lengths 312.5, 283, and 186 kb) with the total length of 781.5 kb. All three molecules of the P. simonii mitogenome had protein-coding capability. Whole-genome alignment analyses of four Populus species revealed the fission of poplar mitogenome in P. simonii. Comparative repeat analyses of four Populus mitogenomes showed that there were no repeats longer than 350 bp in Populus mitogenomes, contributing to the stability of genome sizes and gene contents in the genus Populus. As the first reported multi-circular mitogenome in Populus, this study of P. simonii mitogenome are imperative for better elucidating their biological functions, replication and recombination mechanisms, and their unique evolutionary trajectories in Populus.

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“…This phenomenon indicates high A/T content at the third codon position in the mitogenome of P. deltoides, which is very similar to what has been reported in the mitogenomes of other land plants. The strong AT bias of the third codon is considered to be a universal phenomenon in higher plants (Bi et al 2020;Wang et al 2021;Yang et al 2021).…”

Section: Codon Usage Analysis Of Pcgsmentioning

confidence: 99%

Assembly and analysis of the Populus deltoides mitochondrial genome: the first report of a multicircular mitochondrial conformation for the genus Populus

Qu¹,

Zhou²,

Bi³

et al. 2022

J. For. Res.

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Genomics research of Populus deltoides, an important timber species that is widely planted worldwide, is an important part of poplar breeding. Currently, the nuclear and chloroplast genome of P. deltoides have been sequenced, but its mitochondrial genome (mitogenome) has not been reported. To further explore the evolution and phylogeny of P. deltoides, the mitogenome of P. deltoides I-69 was assembled using reads from Nanopore and Illumina sequencing platforms and found to consist of 802,637 bp and three circular chromosomes (336,205, 280,841, and 185,591 bp) containing 58 genes (34 protein-coding genes, 21 tRNA genes, and 3 rRNA genes). RNA analysis in combination with several species showed significantly fewer RNA editing sites in the mitogenomes of poplar and other angiosperms than in gymnosperms. Sequence transfer analysis showed extensive mitogenome rearrangements in Populus species, and with evolution from lower to higher plants, tRNA transfer from chloroplasts to mitochondria became increasingly frequent. In a phylogenetic analysis, the evolutionary status of P. deltoides was determined, and the section Populus was supported. Our results based on the first report of a multi-circular conformation of the Populus mitogenome provide a basis for further study of the evolution and genetics of P. deltoides and other Populus species and for breeding programs.

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Comprehensive analysis of complete mitochondrial genome of Sapindus mukorossi Gaertn.: an important industrial oil tree species in China

Cited by 21 publications

References 79 publications

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

Assembly and analysis of the Populus deltoides mitochondrial genome: the first report of a multicircular mitochondrial conformation for the genus Populus

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