Comparative chloroplast genome analysis of Citrus (Rutaceae) species: Insights into genomic characterization, phylogenetic relationships, and discrimination of subgenera

Shi, Wenbo; Song, Weicai; Liu, Jin; Shi, Chao; Wang, Shuo

doi:10.1016/j.scienta.2023.111909

Cited by 19 publications

(9 citation statements)

References 92 publications

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“…Pseudogenization also occurred in cemA and ycf15 in Afraegle paniculata and Aegle marmelos, respectively. Furthermore, for Atalantia kwangtungenensis, we confirmed the previously reported pseudogenization of accD gene 14 and newly identified a pseudogenization event in ycf1 gene (Supplementary Fig. S8).…”

Section: Variability In Structural Variations and Pseudogenization Ac...supporting

confidence: 88%

Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Witharana,

Iwasaki,

San

et al. 2024

Preprint

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The chloroplast (cp) genome sequence, which is a widely used and affordable tool, is utilized for plant classification. However, its effectiveness remains unclear. This study contrasts the phylogenetics derived from whole cp genome sequences with those obtained using Read2Tree, another cost-efficient method capable of extracting multiple conserved nuclear gene sequences. To explore this topic, we focused on the Aurantioideae subfamily, which includesCitrusand its relatives, where phylogenetic trees based on nuclear DNA from high-throughput sequencing are available. In intergeneric relationships, phylogenetic trees generated with Read2Tree were consistent with previous high-precision nuclear DNA-based trees but differed from those generated using whole cp genome sequences. Thus, even in plants in which past polyploidization or hybridization between distantly related species had not been previously assumed, the two phylogenetic trees did not coincide. Both techniques present unique pros and cons, leaving it unclear which technique is superior for understanding a plant’s evolutionary history. However, integrating both approaches is more useful for effectively classifying plants than it is for understanding the unified evolutionary history based on phylogenetics. We propose that integrating these two cost-effective methods by utilizing the same raw sequencing data is a mainstream approach in DNA-based plant classification.

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Section: Variability In Structural Variations and Pseudogenization Ac...supporting

confidence: 88%

Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Witharana,

Iwasaki,

San

et al. 2024

Preprint

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“…In some species, the trnL-UAG region also showed higher sequence differences [ 40 ]. In general, tRNA genes are always highly conserved, and the intergenic region may have a relatively faster evolutionary rate [ 41 , 42 ]; for example, rpl32-trnL (UAG) was highly variable in many species [ 42 , 43 , 44 ]. Ka/Ks analysis showed that ccsA , matK , rbcL , and ycf1 were affected by positive selection in D. grandiflora , D. hamata , D. hypoglauca , and D. scabra , indicating that these genes may be related to environmental adaptation during the evolution of Deutzia plants.…”

Section: Discussionmentioning

confidence: 99%

Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species

Cai,

Ren,

et al. 2023

IJMS

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In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were typical circular genomes 156,860–157,025 bp in length, with 37.58–37.6% GC content. Repeat analysis showed that the Deutzia species had 41–45 scattered repeats and 199–201 simple sequence repeats. Comparative genomic and pi analyses indicated that the genomes are conservative and that the gene structures are stable. According to the phylogenetic tree, Deutzia species appear to be closely related to Kirengeshoma palmata and Philadelphus. By combining chloroplast genomic and transcriptomic analyses, 29–31 RNA editing events and 163–194 orthologous genes were identified. The ndh, rpo, rps, and atp genes had the most editing sites, and all RNA editing events were of the C-to-U type. Most of the orthologous genes were annotated to the chloroplast, mitochondria, and nucleus, with functions including energy production and conversion, translation, and protein transport. Genes related to the biosynthesis of monoterpenoids and flavonoids were also identified from the transcriptome of Deutzia spp. Our results will contribute to further studies of the genomic information and potential uses of the Deutzia spp.

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“…Citrus occur naturally in certain tropical and sub-tropical regions and are now widely cultivated around the world due to their high economic and nutritional value (Shi et al 2023;Wu et al 2014). Australian Citrus are adapted to xerophytic and rainforest climatic conditions, and are an important genetic resource, as they have many bene cial traits, including tolerance to drought, salt and diseases, shortened fruiting period, and high phenotypic diversity.…”

Section: Introductionmentioning

confidence: 99%

The Genomes of Australian Wild Limes

Nakandala,

Furtado,

Masouleh

et al. 2024

Preprint

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Australian wild limes occur in highly diverse range of environments and are a unique genetic resource within the genus Citrus. Here we compare the haplotype-resolved genome assemblies of six Australian native limes, including four new assemblies generated using PacBio HiFi and Hi-C sequencing data. The size of the genomes was between 315 and 391 Mb with contig N50s from 29.5 to 35 Mb. Gene completeness of the assemblies was estimated to be from 98.4–99.3% and the annotations from 97.7–98.9% based upon BUSCO, confirming the high contiguity and completeness of the assembled genomes. High collinearity was observed among the genomes and the two haplotype assemblies for each species. Gene duplication and evolutionary analysis demonstrated that the Australian citrus have undergone only one ancient whole-genome triplication event during evolution. The highest number of species-specific and expanded gene families were found in C. glauca and they were primarily enriched in purine, thiamine metabolism, amino acids and aromatic amino acids metabolism which might help C. glauca to mitigate drought, salinity, and pathogen attacks in the drier environments in which this species is found. Unique genes related to terpene biosynthesis, glutathione metabolism, and toll-like receptors in C. australasica, and starch and sucrose metabolism genes in both C. australis and C. australasica might be important candidate genes for HLB tolerance in these species. Expanded gene families were not lineage specific, however, a greater number of genes related to plant-pathogen interactions, predominantly disease resistant protein, was found in C. australasica and C. australis.

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Comparative chloroplast genome analysis of Citrus (Rutaceae) species: Insights into genomic characterization, phylogenetic relationships, and discrimination of subgenera

Cited by 19 publications

References 92 publications

Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species

The Genomes of Australian Wild Limes

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