Comparative analysis of the complete chloroplast genome sequences of three Amaranthus species

Hong, Saw-See; Cheon, Kyeong‐Sik; Yoo, Ki-Oug; Lee, Hyun-Oh; Mekapogu, Manjulatha; Cho, Kwang-Soo

doi:10.1017/s1479262118000485

Cited by 16 publications

(12 citation statements)

References 37 publications

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“…The ycf15 gene in the two reverse repeats was lost in S. przewalskii and S. bifolia , implying that their chloroplast genomes contained 131 genes. Our result was different from the previous result obtained for Gentianaceae ( Dong et al, 2020 ), which showed that the chloroplast genome of Gentianaceae had 67–80 protein-coding genes, 30 tRNA genes, and four rRNA genes. This difference mainly arose due to gene deletion between genera.…”

Section: Resultscontrasting

confidence: 99%

“…As can be seen from the comparison of chloroplast sections, such differences mainly occurred in the large single-copy (LSC) and IR regions. The chloroplast genome length of angiosperms is generally 115–165 kb and that of Gentianaceae is 137–154 kb, which is consistent with the length characteristics of angiosperms and Gentianaceae ( Li et al, 2018 ; Dong et al, 2020 ). Compared with other genera of Gentianaceae, the average chloroplast genome length of Swertia L. was similar to that of Halenia (153 kb), but shorter than that of Paedera (154 kb) ( Dong et al, 2020 ).…”

Section: Resultssupporting

confidence: 73%

“…The chloroplast genome length of angiosperms is generally 115–165 kb and that of Gentianaceae is 137–154 kb, which is consistent with the length characteristics of angiosperms and Gentianaceae ( Li et al, 2018 ; Dong et al, 2020 ). Compared with other genera of Gentianaceae, the average chloroplast genome length of Swertia L. was similar to that of Halenia (153 kb), but shorter than that of Paedera (154 kb) ( Dong et al, 2020 ). The chloroplast genomes of the Swertia L. species contained two reverse repeats, IRa and IRb, which divided the whole genome into four parts; the remainder comprised LSC and small single-copy (SSC) regions ( Figure 1 ).…”

Section: Resultssupporting

confidence: 73%

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Comparative chloroplast genome analyses of 23 species in Swertia L. (Gentianaceae) with implications for its phylogeny

Yang

Li²,

Zhou³

2022

Front. Genet.

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Swertia L. is a large genus in the family Gentianaceae. Different chloroplast gene segments have been used to study systematic evolutionary relationships between species of Swertia L. However, as gene fragment–based phylogenies lack sufficient resolution, the systematic evolutionary relationships between Swertia L. species have remained unclear. We sequenced and annotated the complete chloroplast genomes of four Swertia species, namely, S. bifolia, S. tetraptera, S. franchetian, and S. przewalskii, using next generation sequencing and the plastid genome annotator tool. The chloroplast genome sequences of 19 additional species of Swertia L. were downloaded from the NCBI database and also assessed. We found that all 23 Swertia L. species had a similar genetic structure, that is, a ring tetrad structure, but with some clear differences. The chloroplast genomes of the 23 Swertia L. species were 149036–153691 bp long, averaging 152385 bp; the genomes contained 134 functional genes: 38 tRNA, eight rRNA, and 88 protein-encoding genes. A comparative analysis showed that chloroplasts genome of Swertia was conserved in terms of genome structure, codon preference, and repeat sequences, but it differed in terms of genome sizes, gene contents, and SC/IR boundary. Using Swertia wolfangiana as a reference, we found clear divergences in most of the non-coding and intergenic regions of the complete chloroplast genomes of these species; we also found that rpoC1, ccsA, ndhI, ndhA, and rps15 protein-coding genes had large variations. These highly variable hotspots will be useful for future phylogenetic and population genetic studies. Phylogenetic analysis with high bootstrap support showed that Swertia L. was not monophyletic. The classification of subgen. Swertia and subgen. Ophelia was supported by molecular data, which also partly supported the division of sect. Ophelia, sect. Platynema, sect. Poephila, sect. Swertia, and sect. Macranthos. However, the systematic positions of other groups and species require further exploration. The Swertia L formed at 29.60 Ma. Speciation of 10 species occurred in succession after 12 Ma and 13 species occurred in succession after 2.5 Ma. Our analysis provides insight into the unresolved evolutionary relationships of Swertia L. species.

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Section: Resultscontrasting

confidence: 99%

Section: Resultssupporting

confidence: 73%

Section: Resultssupporting

confidence: 73%

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Comparative chloroplast genome analyses of 23 species in Swertia L. (Gentianaceae) with implications for its phylogeny

Yang

Li²,

Zhou³

2022

Front. Genet.

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“…The pseudogenization of the ycf1 gene may be interpreted as wastage in the course of species evolution, or as the fact that the species does not specifically need the gene. Moreover, the pseudogenization of ycf1 was also detected in the genera Paeonia and Aconitum [ 37 , 38 , 39 ].…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications

Wei

Li²

2022

Genes

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Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.

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“…Thirty-one complete chloroplast genome sequences of Amaranthaceae including two Sueada chloroplast genomes (Kim et al 2016;Devi and Thongam 2017;Hong et al 2017;Park et al 2018;Hong et al 2019;Kim et al 2019aKim et al , 2019bMaughan et al 2019) were aligned by MAFFT 7.388 (Katoh and Standley 2013) after rearranging SSC and LSC regions of Chenopodium quinoa 'Real Blanca' for constructing neighbor joining (bootstrap repeat is 10,000) and maximum likelihood trees (bootstrap repeat is 1,000) using MEGA X (Kumar et al 2018). Phylogenetic trees show that two Suaeda chloroplast genomes were clustered with high bootstrap support ( Figure 1).…”

mentioning

confidence: 99%

The complete chloroplast genome of Suaeda japonica Makino (Amaranthaceae)

Kim¹,

Park²,

Chung

2019

Mitochondrial DNA Part B

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Suaeda japonica Makino is an annual herb in seashore in Korea and Japan. In this study, we presented the first complete chloroplast genome of S. japonica which is 152,109 bp long and has four subregions: 83,618 bp of large single copy (LSC) and 18,101 bp of small single copy (SSC) regions are separated by 25,195 bp of inverted repeat (IR) regions including 128 genes (83 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.4% and those in the LSC, SSC, and IR regions are 34.2%, 29.2%, and 42.7%, respectively. Phylogenetic trees show that two Suaeda chloroplast genomes were clustered and clade of Betoidae, Chenopodioidae, and Amarantheae are successfully resolved with high bootstrap supports. Our chloroplast genome will contribute for phylogeny of Amaranthaceae in detail.

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Comparative analysis of the complete chloroplast genome sequences of three Amaranthus species

Cited by 16 publications

References 37 publications

Comparative chloroplast genome analyses of 23 species in Swertia L. (Gentianaceae) with implications for its phylogeny

Comparative chloroplast genome analyses of 23 species in Swertia L. (Gentianaceae) with implications for its phylogeny

The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications

The complete chloroplast genome of Suaeda japonica Makino (Amaranthaceae)

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