The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

Ren, Weichao; Jiang, Zhehui; Zhang, Meiqi; Kong, Lingyang; Zhang, Houliang; Liu, Yunwei; Fu, Qifeng; Ma, Wei

doi:10.3389/fpls.2022.987443

Cited by 2 publications

References 97 publications

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Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae)

Caycho,

La Torre,

Orjeda

2023

BMC Plant Biol

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Background Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. Results In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. Conclusions The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.

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Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae)

Caycho,

La Torre,

Orjeda

2023

BMC Plant Biol

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Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (Subfamily: Caesalpinioideae)

Caycho,

Torre,

Orjeda

2023

Preprint

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Background Neltuma pallida is a tree that grows in arid soils in northwestern Peru. Being a predominant species of the Equatorial Dry Forest ecoregion, it has a high economic and ecological importance for people and environment. Despite this, the species is severely threatened and there are few genetic and genomic studies about it, making it difficult to propose evidence-based conservation strategies.Results In this work, the chloroplast genome of a N. pallida specimen was assembled, annotated, analyzed and compared with those of related species. The length of the assembled chloroplast genome was 162381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC% for the genome was 35.97%, although this is variable between regions, with a higher GC% found in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 18 contained at least one intron in their sequence. A large number of repetitive sequences of different types were identified in the assembled genome, being the most frequent the tandem repeats (> 300), especially microsatellites (SSR). The phylogenetic reconstruction of Prosopis s.l. showed that this group is monophyletic. N. pallida was closely related to P. cineraria, N. juliflora and N. glandulosa, forming a subclade with these species. When comparing the chloroplast genome sequence of N. pallida with N. juliflora, P. farcta and Strombocarpa tamarugo, it was found that the sequences were highly similar.Conclusions The chloroplast genome of N. pallida is composed of 162381 bp with the classical quadripartite structure and GC% of 35.97%, a value similar to that of other closely related species. Also, the genetic structure of the genome was found to be similar to other members of Prosopis s.l. In the chloroplast genome of N. pallida, more than 800 repetitive sequences were identified, being the most common the tandem repeats. N. pallida showed closeness to the other Neltuma spp., forming a subclade within the Prosopis s.l. group. The divergence analysis indicated that there were little differences when comparing the Prosopis s.l. chloroplast genomes, evidencing high levels of conservation between these species.

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The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

Cited by 2 publications

References 97 publications

Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae)

Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae)

Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (Subfamily: Caesalpinioideae)

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