Abstract
Sporadic rains in the Atacama Desert reveal a high biodiversity of plant species that only occur there. One of these rare species is the “Red añañuca” (Zephyranthes phycelloides), formerly known as Rhodophiala phycelloides. Many species of Zephyranthes in the Atacama Desert are dangerously threatened, due to massive extraction of bulbs and cutting of flowers. Therefore, studies of the biodiversity of these endemic species, which are essential for their conservation, should be conducted sooner rather than later. There are some chloroplast genomes available for Amaryllidaceae species, however there is no complete chloroplast genome available for any of the species of Zephyranthes subgenus Myostemma. The aim of the present work was to characterize and analyze the chloroplast of Z. phycelloides by NGS sequencing. The chloroplast genome of the Z. phycelloides consists of 158,107 bp, with typical quadripartite structures: a large single copy (LSC, 86,129 bp), a small single copy (SSC, 18,352 bp), and two inverted repeats (IR, 26,813 bp). One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. The number of SSRs was 64 in Z. phycelloides and a total of 43 repeats were detected. The phylogenetic analysis of Z. phycelloides shows a distinct subclade with respect to Z. mesochloa. The average nucleotide variability (Pi) between Z. phycelloides and Z. mesochloa was of 0.02000, and seven loci with high variability were identified: psbA, trnSGCU-trnGUCC, trnDGUC-trnYGUA, trnLUAA-trnFGAA, rbcL, psbE-petL and ndhG-ndhI. The differences between the species are furthermore confirmed by the high amount of SNPs between these two species. Here, we report for the first time the complete cp genome of one species of the Zephyranthes subgenus Myostemma, which can be used for phylogenetic and population genomic studies.
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Claims 15
Claim · model-written summary
The chloroplast genome measured 158,107 bp.
- Taxon
- Z. phycelloides
Zephyranthes phycelloidese0 - Outcome
- chloroplast genomee0
- Value
- 158,107 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The chloroplast genome of the Z. phycelloides consists of 158,107 bp”
Claim · model-written summary
The large single copy region measured 86,129 bp.
Not reportedTaxon
Verbatim
e0“a large single copy (LSC, 86,129 bp)”
Claim · model-written summary
The small single copy region measured 18,352 bp.
Not reportedTaxon
Verbatim
e0“a small single copy (SSC, 18,352 bp)”
Claim · model-written summary
The inverted repeats measured 26,813 bp.
Not reportedTaxon
Verbatim
e0“two inverted repeats (IR, 26,813 bp)”
Claim · model-written summary
The chloroplast genome had 87 coding genes.
Not reportedTaxon
Verbatim
e0“One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes”
Claim · model-written summary
The chloroplast genome had 8 rRNA genes.
Not reportedTaxon
Verbatim
e0“One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes”
Claim · model-written summary
The chloroplast genome had 38 tRNA genes.
Not reportedTaxon
Verbatim
e0“One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes”
Claim · model-written summary
The chloroplast genome had 4 pseudogenes.
Not reportedTaxon
Verbatim
e0“One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes”
Claim · model-written summary
64 SSRs were found in Z. phycelloides.
- Taxon
- Z. phycelloidesZephyranthes phycelloidese0
- Outcome
- SSRse0
- Value
- 64e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The number of SSRs was 64 in Z. phycelloides”
Claim · model-written summary
43 repeats were detected.
Not reportedTaxon
Verbatim
e0“a total of 43 repeats were detected”
Claim · model-written summary
Z. phycelloides formed a distinct subclade relative to Z. mesochloa.
- Taxon
- Z. phycelloidesZephyranthes phycelloidese0
- Outcome
- distinct subcladee0
- Comparator
- Z. mesochloae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Z. phycelloides shows a distinct subclade with respect to Z. mesochloa”
Claim · model-written summary
Average nucleotide variability between the two species was 0.02000.
- Taxon
- Z. phycelloidesZephyranthes phycelloidese0
- Outcome
- average nucleotide variability (Pi)e0
- Value
- 0.02000e0
- Comparator
- Z. mesochloae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“average nucleotide variability (Pi) between Z. phycelloides and Z. mesochloa was of 0.02000”
Claim · model-written summary
Seven highly variable loci were identified.
Not reportedTaxon
Verbatim
e0“seven loci with high variability were identified: psbA, trnSGCU-trnGUCC, trnDGUC-trnYGUA, trnLUAA-trnFGAA, rbcL, psbE-petL and ndhG-ndhI”
Claim · model-written summary
Many SNPs distinguished the two species.
- Outcome
- SNPse0
Not reportedTaxon
Verbatim
e0“high amount of SNPs between these two species”
Claim · model-written summary
The complete cp genome of a Zephyranthes subgenus Myostemma species was reported as a resource.
- Taxon
- Zephyranthes
.JPG?width=60)
Zephyranthese0 - Outcome
- complete cp genomee0
- Value
- one speciese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.JPG?width=500)
Verbatim
e0“the first time the complete cp genome of one species of the Zephyranthes subgenus Myostemma”