Abstract
Yeyong mustard is a mustard vegetable belonging to the Brassicaceae family and the Brassica genus. This study assembled, annotated, and analyzed the chloroplast genome of Brassica juncea L., aiming to clarify its systematic evolutionary relationship with other cruciferous plants. The study used the Illumina NovaSeq 6000 platform to sequence the entire chloroplast genome of leaf mustard, and systematically analyzed its genome structure, repeat sequences, nucleic acid diversity, and codon preferences using bioinformatics methods. At the same time, the phylogenetic relationships were constructed by combining the leaf chloroplast genome sequences of other cruciferous plants. The results showed that the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%, exhibiting a typical tetrad structure; a total of 132 coding genes were annotated, including 87 mRNA genes, 37 tRNA genes, and eight rRNA genes, and no pseudogenes were found. Codon preference analysis shows that leucine (Leu) has the highest frequency of use, with 32 codons having a relative synonymous codon usage (RSCU) greater than 1, mostly ending in A or U; there are 37 scattered repetitive sequences and 315 simple repetitive sequences in the genome. Ka/Ks analysis showed that the chloroplast genes of leaf mustard were subjected to purification selection as a whole, while genes such as nadhF and petD showed positive selection, which is speculated to be related to adaptive evolution. The results of the phylogenetic analysis further confirm that the chloroplast genome of leaf mustard has a typical tetrad structure and is relatively conserved. It is most closely related to mustard greens in terms of evolutionary relationship, followed by Brassica plants such as nori and turnip, and is also closely related to Brassica plants such as European rapeseed. This study elucidated the conservative characteristics and evolutionary patterns of the chloroplast genome in mustard leaves, providing theoretical support for the phylogenetic research of the Brassicaceae family and the development and utilization of germplasm resources.
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Claims 17
Claim · model-written summary
The chloroplast genome of leaf mustard had a total length of 153,490 bp.
Verbatim
e1“the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%”
Claim · model-written summary
The chloroplast genome of leaf mustard had a GC content of 36.36%.
Verbatim
e1“the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%”
Claim · model-written summary
The leaf mustard chloroplast genome exhibited a typical tetrad structure.
- Taxon
- Brassica juncea
Brassica junceat0 - Outcome
- typical tetrad structuree1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“exhibiting a typical tetrad structure”
t0“Brassica juncea”
Claim · model-written summary
A total of 132 coding genes were annotated in the leaf mustard chloroplast genome.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- coding genese1
- Value
- 132e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“132 coding genes”
t0“Brassica juncea”
Claim · model-written summary
The annotated genes included 87 mRNA genes.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- mRNA genese1
- Value
- 87e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“87 mRNA genes”
t0“Brassica juncea”
Claim · model-written summary
The annotated genes included 37 tRNA genes.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- tRNA genese1
- Value
- 37e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“37 tRNA genes”
t0“Brassica juncea”
Claim · model-written summary
The annotated genes included eight rRNA genes.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- rRNA genese1
- Value
- eighte1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“eight rRNA genes”
t0“Brassica juncea”
Claim · model-written summary
No pseudogenes were found in the leaf mustard chloroplast genome.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- no pseudogenes were founde1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“no pseudogenes were found”
t0“Brassica juncea”
Claim · model-written summary
Leucine had the highest frequency of codon use in leaf mustard.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- frequency of usee1
- Direction
- higheste1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“leucine (Leu) has the highest frequency of use”
t0“Brassica juncea”
Claim · model-written summary
Thirty-two codons had relative synonymous codon usage greater than 1, mostly ending in A or U.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- codons having a relative synonymous codon usage (RSCU) greater than 1e1
- Value
- 32e1
- Qualifier
- mostly ending in A or Ue1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“32 codons having a relative synonymous codon usage (RSCU) greater than 1, mostly ending in A or U”
t0“Brassica juncea”
Claim · model-written summary
The genome contained 37 scattered repetitive sequences.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- scattered repetitive sequencese1
- Value
- 37e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“37 scattered repetitive sequences”
t0“Brassica juncea”
Claim · model-written summary
The genome contained 315 simple repetitive sequences.
- Taxon
- Brassica junceaBrassica junceat0
- Outcome
- simple repetitive sequencese1
- Value
- 315e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“315 simple repetitive sequences”
t0“Brassica juncea”
Claim · model-written summary
Ka/Ks analysis showed the chloroplast genes of leaf mustard were under purifying selection as a whole.
Verbatim
e1“the chloroplast genes of leaf mustard were subjected to purification selection as a whole”
Claim · model-written summary
Genes such as nadhF and petD showed positive selection, speculated to be related to adaptive evolution.
Verbatim
e1“genes such as nadhF and petD showed positive selection, which is speculated to be related to adaptive evolution”
e2“the chloroplast genes of leaf mustard”
Claim · model-written summary
Leaf mustard is most closely related to mustard greens in evolutionary relationship.
Verbatim
e1“It is most closely related to mustard greens in terms of evolutionary relationship”
Claim · model-written summary
Leaf mustard is followed in relatedness by Brassica plants such as nori and turnip and is also closely related to European rapeseed.
Verbatim
e1“followed by Brassica plants such as nori and turnip, and is also closely related to Brassica plants such as European rapeseed”
Claim · model-written summary
The leaf mustard chloroplast genome is relatively conserved.
Verbatim
e1“is relatively conserved”
e2“the chloroplast genome of leaf mustard has a typical tetrad structure”