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Phenotype and transcriptome analysis reveals chloroplast development and pigment biosynthesis together influenced the leaf color formation in mutants of Anthurium andraeanum 'Sonate'.

Yang Y, Chen X, Xu B, Li Y, Ma Y, Wang G - Front Plant Sci (2015)

Bottom Line: Knowledge of mechanisms in anthuriums to produce leaves with different shades of green would help to effectively select desirable traits.From the 27,539 (67.1%) unigenes with annotated functions, 858 significantly differently expressed genes (DEGs) were identified, consisting of 446 up-regulated genes and 412 down-regulated genes.And the possible formation pathway of leaf color mutant of A. andraeanum 'Sonate' is deduced based on our results.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Leaf color is one of the well-sought traits in breeding program for Anthurium andraeanum Lind. Knowledge of mechanisms in anthuriums to produce leaves with different shades of green would help to effectively select desirable traits. In this study, the micro- and ultra-structural and physiological features of leaves on wild type and leaf color mutants (dark green, rubescent, etiolated, albino) in A. andraeanum 'Sonate' were analyzed. Results show that chloroplasts of leaf color mutants exhibited abnormal morphology and distribution. Using next generation sequencing technology followed by de novo assembly, leaf transcriptomes comprising of 41,017 unigenes with an average sequence length of 768 bp were produced from wild type and rubescent mutant. From the 27,539 (67.1%) unigenes with annotated functions, 858 significantly differently expressed genes (DEGs) were identified, consisting of 446 up-regulated genes and 412 down-regulated genes. Genes that affect chloroplasts development and division, and chlorophyll biosynthesis were included in the down-regulated DEGs. Quantitative real-time PCR (qRT-PCR) analysis validated that the expression level of those genes was significantly lower in the rubescent, etiolated, and albino mutant compared to wild type plants, which concurs with the differences in micro- and ultra-structures and physiological features between these two types of plants. Conclusively, the leaf color formation is greatly affected by the activity of chloroplast development and pigment biosynthesis. And the possible formation pathway of leaf color mutant of A. andraeanum 'Sonate' is deduced based on our results.

No MeSH data available.


Related in: MedlinePlus

Length distributions of unigenes.
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Figure 5: Length distributions of unigenes.

Mentions: From the above described micro- and ultra-morphology and physiological features, we proposed that the expression pattern of genes responsible for chloroplast development and division and pigment biosynthesis may have been altered in mutants. To testify our hypothesis, transcriptome comparison was carried out. Because the 4 leaf color mutants came from an original mutant, we supposed they should share the same mechanism in leaf color formation, thus each of them could represent all of them. The dark green was more complex: it had chloroplast with normal function meanwhile showed characteristics of mutants. In contrast, the other 3 mutants (rubescent, etiolated, and albino) displayed similar and relatively simple phenotype (but showed difference in mutation degree: weak, moderate and severe, respectively). Thus, here rubescent was selected as the representative mutant to compared with the wild type to explore the mechanism of the leaf color mutation based on transcriptome analysis. As a result, approximately 4 Gbp of sequence data was produced. A total of 39,119,350 and 45,807,980 raw reads were obtained respectively by sequencing the cDNA libraries prepared from the wild type and rubescent mutant leaves. After trimming of the adapter sequences, and removal of low quality reads with N greater than 5%, the remaining 39,107,374 clean paired-end reads with 3,790,089,187 nucleotides in wild type library, and 45,794,218 paired-end reads with 4,445,749,574 nucleotides in rubescent mutant library, were generated, respectively. Using de novo assembly, 48,284 contigs consisting of 37,289,226 nucleotides were produced, with an average length of 772 bp and N50 (represents median length of all contigs) of 1155 bp. The length distribution of the assembled contigs was shown in Figure S1. At last, all of the assembled contigs were further scaffolded into 41,017 unigenes with a N50 length of 1172 bp and the mean unigene size was 768 bp (Table S2). The majority (50.3%) of the unigenes were longer than 500 bp. The specific length distributions of unigenes were given in Figure 5. This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GBKP00000000.


Phenotype and transcriptome analysis reveals chloroplast development and pigment biosynthesis together influenced the leaf color formation in mutants of Anthurium andraeanum 'Sonate'.

Yang Y, Chen X, Xu B, Li Y, Ma Y, Wang G - Front Plant Sci (2015)

Length distributions of unigenes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356079&req=5

Figure 5: Length distributions of unigenes.
Mentions: From the above described micro- and ultra-morphology and physiological features, we proposed that the expression pattern of genes responsible for chloroplast development and division and pigment biosynthesis may have been altered in mutants. To testify our hypothesis, transcriptome comparison was carried out. Because the 4 leaf color mutants came from an original mutant, we supposed they should share the same mechanism in leaf color formation, thus each of them could represent all of them. The dark green was more complex: it had chloroplast with normal function meanwhile showed characteristics of mutants. In contrast, the other 3 mutants (rubescent, etiolated, and albino) displayed similar and relatively simple phenotype (but showed difference in mutation degree: weak, moderate and severe, respectively). Thus, here rubescent was selected as the representative mutant to compared with the wild type to explore the mechanism of the leaf color mutation based on transcriptome analysis. As a result, approximately 4 Gbp of sequence data was produced. A total of 39,119,350 and 45,807,980 raw reads were obtained respectively by sequencing the cDNA libraries prepared from the wild type and rubescent mutant leaves. After trimming of the adapter sequences, and removal of low quality reads with N greater than 5%, the remaining 39,107,374 clean paired-end reads with 3,790,089,187 nucleotides in wild type library, and 45,794,218 paired-end reads with 4,445,749,574 nucleotides in rubescent mutant library, were generated, respectively. Using de novo assembly, 48,284 contigs consisting of 37,289,226 nucleotides were produced, with an average length of 772 bp and N50 (represents median length of all contigs) of 1155 bp. The length distribution of the assembled contigs was shown in Figure S1. At last, all of the assembled contigs were further scaffolded into 41,017 unigenes with a N50 length of 1172 bp and the mean unigene size was 768 bp (Table S2). The majority (50.3%) of the unigenes were longer than 500 bp. The specific length distributions of unigenes were given in Figure 5. This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GBKP00000000.

Bottom Line: Knowledge of mechanisms in anthuriums to produce leaves with different shades of green would help to effectively select desirable traits.From the 27,539 (67.1%) unigenes with annotated functions, 858 significantly differently expressed genes (DEGs) were identified, consisting of 446 up-regulated genes and 412 down-regulated genes.And the possible formation pathway of leaf color mutant of A. andraeanum 'Sonate' is deduced based on our results.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Leaf color is one of the well-sought traits in breeding program for Anthurium andraeanum Lind. Knowledge of mechanisms in anthuriums to produce leaves with different shades of green would help to effectively select desirable traits. In this study, the micro- and ultra-structural and physiological features of leaves on wild type and leaf color mutants (dark green, rubescent, etiolated, albino) in A. andraeanum 'Sonate' were analyzed. Results show that chloroplasts of leaf color mutants exhibited abnormal morphology and distribution. Using next generation sequencing technology followed by de novo assembly, leaf transcriptomes comprising of 41,017 unigenes with an average sequence length of 768 bp were produced from wild type and rubescent mutant. From the 27,539 (67.1%) unigenes with annotated functions, 858 significantly differently expressed genes (DEGs) were identified, consisting of 446 up-regulated genes and 412 down-regulated genes. Genes that affect chloroplasts development and division, and chlorophyll biosynthesis were included in the down-regulated DEGs. Quantitative real-time PCR (qRT-PCR) analysis validated that the expression level of those genes was significantly lower in the rubescent, etiolated, and albino mutant compared to wild type plants, which concurs with the differences in micro- and ultra-structures and physiological features between these two types of plants. Conclusively, the leaf color formation is greatly affected by the activity of chloroplast development and pigment biosynthesis. And the possible formation pathway of leaf color mutant of A. andraeanum 'Sonate' is deduced based on our results.

No MeSH data available.


Related in: MedlinePlus