Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes
Abstract Background Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA se...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2017-10-01
|
Series: | Plant Methods |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s13007-017-0237-8 |
id |
doaj-2a650300b7904df7ab6268066d302686 |
---|---|
record_format |
Article |
spelling |
doaj-2a650300b7904df7ab6268066d3026862020-11-24T21:41:38ZengBMCPlant Methods1746-48112017-10-0113111010.1186/s13007-017-0237-8Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomesTomohiro Yanagi0Kenta Shirasawa1Mayuko Terachi2Sachiko Isobe3Faculty of Agriculture, Kagawa UniversityKazusa DNA Research InstituteFaculty of Agriculture, Kagawa UniversityKazusa DNA Research InstituteAbstract Background Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry. Results Three hundred and ten somatic chromosomes of the Japanese octoploid strawberry ‘Reiko’ were individually selected under a light microscope using a microdissection system. DNA from 288 of the dissected chromosomes was successfully amplified using a DNA amplification kit. Using next-generation sequencing, we decoded the base sequences of the amplified DNA segments, and on the basis of mapping, we identified DNA sequences from 144 samples that were best matched to the reference genomes of the octoploid strawberry, F. × ananassa, and the diploid strawberry, F. vesca. The 144 samples were classified into seven pseudo-molecules of F. vesca. The coverage rates of the DNA sequences from the single chromosome onto all pseudo-molecular sequences varied from 3 to 29.9%. Conclusion We demonstrated an efficient method for sequence analysis of allopolyploid plants using microdissected single chromosomes. On the basis of our results, we believe that whole-genome analysis of allopolyploid plants can be enhanced using methodology that employs microdissected single chromosomes.http://link.springer.com/article/10.1186/s13007-017-0237-8Strawberry (Fragaria × ananassa Duch.)AllopolyploidChromosome microdissectionSequence analysisMapping |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Tomohiro Yanagi Kenta Shirasawa Mayuko Terachi Sachiko Isobe |
spellingShingle |
Tomohiro Yanagi Kenta Shirasawa Mayuko Terachi Sachiko Isobe Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes Plant Methods Strawberry (Fragaria × ananassa Duch.) Allopolyploid Chromosome microdissection Sequence analysis Mapping |
author_facet |
Tomohiro Yanagi Kenta Shirasawa Mayuko Terachi Sachiko Isobe |
author_sort |
Tomohiro Yanagi |
title |
Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes |
title_short |
Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes |
title_full |
Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes |
title_fullStr |
Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes |
title_full_unstemmed |
Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes |
title_sort |
sequence analysis of cultivated strawberry (fragaria × ananassa duch.) using microdissected single somatic chromosomes |
publisher |
BMC |
series |
Plant Methods |
issn |
1746-4811 |
publishDate |
2017-10-01 |
description |
Abstract Background Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry. Results Three hundred and ten somatic chromosomes of the Japanese octoploid strawberry ‘Reiko’ were individually selected under a light microscope using a microdissection system. DNA from 288 of the dissected chromosomes was successfully amplified using a DNA amplification kit. Using next-generation sequencing, we decoded the base sequences of the amplified DNA segments, and on the basis of mapping, we identified DNA sequences from 144 samples that were best matched to the reference genomes of the octoploid strawberry, F. × ananassa, and the diploid strawberry, F. vesca. The 144 samples were classified into seven pseudo-molecules of F. vesca. The coverage rates of the DNA sequences from the single chromosome onto all pseudo-molecular sequences varied from 3 to 29.9%. Conclusion We demonstrated an efficient method for sequence analysis of allopolyploid plants using microdissected single chromosomes. On the basis of our results, we believe that whole-genome analysis of allopolyploid plants can be enhanced using methodology that employs microdissected single chromosomes. |
topic |
Strawberry (Fragaria × ananassa Duch.) Allopolyploid Chromosome microdissection Sequence analysis Mapping |
url |
http://link.springer.com/article/10.1186/s13007-017-0237-8 |
work_keys_str_mv |
AT tomohiroyanagi sequenceanalysisofcultivatedstrawberryfragariaananassaduchusingmicrodissectedsinglesomaticchromosomes AT kentashirasawa sequenceanalysisofcultivatedstrawberryfragariaananassaduchusingmicrodissectedsinglesomaticchromosomes AT mayukoterachi sequenceanalysisofcultivatedstrawberryfragariaananassaduchusingmicrodissectedsinglesomaticchromosomes AT sachikoisobe sequenceanalysisofcultivatedstrawberryfragariaananassaduchusingmicrodissectedsinglesomaticchromosomes |
_version_ |
1725920898725183488 |