DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees
Abstract This study introduces a new method to construct phylogenetic trees by combining both of the Simple Sequence Repeats (SSRs) and sequence alignments. The purpose of this work is to present the DendroSSR program and show it via a case study involving diverse Aspergillus species. To show how th...
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| Format: | Article |
| Language: | English |
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Instituto Internacional de Ecologia
2023-10-01
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| Series: | Brazilian Journal of Biology |
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| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842023000100873&tlng=en |
| _version_ | 1797658814802034688 |
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| author | M. Alhawatema |
| author_facet | M. Alhawatema |
| author_sort | M. Alhawatema |
| collection | DOAJ |
| description | Abstract This study introduces a new method to construct phylogenetic trees by combining both of the Simple Sequence Repeats (SSRs) and sequence alignments. The purpose of this work is to present the DendroSSR program and show it via a case study involving diverse Aspergillus species. To show how the DendroSSR program works to resolve complicated species relationships in phylogenetic trees, we employed the Aspergillus species as an example of a research case. The DendroSSR employs a technique containing multiple phases beginning with, detecting SSRs, computing SSRs similarities, sequences alignment, building a distance matrix based on SSRs similarity and sequences alignments, and then hierarchical clustering, and presenting the findings in a dendrogram. Sometimes sequence alignments alone may not give adequate information to generate a phylogenetic tree to resolve complicated species relationships. Therefore, establishing a distance matrix that is formed of addition of SSRs similarity across sequences to the traditional sequence alignment helps the process substantially and resolves the connections of complex species on phylogenetic trees. Additionally, it may be hard to distinguish complex relationships across species when studying conserved sequences, which could lead to an incomplete representation of their evolutionary relationships. These limitations are addressed by DendroSSR, which offers a technique to produce phylogenetic trees by incorporating SSRs similarity across species into the approach of generating phylogenetic trees. As it is known, SSRs are extensively scattered across the genomes of species and exhibit a great variation. Therefore, SSRs may support the knowledge gathered from sequence alignments by providing more information on genetic variation and even evolutionary relationships. The use of DendroSSR analysis might be considered for creating phylogenetic trees as a complementary or secondary strategy among the species under examination in circumstances where traditional phylogenetic analysis fails to clarify the species complex phylogenetic relationships. |
| first_indexed | 2024-03-11T18:04:46Z |
| format | Article |
| id | doaj.art-094607a591b24031870c221bea962906 |
| institution | Directory Open Access Journal |
| issn | 1678-4375 |
| language | English |
| last_indexed | 2024-03-11T18:04:46Z |
| publishDate | 2023-10-01 |
| publisher | Instituto Internacional de Ecologia |
| record_format | Article |
| series | Brazilian Journal of Biology |
| spelling | doaj.art-094607a591b24031870c221bea9629062023-10-17T07:41:50ZengInstituto Internacional de EcologiaBrazilian Journal of Biology1678-43752023-10-018310.1590/1519-6984.275386DendroSSR: SSRs and sequence alignment as tools for building phylogeny treesM. Alhawatemahttps://orcid.org/0009-0002-4614-8070Abstract This study introduces a new method to construct phylogenetic trees by combining both of the Simple Sequence Repeats (SSRs) and sequence alignments. The purpose of this work is to present the DendroSSR program and show it via a case study involving diverse Aspergillus species. To show how the DendroSSR program works to resolve complicated species relationships in phylogenetic trees, we employed the Aspergillus species as an example of a research case. The DendroSSR employs a technique containing multiple phases beginning with, detecting SSRs, computing SSRs similarities, sequences alignment, building a distance matrix based on SSRs similarity and sequences alignments, and then hierarchical clustering, and presenting the findings in a dendrogram. Sometimes sequence alignments alone may not give adequate information to generate a phylogenetic tree to resolve complicated species relationships. Therefore, establishing a distance matrix that is formed of addition of SSRs similarity across sequences to the traditional sequence alignment helps the process substantially and resolves the connections of complex species on phylogenetic trees. Additionally, it may be hard to distinguish complex relationships across species when studying conserved sequences, which could lead to an incomplete representation of their evolutionary relationships. These limitations are addressed by DendroSSR, which offers a technique to produce phylogenetic trees by incorporating SSRs similarity across species into the approach of generating phylogenetic trees. As it is known, SSRs are extensively scattered across the genomes of species and exhibit a great variation. Therefore, SSRs may support the knowledge gathered from sequence alignments by providing more information on genetic variation and even evolutionary relationships. The use of DendroSSR analysis might be considered for creating phylogenetic trees as a complementary or secondary strategy among the species under examination in circumstances where traditional phylogenetic analysis fails to clarify the species complex phylogenetic relationships.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842023000100873&tlng=enDendroSSRsimple sequence repeats (SSRs)phylogenetic treesAspergillus speciesUPGMA |
| spellingShingle | M. Alhawatema DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees Brazilian Journal of Biology DendroSSR simple sequence repeats (SSRs) phylogenetic trees Aspergillus species UPGMA |
| title | DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees |
| title_full | DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees |
| title_fullStr | DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees |
| title_full_unstemmed | DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees |
| title_short | DendroSSR: SSRs and sequence alignment as tools for building phylogeny trees |
| title_sort | dendrossr ssrs and sequence alignment as tools for building phylogeny trees |
| topic | DendroSSR simple sequence repeats (SSRs) phylogenetic trees Aspergillus species UPGMA |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842023000100873&tlng=en |
| work_keys_str_mv | AT malhawatema dendrossrssrsandsequencealignmentastoolsforbuildingphylogenytrees |