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Title: Chloroinformatics
Author: Amiryousefi, Ali
Contributor: University of Helsinki, Faculty of Biological and Environmental Sciences
Doctoral Program in Plant Sciences
Publisher: Helsingin yliopisto
Date: 2019-03-19
Thesis level: Doctoral dissertation (article-based)
Abstract: Chloroplasts are cytoplasmic organelles chiefly responsible for the photosynthesis. Their genes have been used extensively during the past decades in phylogenetic analyses of various photosynthetic eukaryotes, particularly plants. The genomic content of this organelle and its very architecture can be used for a deeper insight in evolution and towards robust phylogenetic hypotheses. Ever since this importance was recognized concurrently with the advancements of methods in both providing a basic genetic material through sequencing and advanced methods to analyze the data, we have witnessed the introduction of a couple of thousands plastid genomes up to this date. This process, by no means is in its decline or even stationary state, as this pace is projected to be accelerated in the coming years, with the inevitable advances in our technologies and our need to understand the nature as accurate as possible. The aim of this study as represented in the sequel chapters is twofold; 1) to introduce the complete chloroplast genomes of two species from the euasterid clade and provide their phylogenetic analyses; Solanum dulcamara L. as a native Old World diploid member of the nightshade family, and Ambrosia trifida L. as a recognized invasive plant originated and evolved from North America. 2) To provide two analytical tools for more advanced treatment of the genetic information of plastids in bioinformatics. By comparative analysis for bittersweet and giant ragweed, the result show that synteny and the genomic content of both belonging to the families Solanaceae and Asteraceae, respectively, have a conserved structure. We also noted that many submitted annotations in the nightshade family are far from acceptable quality, and further on, we improved them with reannotation of the existing sequences. On the other hand, a novel tool (IRscope) to detect and plot the Inverted Repeat (IR) regions of the chloroplast genome was introduced. IRscope, with the help of iterative search algorithm, allows the depiction of genes in the vicinity of the Junction Sites (JS), of up to ten different chloroplast genomes of embryophytes (land plants). Moreover, we constructed an online calculative suite (iMEC) to return the result of the seven different molecular markers against the provided input file. This tool is useful particularly in studies aimed to assess the efficiency of different marker systems linked to plastid genome variation.Viherhiukkaset ovat yhteyttämisestä vastaavia soluelimiä. Niiden geenejä on laajalti käytetty viime vuosikymmenien ajan erilaisten aitotumallisten, erityisesti kasvien, fylogeneettisissä tutkimuksissa. Viherhiukkasen genominen vaihtelu tarjoaa näkökulmaa kasvien evoluutioon ja edesauttaa fylogeneettisia tutkimuksia. Edistyneiden data-analyysimenetelmien kehitys on mahdollistanut viherhiukkasten perustanlaatuisen geneettisen tutkimuksen. Tuhansia soluelingenomeja on tutkittu ja yhä usempia soluelingenomeja tutkitaan parhaillaan. Tämän alan tutkimus edistyy nopeaa vauhtia kehittyvien tutkimusmenetelmien kehittyessä. Tämän tutkimuksen tarkoituksena oli 1) Analysoida ja verrata kahden eri euasterid-lajin viherhiukkas-genomia: punakoiso (Solanum dulcamara) vs. sormituoksukki (Ambrosia trifida). 2) Kehittää analyyttisiä työkaluja hiukkastutkimuksen genetiikan bioinformatiiviseen tutkimukseen vertailemalla kelasköynnöksia ja tuoksukkeja, osoitimme että niiden genomeilla on samankaltainen rakenne. Tutkimuksen aikana kehitettiin useita uusia bioinformatiikan työkaluja hiukkasten genomisen vaihtelevuuden tutkimiseen.
Subject: Bioinformatics
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