{"id":15648,"date":"2022-06-22T10:40:21","date_gmt":"2022-06-22T03:40:21","guid":{"rendered":"https:\/\/bgrssb.icgbio.ru\/2022\/?p=15648"},"modified":"2022-09-20T10:32:44","modified_gmt":"2022-09-20T03:32:44","slug":"the-low-level-of-variability-is-depicted-in-plastomes-of-early-soybean-varieties","status":"publish","type":"post","link":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/2022\/06\/22\/the-low-level-of-variability-is-depicted-in-plastomes-of-early-soybean-varieties\/","title":{"rendered":"The low level of variability is depicted in plastomes of early soybean varieties"},"content":{"rendered":"<p><em>by Valeryia Aleksandrovich | Maryna Siniauskaya | Aleh Liaudanski | Yahor Mishuk | Tatjana Shatarnova |<\/em><br \/>\n<em>Nina Danilenko | Oleg Davydenko | Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of<\/em><br \/>\n<em>Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology, NAS, Minsk, Belarus |<\/em><br \/>\n<em>Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology, NAS, Minsk,<\/em><br \/>\n<em>Belarus | Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology,<\/em><br \/>\n<em>NAS, Minsk, Belarus<\/em><\/p>\n<p><strong>Motivation and Aim<\/strong>: The chloroplast genome of land plants is usually conservative in<br \/>\nstructure, but variable in sequence. Today the information about the complete plastidial<br \/>\nsequences is growing fast. Intraspecific diversity of organelle DNA became apparent and<br \/>\npossibly plays an important role in successful breeding and creation of the new varieties in<br \/>\nplants. Here we report about the sequencing of complete plastomes of 24 early-maturing<br \/>\nsoybean (Glycine max (L.) Merr.) cultivars. The aim of our study was to evaluate the level of<br \/>\nchloroplast genomes diversity in specific group of Glycine max varieties.<br \/>\n<strong>Methods and Algorithms<\/strong>: DNA was obtained from the 7-day-old seedlings by phenolchlorophorm extraction from the chloroplast fraction, isolated by differential centrifugation.<br \/>\nThe chloroplast DNA was then sequenced on Illumina MiSeq. The NGS data processing<br \/>\nalgorithm included reads alignment on reference G. max plastid sequence (MW357264.1)<br \/>\nusing Burrows-Wheeler Alignment Tool followed by converting to .bam format and sorting<br \/>\nwith Samtools. Variant calling was performed with GATK HaplotypeCaller followed by<br \/>\nfiltering with Bcftools.<br \/>\n<strong>Results<\/strong>: Analysis of 24 complete soybean chloroplast genome sequences demonstrated the<br \/>\ndrastically low level of genetic diversity in studied varieties. Only 3 SSRs, 1 INDEL and 5<br \/>\nSNP were revealed between samples. 4 SNPs were located in coding sequences of atpB,<br \/>\nrps4, accD and rps3 genes. All of them were synonymic. The studied chloroplast genomes<br \/>\ncan be subdivided into 3 haplotypes based on found polymorphisms.<br \/>\n<strong>Conclusion<\/strong>: Here we report about low level of variability in chloroplast DNA of Glycine max.<br \/>\nPossibly it is the result of the founder effect \u2013 evidently a narrow range of ancestors was<br \/>\nused while this group of varieties was created.<br \/>\n<strong>Acknowledgements<\/strong>: The study was carried out as a part of the State Scientific Research<br \/>\nProgram \u00abBiotechnologies\u00bb 2021\u20132023, Subprogram 2 \u00abStructural and functional<br \/>\ngenomics\u00bb, assignment 2.1.3<\/p>\n<a href=\"https:\/\/bgrssb.icgbio.ru\/2022\/wp-content\/uploads\/sites\/3\/2022\/06\/The-low-level-of-variability-is-depicted-in-plastomes-of-early-soybean-varieties.pdf\" class=\"pdfemb-viewer\" style=\"\" data-width=\"max\" data-height=\"max\"  data-toolbar=\"bottom\" data-toolbar-fixed=\"off\">The low level of variability is depicted in plastomes of early soybean varieties<br\/><\/a>\n","protected":false},"excerpt":{"rendered":"<p>by Valeryia Aleksandrovich | Maryna Siniauskaya | Aleh Liaudanski | Yahor Mishuk | Tatjana Shatarnova | Nina Danilenko | Oleg Davydenko | Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology, NAS, [&hellip;]<\/p>\n","protected":false},"author":3967,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[10],"tags":[104,105,106,107],"_links":{"self":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/posts\/15648"}],"collection":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/users\/3967"}],"replies":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/comments?post=15648"}],"version-history":[{"count":1,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/posts\/15648\/revisions"}],"predecessor-version":[{"id":15650,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/posts\/15648\/revisions\/15650"}],"wp:attachment":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/media?parent=15648"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/categories?post=15648"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/ru\/wp-json\/wp\/v2\/tags?post=15648"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}