Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

Abstract

BackgroundRetroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not copied to the new location in this mechanism, the duplicated gene copies (retrocopies) become pseudogenized. However, few can still survive, e.g. by recruiting novel regulatory elements from the region of insertion. Subsequently, these duplicated genes can contribute to the formation of lineage-specific traits and phenotypic diversity. Despite the numerous studies of the functional retrocopies (retrogenes) in animals and plants, very little is known about their presence in green algae, including morphologically diverse species. The current availability of the genomes of both uni- and multicellular algae provides a good opportunity to conduct a genome-wide investigation in order to fill the knowledge gap in retroposition phenomenon in this lineage.ResultsHere we present a comparative genomic analysis of uni- and multicellular algae, Chlamydomonas reinhardtii and Volvox carteri, respectively, to explore their retrogene complements. By adopting a computational approach, we identified 141 retrogene candidates in total in both genomes, with their fraction being significantly higher in the multicellular Volvox. Majority of the retrogene candidates showed signatures of functional constraints, thus indicating their functionality. Detailed analyses of the identified retrogene candidates, their parental genes, and homologs of both, revealed that most of the retrogene candidates were derived from ancient retroposition events in the common ancestor of the two algae and that the parental genes were subsequently lost from the respective lineages, making many retrogenes ‘orphan’.ConclusionWe revealed that the genomes of the green algae have maintained many possibly functional retrogenes in spite of experiencing various molecular evolutionary events during a long evolutionary time after the retroposition events. Our first report about the retrogene set in the green algae provides a good foundation for any future investigation of the repertoire of retrogenes and facilitates the assessment of the evolutionary impact of retroposition on diverse morphological traits in this lineage.ReviewersThis article was reviewed by William Martin and Piotr Zielenkiewicz.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0138-1) contains supplementary material, which is available to authorized users.

Multiple gene movements into and out of haploid sex chromosomes

“…identified 16 orphan retrogenes in S. japonica . Recent studies have revealed that retrocopies often replace their parental genes in animal and green lineage genomes [45, 47, 48]. The results presented here indicate that this phenomenon may have a significance in additional eukaryotic supergroups, in this case the stramenopiles.…”

Living Organisms Author Their Read-Write Genomes in Evolution

“…Many novel domain arrangements have been found to originate at the RNA level and involve the insertion of reverse-transcribed cDNA copies into the genome (“retroposition”) to generate loci encoding chimeric fusion proteins [ 343 , 344 , 345 , 346 , 347 , 348 , 349 , 350 , 351 , 352 , 353 , 354 ]. Retroposed coding sequences have been documented in nematodes [ 355 ], multicellular green algae Volvox carteri and Chlamydomonas reinhardtii [ 356 ], plants [ 357 ], silkworm [ 358 ], non-mammalian chordates [ 359 ], zebrafish [ 360 ], mammals [ 361 ], and primates [ 362 , 363 ]. Retrocopying is reported to have played a special role in the evolution of highly variable sex chromosomes [ 364 ].…”

Progress of CRISPR‐Cas Based Genome Editing in Photosynthetic Microbes

“…Adding to the proposed Cas9 cytotoxicity, the diminished expression of Cas9 due to yet unknown factors might be responsible for the feeble efficiency of the tool as observed in C. reinhardtii and N. oceanica . Moreover, the presence of introns and their role in regulating gene expressions in eukaryotes could also be detrimental, e.g., the genome of Chlamydomonas contains about 8.5 introns per gene . Similarly, genomes from micro‐algae such as Nannochloropsis , Phaeodactylum and Thalassiosira contain 1.7, 0.8 and 1.5 introns per gene, respectively .…”