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      Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga, Haematococcus pluvialis

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          Abstract

          Haematococcus pluvialis is a freshwater species of Chlorophyta, family Haematococcaceae. It is well known for its capacity to synthesize high amounts of astaxanthin, which is a strong antioxidant that has been utilized in aquaculture and cosmetics. To improve astaxanthin yield and to establish genetic resources for H. pluvialis, we performed whole-genome sequencing, assembly, and annotation of this green microalga. A total of 83.1 Gb of raw reads were sequenced. After filtering the raw reads, we subsequently generated a draft assembly with a genome size of 669.0 Mb, a scaffold N50 of 288.6 kb, and predicted 18,545 genes. We also established a robust phylogenetic tree from 14 representative algae species. With additional transcriptome data, we revealed some novel potential genes that are involved in the synthesis, accumulation, and regulation of astaxanthin production. In addition, we generated an isoform-level reference transcriptome set of 18,483 transcripts with high confidence. Alternative splicing analysis demonstrated that intron retention is the most frequent mode. In summary, we report the first draft genome of H. pluvialis. These genomic resources along with transcriptomic data provide a solid foundation for the discovery of the genetic basis for theoretical and commercial astaxanthin enrichment.

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          Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

          The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.
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            Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

            Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 transcripts from 6 tissues capturing ∼70% of the genes annotated in maize RefGen_v3 genome. A large proportion of transcripts (57%) represent novel, sometimes tissue-specific, isoforms of known genes and 3% correspond to novel gene loci. In other cases, the identified transcripts have improved existing gene models. Averaging across all six tissues, 90% of the splice junctions are supported by short reads from matched tissues. In addition, we identified a large number of novel long non-coding RNAs and fusion transcripts and found that DNA methylation plays an important role in generating various isoforms. Our results show that characterization of the maize B73 transcriptome is far from complete, and that maize gene expression is more complex than previously thought.
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              Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

              Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
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                Author and article information

                Contributors
                Role: Associate Editor
                Journal
                Genome Biol Evol
                Genome Biol Evol
                gbe
                Genome Biology and Evolution
                Oxford University Press
                1759-6653
                January 2019
                29 November 2018
                29 November 2018
                : 11
                : 1
                : 166-173
                Affiliations
                [1 ]Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
                [2 ]Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
                [3 ]Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China
                [4 ]Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
                [5 ]BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
                [6 ]Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
                [7 ]These authors contributed equally to this work
                Author notes

                Data deposition: The raw sequence data generated from this study have been deposited in the Genome Sequence Archive (GSA) database in the BIG Data Center ( http://gsa.big.ac.cn/index.jsp) under the accession number of PRJCA000614. The long reads sequenced by the PacBio platform were deposited in NCBI with the SRA accession number of SRP134137.

                Corresponding authors: E-mails: huzl@ 123456szu.edu.cn ; shiqiong@ 123456genomics.cn
                Article
                evy263
                10.1093/gbe/evy263
                6330051
                30496415
                881c0ec1-7ebf-494c-b9b1-65297936eb9a
                © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 26 November 2018
                Page count
                Pages: 8
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 31470431
                Award ID: 31400313
                Award ID: 31470389
                Award ID: 31700309
                Funded by: Guangdong Natural Science Foundation for Major Cultivation Project
                Award ID: 2014A030308017
                Award ID: 2017A030310255
                Funded by: Shenzhen Grant Plan for Science & Technology
                Award ID: JSGG20130411160539208
                Award ID: NYSW20140327010012
                Award ID: CKCY2016042710211071
                Award ID: JCYJ20170302144605664
                Categories
                Genome Report

                Genetics
                genome sequencing,assembly,annotation,astaxanthin,haematococcus pluvialis
                Genetics
                genome sequencing, assembly, annotation, astaxanthin, haematococcus pluvialis

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