Cryptomonas pyrenoidifera organellar genomes and estimation of its ITS2 sequence diversity using lineage directed barcode primers

IF 1.5 4区 生物学 Q3 MARINE & FRESHWATER BIOLOGY Phycologia Pub Date : 2023-05-01 DOI:10.1080/00318884.2023.2202069
Lucie O. Hornberger, Isabella J. Maggard, R. Matthews, A. B. Cahoon
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Abstract

ABSTRACT Cryptomonas is a common metropolitan freshwater microalgal genus that is easily recognizable due to its distinctive asymmetric cellular morphology and swimming pattern. There are currently 71 recognized Cryptomonas species but these can be difficult to identify by cellular morphology alone. This makes estimation of Cryptomonas diversity from environmental samples challenging as it requires culturing of strains followed by sequencing of genetic markers for clear identifications. In this paper we describe the isolation and culture of Cryptomonas pyrenoidifera from a small ephemeral pool in Southwestern Virginia, USA, with an annual recurrent population of this genus. Genomic resources from this isolate, including complete chloroplast and mitochondrial genomes, and nuclear and nucleomorph rRNA regions, were completed and archived. Metabarcoding, using lineage-directed primers designed to amplify the ITS2 region of Cryptomonas, was used to estimate an intra-specific variation of 99.3% for the C. pyrenoidifera ITS2 barcode from this natural environment. Metabarcoding also revealed that at least twelve phylogenetic species were present in this body of water. Our results provide new genomic resources for C. pyrenoidifera and suggest that metabarcoding with the ITS2 marker is a feasible approach to estimating Cryptomonas diversity and identification.
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利用谱系定向条形码引物分析pyrenoidifera隐单胞菌的胞体基因组及其ITS2序列多样性
隐单胞菌是一种常见的都市淡水微藻属,由于其独特的不对称细胞形态和游动模式而易于识别。目前已知的隐单胞菌有71种,但仅凭细胞形态很难识别。这使得从环境样本中估计隐单胞菌的多样性具有挑战性,因为它需要培养菌株,然后对遗传标记进行测序以明确鉴定。在本文中,我们描述了从美国弗吉尼亚州西南部一个小的短暂池中分离和培养的pyrenoidifera隐单胞菌,该属每年都有复发种群。该分离物的基因组资源,包括完整的叶绿体和线粒体基因组,以及核和核形态rRNA区域,已完成并存档。利用设计用于扩增隐单胞菌ITS2区的定向引物进行元条形码编码,估计C. pyrenoidifera ITS2条形码在自然环境下的种内变异率为99.3%。元条形码还显示,该水体中存在至少12种系统发育物种。本研究结果为隐单胞菌提供了新的基因组资源,表明利用ITS2标记进行元条形码编码是估计隐单胞菌多样性和鉴定的一种可行方法。
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来源期刊
Phycologia
Phycologia 生物-海洋与淡水生物学
CiteScore
3.10
自引率
18.80%
发文量
54
审稿时长
3 months
期刊介绍: Phycologia is published bimonthly by the International Phycological Society and serves as a publishing medium for information about any aspect of phycology. Membership in the Society is not necessary for publication. Submitted manuscripts cannot be previously published or submitted elsewhere. Copyright ownership of all accepted papers is held by the International Phycological Society.
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