Dataset Information

Complete Genome Sequence of Floricoccus penangensis ML061-4 Isolated from Assam Tea Leaf [Camellia sinensis var. assamica (J.W.Mast.) Kitam.].

ABSTRACT: Floricoccus penangensis is a Gram-positive coccoid organism that is a member of the lactic acid bacteria. F. penangensis ML061-4 was originally isolated from the surface of an Assam tea leaf, and its genome is herein shown to contain gene clusters predicted to be involved in complex carbohydrate metabolism and biosynthesis of secondary metabolites.

SUBMITTER: Rungsirivanich P

PROVIDER: S-EPMC10367601 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

Complete Genome Sequence of Floricoccus penangensis ML061-4 Isolated from Assam Tea Leaf [Camellia sinensis var. assamica (J.W.Mast.) Kitam.].

Rungsirivanich Patthanasak P Parlindungan Elvina E Mahony Jennifer J O'Neill Ian I McDonnell Brian B Bottacini Francesca F Supandee Witsanu W Thongwai Narumol N van Sinderen Douwe D

Journal of genomics 20230716

Floricoccus penangensis is a Gram-positive coccoid organism that is a member of the lactic acid bacteria. F. penangensis ML061-4 was originally isolated from the surface of an Assam tea leaf, and its genome is herein shown to contain gene clusters predicted to be involved in complex carbohydrate metabolism and biosynthesis of secondary metabolites. ...[more]

PMID: 37497281

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Project description:Flavonoids and caffeine are the major secondary metabolites with beneficial bioactivity for human health in tea plants, and their biosynthesis pathway and regulatory networks have been well-deciphered. However, the accumulation traits of flavonoids and caffeine in different tea cultivars was insufficient in investigation. In this study, metabolomic and transcriptomic analyses were performed to investigate the differences of flavonoids and caffeine accumulation and regulation between Chinese varieties, including the 'BTSC' group with green leaf, the 'BTZY' group with purple foliage, and the 'MYC' group comprising Assam varieties with green leaf. The results showed that most of the flavonoids were down-regulated in the 'MYC' group; however, the total anthocyanin contents were higher than that of the 'BTSC' group while lower than that of the 'BTZY' group. An ANS (Anthocyanin synthase) was significantly up-regulated and supposed to play a key role for anthocyanin accumulation in the 'BTZY' group. In addition, the results showed that esterified catechins were accumulated in the 'BTSC' and 'BTZY' groups with high abundance. In addition, SCPL1A (Type 1A serine carboxypeptidase-like acyltransferases gene) and UGGT (UDP glucose: galloyl-1-O-β-d-glucosyltransferase gene) potentially contributed to the up-accumulation of catechins esterified by gallic acid. Interestingly, the results found that much lower levels of caffeine accumulation were observed in the 'MYC' group. RT-qPCR analysis suggested that the expression deficiency of TCS1 (Tea caffeine synthase 1) was the key factor resulting in the insufficient accumulation of caffeine in the 'MYC' group. Multiple MYB/MYB-like elements were discovered in the promoter region of TCS1 and most of the MYB genes were found preferentially expressed in 'MYC' groups, indicating some of which potentially served as negative factor(s) for biosynthesis of caffeine in tea plants. The present study uncovers the characteristics of metabolite accumulation and the key regulatory network, which provide a research reference to the selection and breeding of tea varieties.

Project description:Camellia sinensis var. Assamica cv. Duntsa (C.duntsa), a valuable Theaceae from Hunan Province, has been looked at as a precious tea resource by local farmers because of its economic and ecological value. Genomics study on C.duntsa is essential for the domestication and enhancement of tea tree varieties. In the present study, we used a hybrid approach based on Illumina and PacBio data to sequence and assemble the mitochondrial genome of C.duntsa. The mitochondrial genome of C.duntsa was estimated to be 1,081,996 base pairs (bp) and eighty-one genes consisting of one pseudogene, three ribosomal RNA (rRNA) genes, thirty transfer RNA (tRNA) genes, and forty-seven protein-coding genes (PCGs). Tetramer repetitions made up 43.90% of simple sequence repeats (SSRs). The codon usage bias of the Theaceae mitochondrial gene atp9 was altered by mutation, but the codon usage of other genes was shaped by natural selection. Besides, there are eighteen gene-containing homologous regions between the chloroplast and mitochondrial genomes of C. duntsa.Some genomes including atp8, cox1, cox3, nad7, nad9, rpl16, rpl2, rps19, rps4, and sdh4 are absent in the mitochondrial genome of several Theaceae plant. However, C. duntsa maintains these genes integrity and functionality. Another gene, rps16, is either lacking from the mitochondrial genome of C. duntsa or is present as a pseudogene. C. duntsa and C. sinensis (OM809792) are very similar, as shown by a collinear match across four species of Theaceae; the most conservative genes are nad5, atp9, cox2, rps3, trnA-TGC, trnI-GAT, rrn18, trnV-GAC, and ccmFN. Similarly, the genome's phylogenetic trees revealed that C. duntsa was the sister species to C. sinensis. The results confirmed that the C. duntsa and C. sinensis (OM809792) mitochondrial genome underwent gene rearrangement.In general, our results shows that genomic information from organelles can help us understand plant phylogeny and can also be used to make molecular markers and study how genetic traits change over time. Our research will contribute to the population genetics and evolution of tea plant.

Dataset Information

Complete Genome Sequence of Floricoccus penangensis ML061-4 Isolated from Assam Tea Leaf [Camellia sinensis var. assamica (J.W.Mast.) Kitam.].

Publications

Complete Genome Sequence of <i>Floricoccus penangensis</i> ML061-4 Isolated from Assam Tea Leaf [<i>Camellia sinensis</i> var. <i>assamica</i> (J.W.Mast.) Kitam.].

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