Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

AbstractSacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

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Genome-wide Identification and Expression Analysis of CaM/CML Gene Family in Sacred Lotus (Nelumbo nucifera)

Plant Molecular Biology Reporter ◽

10.1007/s11105-021-01330-6 ◽

2022 ◽

Author(s):

Li Gao ◽

Rebecca Njeri Damaris ◽

Feng Yu ◽

Pingfang Yang

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Nelumbo Nucifera ◽

Sacred Lotus ◽

Genome Wide

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Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications

Genes ◽

10.3390/genes9110563 ◽

2018 ◽

Vol 9 (11) ◽

pp. 563 ◽

Cited By ~ 6

Author(s):

Anna Szczepaniak ◽

Michał Książkiewicz ◽

Jan Podkowiński ◽

Katarzyna Czyż ◽

Marek Figlerowicz ◽

...

Keyword(s):

Selection Pressure ◽

Coenzyme A ◽

Phylogenetic Inference ◽

Whole Genome ◽

Evolutionary Patterns ◽

Acetyl Coenzyme A ◽

Acetyl Coenzyme ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Acetyl Coenzyme A Carboxylase

Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.

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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

Scientific Reports ◽

10.1038/s41598-021-95822-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shashi Sharma ◽

Paban Kumar Dash ◽

Sushil Kumar Sharma ◽

Ambuj Srivastava ◽

Jyoti S. Kumar ◽

...

Keyword(s):

Genome Sequence ◽

Sequence Data ◽

Central India ◽

Madhya Pradesh ◽

Whole Genome Sequence ◽

Health Economy ◽

Whole Genome ◽

Evolutionary Patterns ◽

First Case ◽

Multiple Introduction

AbstractCOVID-19 has emerged as global pandemic with largest damage to the public health, economy and human psyche.The genome sequence data obtained during the ongoing pandemic are valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome information of circulating SARS-CoV-2 strains in India will enable the scientific community to understand the emergence of new variants and their impact on human health. The first case of COVID-19 was detected in Chambal region of Madhya Pradesh state in mid of March 2020 followed by multiple introduction events and expansion of cases within next three months. More than 5000 COVID-19 suspected samples referred to Defence Research and Development Establishment, Gwalior, Madhya Pradesh were analyzed during the nation -wide lockdown and unlock period. A total of 136 cases were found positive over a span of three months that included virus introduction to the region and its further spread. Whole genome sequences employing Oxford nanopore technology were generated for 26 SARS-CoV-2 circulating in 10 different districts in Madhya Pradesh state of India. This period witnessed index cases with multiple travel histories responsible for introduction of COVID-19 followed by remarkable expansion of virus. The genome wide substitutions including in important viral proteins were identified. The detailed phylogenetic analysis revealed the circulating SARS-CoV-2 clustered in multiple clades including A2a, A4 and B. The cluster-wise segregation was observed, suggesting multiple introduction links and subsequent evolution of virus in the region. This is the first comprehensive whole genome sequence analysis from central India, which revealed the emergence and evolution of SARS-CoV-2 during thenation-wide lockdown and unlock.

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