scholarly journals GFAP: ultra-fast and accurate gene functional annotation software for plants

2022 ◽  
Author(s):  
Dong Xu ◽  
Kangming Jin ◽  
Heling Jiang ◽  
Desheng Gong ◽  
Jinbao Yang ◽  
...  
Keyword(s):  
Plant Species ◽  
Sequence Alignment ◽  
Related Species ◽  
Functional Annotation ◽  
Gene Annotation ◽  
Protein Domain ◽  
Species Number ◽  
Closely Related Species ◽  
Video Tutorials ◽  
Testing Data

Sequence alignment is the basis of gene functional annotation for unknow sequences. Selecting closely related species as the reference species should be an effective way to improve the accuracy of gene annotation for plants, compared with only based on one or some model plants. Therefore, limited species number in previous software or website is disadvantageous for plant gene annotation. Here, we collected the protein sequences of 236 plant species with known genomic information from 63 families. After that, these sequences were annotated by pfam, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases to construct our databases. Furthermore, we developed the software, Gene Annotation Software for Plants (GFAP), to perform gene annotation using our databases. GFAP, an open-source software running on Windows and MacOS systems, is an efficient and network independent tool. GFAP can search the protein domain, GO and KEGG information for 43000 genes within 4 minutes. In addition, GFAP can also perform the sequence alignment, statistical analysis and drawing. The website of https://gitee.com/simon198912167815/gfap-database provides the software, databases, testing data and video tutorials for users. GFAP contained large amount of plant-species information. We believe that it will become a powerful tool in gene annotation using closely related species for phytologists.

Wetland Plants of Queensland

2002 ◽  
Author(s):  
KM Stephens ◽  
RM Dowling
Keyword(s):  
Plant Species ◽  
Related Species ◽  
Wetland Plants ◽  
Distribution Map ◽  
Artificial Wetlands ◽  
Closely Related Species ◽  
Field Guide ◽  
Practical Field ◽  
Technical Terms

This practical field guide describes and illustrates in colour 90 common and widespread wetland plants found in Queensland, and gives a distribution map for each species. To assist those readers who are keen to learn more, the book includes a series of keys to help identify those species that are not illustrated in the book but which may be encountered in the field. The keys also help to identify closely related species. There is also a glossary of technical terms. Creating artificial wetlands for the treatment of wastewater and rehabilitating wetland areas that have been disturbed by roads, bridges, mining, housing and other infrastructure developments requires the use of a range of plant species. Wetland Plants of Queensland is an invaluable resource for all those involved in the reclamation of wetlands or the treatment of wastewater, including farmers, environmentalists and all those with an interest in wetland revegetation.

scholarly journals An annotated key to the species of Gastridium (Poaceae) with distributional novelties to the Italian territory

2019 ◽  
Vol 6 (2) ◽  
Author(s):  
Anna Scoppola
Keyword(s):  
Related Species ◽  
Molecular Basis ◽  
Mediterranean Region ◽  
Species Number ◽  
Herbarium Specimens ◽  
Present Contribution ◽  
Closely Related Species ◽  
Poaceae Family ◽  
Italian Territory

Gastridium is a Mediterranean-paleotropical genus of the Poaceae family, native to Italy. Species number and diversity were imperfectly known until recent taxonomic updates on morphological and molecular basis that enhanced our knowledge of this taxon. The present contribution provides a complete key of the genus, encompassing the four currently known closely related species, G. lainzii, G. phleoides, G. scabrum, and G. ventricosum. The essential features of panicle, spikelets, and florets are specified and briefly discussed. Revisions of ancient and recent herbarium specimens provided three Italian distributional novelties for G. phleoides concerning Liguria, Campania, and Puglia and two for G. scabrum concerning Liguria and Basilicata. In contrast, the distributional ranges of G. scabrum and G. lainzii in the W Mediterranean region remain poorly known and await further investigations.

Microsatellite Marker: Importance and Implications of Cross-genome Analysis for Finger Millet (Eleusine coracana (L.) Gaertn)

2020 ◽  
Vol 9 (3) ◽  
pp. 160-170
Author(s):  
Thumadath P.A. Krishna ◽  
Maharajan Theivanayagam ◽  
Gurusunathan V. Roch ◽  
Veeramuthu Duraipandiyan ◽  
Savarimuthu Ignacimuthu
Keyword(s):  
Molecular Marker ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Genome Analysis ◽  
Related Species ◽  
Finger Millet ◽  
Crop Improvement ◽  
Human Beings ◽  
Closely Related Species ◽  
Genome Amplification

Finger millet is a superior staple food for human beings. Microsatellite or Simple Sequence Repeat (SSR) marker is a powerful tool for genetic mapping, diversity analysis and plant breeding. In finger millet, microsatellites show a higher level of polymorphism than other molecular marker systems. The identification and development of microsatellite markers are extremely expensive and time-consuming. Only less than 50% of SSR markers have been developed from microsatellite sequences for finger millet. Therefore, it is important to transfer SSR markers developed for related species/genus to finger millet. Cross-genome transferability is the easiest and cheapest method to develop SSR markers. Many comparative mapping studies using microsatellite markers clearly revealed the presence of synteny within the genomes of closely related species/ genus. Sufficient homology exists among several crop plant genomes in the sequences flanking the SSR loci. Thus, the SSR markers are beneficial to amplify the target regions in the finger millet genome. Many SSR markers were used for the analysis of cross-genome amplification in various plants such as Setaria italica, Pennisetum glaucum, Oryza sativa, Triticum aestivum, Zea mays and Hordeum vulgare. However, there is very little information available about cross-genome amplification of these markers in finger millet. The only limited report is available for the utilization of cross-genome amplified microsatellite markers in genetic analysis, gene mapping and other applications in finger millet. This review highlights the importance and implication of microsatellite markers such as genomic SSR (gSSR) and Expressed Sequence Tag (EST)-SSR in cross-genome analysis in finger millet. Nowadays, crop improvement has been one of the major priority areas of research in agriculture. The genome assisted breeding and genetic engineering plays a very crucial role in enhancing crop productivity. The rapid advance in molecular marker technology is helpful for crop improvement. Therefore, this review will be very helpful to the researchers for understanding the importance and implication of SSR markers in closely related species.

Genetic Complexity Underlying Hybrid Male Sterility in Drosophila

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 789-796 ◽  
Author(s):  
Kyoichi Sawamura ◽  
John Roote ◽  
Chung-I Wu ◽  
Masa-Toshi Yamamoto
Keyword(s):  
Male Sterility ◽  
Related Species ◽  
Synergistic Effects ◽  
Female Sterility ◽  
Hybrid Male ◽  
Hybrid Female ◽  
Hybrid Male Sterility ◽  
Closely Related Species ◽  
Genetic Complexity ◽  
Recessive Genes

Abstract Recent genetic analyses of closely related species of Drosophila have indicated that hybrid male sterility is the consequence of highly complex synergistic effects among multiple genes, both conspecific and heterospecific. On the contrary, much evidence suggests the presence of major genes causing hybrid female sterility and inviability in the less-related species, D. melanogaster and D. simulans. Does this contrast reflect the genetic distance between species? Or, generally, is the genetic basis of hybrid male sterility more complex than that of hybrid female sterility and inviability? To clarify this point, the D. simulans introgression of the cytological region 34D-36A to the D. melanogaster genome, which causes recessive male sterility, was dissected by recombination, deficiency, and complementation mapping. The 450-kb region between two genes, Suppressor of Hairless and snail, exhibited a strong effect on the sterility. Males are (semi-)sterile if this region of the introgression is made homozygous or hemizygous. But no genes in the region singly cause the sterility; this region has at least two genes, which in combination result in male sterility. Further, the males are less fertile when heterozygous with a larger introgression, which suggests that dominant modifiers enhance the effects of recessive genes of male sterility. Such an epistatic view, even in the less-related species, suggests that the genetic complexity is special to hybrid male sterility.

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