Neural networks for identification of protein coding regions in genomic DNA sequences

Summary Given the increasing number of available genomic sequences, one now faces the task of identifying their functional parts, like the protein coding regions. The gene prediction problem can be addressed in several ways. One of the most promising methods makes use of similarity information between the genomic DNA and previously annotated sequences (proteins, cDNAs and ESTs). Recently, given the huge amount of newly sequenced genomes, new similarity-based methods are being successfully applied in the task of gene prediction. The so-called comparative-based methods lie in the similarities shared by regions of two evolutionary related genomic sequences. Despite the number of different gene prediction approaches in the literature, this problem remains challenging. In this paper we present a new comparative-based approach to the gene prediction problem. It is based on a syntenic alignment of three or more genomic sequences. With syntenic alignment we mean an alignment that is constructed taking into account the fact that the involved sequences include conserved regions intervened by unconserved ones. We have implemented the proposed algorithm in a computer program and confirm the validity of the approach on a benchmark including triples of human, mouse and rat genomic sequences.

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A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽

10.11646/zootaxa.4748.1.10 ◽

2020 ◽

Vol 4748 (1) ◽

pp. 182-194 ◽

Cited By ~ 1

Author(s):

JING ZHANG ◽

ERNST BROCKMANN ◽

QIAN CONG ◽

JINHUI SHEN ◽

NICK V. GRISHIN

Keyword(s):

Dna Sequences ◽

Type Species ◽

Phylogenetic Trees ◽

Type Specimens ◽

African Species ◽

Protein Coding ◽

Coding Regions ◽

As Species ◽

Close Relatives ◽

Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]).

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